diff --git a/404.html b/404.html
index a9fbc08a..2b1e231b 100644
--- a/404.html
+++ b/404.html
@@ -7,8 +7,8 @@
 <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
 <title>Page not found (404) • AlphaSimR</title>
 <script src="https://gaynorr.github.io/AlphaSimR/deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
-<link href="https://gaynorr.github.io/AlphaSimR/deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet">
-<script src="https://gaynorr.github.io/AlphaSimR/deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
+<link href="https://gaynorr.github.io/AlphaSimR/deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="https://gaynorr.github.io/AlphaSimR/deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
 <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
 <!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="https://gaynorr.github.io/AlphaSimR/pkgdown.js"></script><meta property="og:title" content="Page not found (404)">
 <!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
@@ -24,7 +24,7 @@
     
     <a class="navbar-brand me-2" href="https://gaynorr.github.io/AlphaSimR/index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/LICENSE-text.html b/LICENSE-text.html
index a6265dc9..c57e1db3 100644
--- a/LICENSE-text.html
+++ b/LICENSE-text.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>License • AlphaSimR</title><script src="deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="pkgdown.js"></script><meta property="og:title" content="License"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>License • AlphaSimR</title><script src="deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="pkgdown.js"></script><meta property="og:title" content="License"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body>
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/articles/index.html b/articles/index.html
index b44e21c5..9fe1a276 100644
--- a/articles/index.html
+++ b/articles/index.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Articles • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Articles"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Articles • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Articles"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body>
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/articles/intro.html b/articles/intro.html
index 17264152..169fc675 100644
--- a/articles/intro.html
+++ b/articles/intro.html
@@ -8,8 +8,8 @@
 <meta name="description" content="AlphaSimR">
 <title>Introduction to AlphaSimR • AlphaSimR</title>
 <script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
-<link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet">
-<script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
 <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
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 <meta property="og:description" content="AlphaSimR">
@@ -26,7 +26,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -76,7 +76,7 @@
                         <h4 data-toc-skip class="author">Chris
 Gaynor</h4>
             
-            <h4 data-toc-skip class="date">2023-11-01</h4>
+            <h4 data-toc-skip class="date">2023-11-30</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/gaynorr/AlphaSimR/blob/HEAD/vignettes/intro.Rmd" class="external-link"><code>vignettes/intro.Rmd</code></a></small>
       <div class="d-none name"><code>intro.Rmd</code></div>
diff --git a/articles/intro_files/figure-html/unnamed-chunk-12-1.png b/articles/intro_files/figure-html/unnamed-chunk-12-1.png
index b36b234d..a2bac7d8 100644
Binary files a/articles/intro_files/figure-html/unnamed-chunk-12-1.png and b/articles/intro_files/figure-html/unnamed-chunk-12-1.png differ
diff --git a/articles/traits.html b/articles/traits.html
index 8638a1c8..a14b8304 100644
--- a/articles/traits.html
+++ b/articles/traits.html
@@ -8,8 +8,8 @@
 <meta name="description" content="AlphaSimR">
 <title>Traits in AlphaSimR • AlphaSimR</title>
 <script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
-<link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet">
-<script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
+<link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
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 <meta property="og:description" content="AlphaSimR">
@@ -26,7 +26,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -76,7 +76,7 @@
                         <h4 data-toc-skip class="author">Chris
 Gaynor</h4>
             
-            <h4 data-toc-skip class="date">2023-11-01</h4>
+            <h4 data-toc-skip class="date">2023-11-30</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/gaynorr/AlphaSimR/blob/HEAD/vignettes/traits.Rmd" class="external-link"><code>vignettes/traits.Rmd</code></a></small>
       <div class="d-none name"><code>traits.Rmd</code></div>
diff --git a/authors.html b/authors.html
index 4037260f..290e570d 100644
--- a/authors.html
+++ b/authors.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
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+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Authors and Citation • AlphaSimR</title><script src="deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="pkgdown.js"></script><meta property="og:title" content="Authors and Citation"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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new file mode 100644
index 00000000..e8f21f70
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s(t){i.add(t.name),[].concat(t.requires||[],t.requiresIfExists||[]).forEach((function(t){if(!i.has(t)){var n=e.get(t);n&&s(n)}})),n.push(t)}return t.forEach((function(t){e.set(t.name,t)})),t.forEach((function(t){i.has(t.name)||s(t)})),n}var fi={placement:"bottom",modifiers:[],strategy:"absolute"};function pi(){for(var t=arguments.length,e=new Array(t),i=0;i<t;i++)e[i]=arguments[i];return!e.some((function(t){return!(t&&"function"==typeof t.getBoundingClientRect)}))}function mi(t){void 0===t&&(t={});var e=t,i=e.defaultModifiers,n=void 0===i?[]:i,s=e.defaultOptions,o=void 0===s?fi:s;return function(t,e,i){void 0===i&&(i=o);var s,r,a={placement:"bottom",orderedModifiers:[],options:Object.assign({},fi,o),modifiersData:{},elements:{reference:t,popper:e},attributes:{},styles:{}},l=[],c=!1,h={state:a,setOptions:function(i){var s="function"==typeof 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t=a.elements,e=t.reference,i=t.popper;if(pi(e,i)){a.rects={reference:di(e,$e(i),"fixed"===a.options.strategy),popper:Ce(i)},a.reset=!1,a.placement=a.options.placement,a.orderedModifiers.forEach((function(t){return a.modifiersData[t.name]=Object.assign({},t.data)}));for(var n=0;n<a.orderedModifiers.length;n++)if(!0!==a.reset){var s=a.orderedModifiers[n],o=s.fn,r=s.options,l=void 0===r?{}:r,d=s.name;"function"==typeof o&&(a=o({state:a,options:l,name:d,instance:h})||a)}else a.reset=!1,n=-1}}},update:(s=function(){return new Promise((function(t){h.forceUpdate(),t(a)}))},function(){return r||(r=new Promise((function(t){Promise.resolve().then((function(){r=void 0,t(s())}))}))),r}),destroy:function(){d(),c=!0}};if(!pi(t,e))return h;function d(){l.forEach((function(t){return t()})),l=[]}return h.setOptions(i).then((function(t){!c&&i.onFirstUpdate&&i.onFirstUpdate(t)})),h}}var gi=mi(),_i=mi({defaultModifiers:[Re,ci,Be,_e]}),bi=mi({defaultModifiers:[Re,ci,Be,_e,li,si,hi,je,ai]});const vi=Object.freeze(Object.defineProperty({__proto__:null,afterMain:ae,afterRead:se,afterWrite:he,applyStyles:_e,arrow:je,auto:Kt,basePlacements:Qt,beforeMain:oe,beforeRead:ie,beforeWrite:le,bottom:Rt,clippingParents:Ut,computeStyles:Be,createPopper:bi,createPopperBase:gi,createPopperLite:_i,detectOverflow:ii,end:Yt,eventListeners:Re,flip:si,hide:ai,left:Vt,main:re,modifierPhases:de,offset:li,placements:ee,popper:Jt,popperGenerator:mi,popperOffsets:ci,preventOverflow:hi,read:ne,reference:Zt,right:qt,start:Xt,top:zt,variationPlacements:te,viewport:Gt,write:ce},Symbol.toStringTag,{value:"Module"})),yi="dropdown",wi=".bs.dropdown",Ai=".data-api",Ei="ArrowUp",Ti="ArrowDown",Ci=`hide${wi}`,Oi=`hidden${wi}`,xi=`show${wi}`,ki=`shown${wi}`,Li=`click${wi}${Ai}`,Si=`keydown${wi}${Ai}`,Di=`keyup${wi}${Ai}`,$i="show",Ii='[data-bs-toggle="dropdown"]:not(.disabled):not(:disabled)',Ni=`${Ii}.${$i}`,Pi=".dropdown-menu",Mi=p()?"top-end":"top-start",ji=p()?"top-start":"top-end",Fi=p()?"bottom-end":"bottom-start",Hi=p()?"bottom-start":"bottom-end",Wi=p()?"left-start":"right-start",Bi=p()?"right-start":"left-start",zi={autoClose:!0,boundary:"clippingParents",display:"dynamic",offset:[0,2],popperConfig:null,reference:"toggle"},Ri={autoClose:"(boolean|string)",boundary:"(string|element)",display:"string",offset:"(array|string|function)",popperConfig:"(null|object|function)",reference:"(string|element|object)"};class qi extends W{constructor(t,e){super(t,e),this._popper=null,this._parent=this._element.parentNode,this._menu=z.next(this._element,Pi)[0]||z.prev(this._element,Pi)[0]||z.findOne(Pi,this._parent),this._inNavbar=this._detectNavbar()}static get Default(){return zi}static get DefaultType(){return Ri}static get NAME(){return yi}toggle(){return this._isShown()?this.hide():this.show()}show(){if(l(this._element)||this._isShown())return;const t={relatedTarget:this._element};if(!N.trigger(this._element,xi,t).defaultPrevented){if(this._createPopper(),"ontouchstart"in document.documentElement&&!this._parent.closest(".navbar-nav"))for(const t of[].concat(...document.body.children))N.on(t,"mouseover",h);this._element.focus(),this._element.setAttribute("aria-expanded",!0),this._menu.classList.add($i),this._element.classList.add($i),N.trigger(this._element,ki,t)}}hide(){if(l(this._element)||!this._isShown())return;const t={relatedTarget:this._element};this._completeHide(t)}dispose(){this._popper&&this._popper.destroy(),super.dispose()}update(){this._inNavbar=this._detectNavbar(),this._popper&&this._popper.update()}_completeHide(t){if(!N.trigger(this._element,Ci,t).defaultPrevented){if("ontouchstart"in document.documentElement)for(const t of[].concat(...document.body.children))N.off(t,"mouseover",h);this._popper&&this._popper.destroy(),this._menu.classList.remove($i),this._element.classList.remove($i),this._element.setAttribute("aria-expanded","false"),F.removeDataAttribute(this._menu,"popper"),N.trigger(this._element,Oi,t)}}_getConfig(t){if("object"==typeof(t=super._getConfig(t)).reference&&!o(t.reference)&&"function"!=typeof t.reference.getBoundingClientRect)throw new TypeError(`${yi.toUpperCase()}: Option "reference" provided type "object" without a required "getBoundingClientRect" method.`);return t}_createPopper(){if(void 0===vi)throw new TypeError("Bootstrap's dropdowns require Popper (https://popper.js.org)");let t=this._element;"parent"===this._config.reference?t=this._parent:o(this._config.reference)?t=r(this._config.reference):"object"==typeof this._config.reference&&(t=this._config.reference);const e=this._getPopperConfig();this._popper=bi(t,this._menu,e)}_isShown(){return this._menu.classList.contains($i)}_getPlacement(){const t=this._parent;if(t.classList.contains("dropend"))return Wi;if(t.classList.contains("dropstart"))return Bi;if(t.classList.contains("dropup-center"))return"top";if(t.classList.contains("dropdown-center"))return"bottom";const e="end"===getComputedStyle(this._menu).getPropertyValue("--bs-position").trim();return t.classList.contains("dropup")?e?ji:Mi:e?Hi:Fi}_detectNavbar(){return null!==this._element.closest(".navbar")}_getOffset(){const{offset:t}=this._config;return"string"==typeof t?t.split(",").map((t=>Number.parseInt(t,10))):"function"==typeof t?e=>t(e,this._element):t}_getPopperConfig(){const t={placement:this._getPlacement(),modifiers:[{name:"preventOverflow",options:{boundary:this._config.boundary}},{name:"offset",options:{offset:this._getOffset()}}]};return(this._inNavbar||"static"===this._config.display)&&(F.setDataAttribute(this._menu,"popper","static"),t.modifiers=[{name:"applyStyles",enabled:!1}]),{...t,...g(this._config.popperConfig,[t])}}_selectMenuItem({key:t,target:e}){const i=z.find(".dropdown-menu .dropdown-item:not(.disabled):not(:disabled)",this._menu).filter((t=>a(t)));i.length&&b(i,e,t===Ti,!i.includes(e)).focus()}static jQueryInterface(t){return this.each((function(){const e=qi.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===e[t])throw new TypeError(`No method named "${t}"`);e[t]()}}))}static clearMenus(t){if(2===t.button||"keyup"===t.type&&"Tab"!==t.key)return;const e=z.find(Ni);for(const i of e){const e=qi.getInstance(i);if(!e||!1===e._config.autoClose)continue;const n=t.composedPath(),s=n.includes(e._menu);if(n.includes(e._element)||"inside"===e._config.autoClose&&!s||"outside"===e._config.autoClose&&s)continue;if(e._menu.contains(t.target)&&("keyup"===t.type&&"Tab"===t.key||/input|select|option|textarea|form/i.test(t.target.tagName)))continue;const o={relatedTarget:e._element};"click"===t.type&&(o.clickEvent=t),e._completeHide(o)}}static dataApiKeydownHandler(t){const e=/input|textarea/i.test(t.target.tagName),i="Escape"===t.key,n=[Ei,Ti].includes(t.key);if(!n&&!i)return;if(e&&!i)return;t.preventDefault();const s=this.matches(Ii)?this:z.prev(this,Ii)[0]||z.next(this,Ii)[0]||z.findOne(Ii,t.delegateTarget.parentNode),o=qi.getOrCreateInstance(s);if(n)return t.stopPropagation(),o.show(),void o._selectMenuItem(t);o._isShown()&&(t.stopPropagation(),o.hide(),s.focus())}}N.on(document,Si,Ii,qi.dataApiKeydownHandler),N.on(document,Si,Pi,qi.dataApiKeydownHandler),N.on(document,Li,qi.clearMenus),N.on(document,Di,qi.clearMenus),N.on(document,Li,Ii,(function(t){t.preventDefault(),qi.getOrCreateInstance(this).toggle()})),m(qi);const Vi="backdrop",Ki="show",Qi=`mousedown.bs.${Vi}`,Xi={className:"modal-backdrop",clickCallback:null,isAnimated:!1,isVisible:!0,rootElement:"body"},Yi={className:"string",clickCallback:"(function|null)",isAnimated:"boolean",isVisible:"boolean",rootElement:"(element|string)"};class Ui extends H{constructor(t){super(),this._config=this._getConfig(t),this._isAppended=!1,this._element=null}static get Default(){return Xi}static get DefaultType(){return Yi}static get NAME(){return Vi}show(t){if(!this._config.isVisible)return void g(t);this._append();const e=this._getElement();this._config.isAnimated&&d(e),e.classList.add(Ki),this._emulateAnimation((()=>{g(t)}))}hide(t){this._config.isVisible?(this._getElement().classList.remove(Ki),this._emulateAnimation((()=>{this.dispose(),g(t)}))):g(t)}dispose(){this._isAppended&&(N.off(this._element,Qi),this._element.remove(),this._isAppended=!1)}_getElement(){if(!this._element){const t=document.createElement("div");t.className=this._config.className,this._config.isAnimated&&t.classList.add("fade"),this._element=t}return this._element}_configAfterMerge(t){return t.rootElement=r(t.rootElement),t}_append(){if(this._isAppended)return;const t=this._getElement();this._config.rootElement.append(t),N.on(t,Qi,(()=>{g(this._config.clickCallback)})),this._isAppended=!0}_emulateAnimation(t){_(t,this._getElement(),this._config.isAnimated)}}const Gi=".bs.focustrap",Ji=`focusin${Gi}`,Zi=`keydown.tab${Gi}`,tn="backward",en={autofocus:!0,trapElement:null},nn={autofocus:"boolean",trapElement:"element"};class sn extends H{constructor(t){super(),this._config=this._getConfig(t),this._isActive=!1,this._lastTabNavDirection=null}static get Default(){return en}static get DefaultType(){return nn}static get NAME(){return"focustrap"}activate(){this._isActive||(this._config.autofocus&&this._config.trapElement.focus(),N.off(document,Gi),N.on(document,Ji,(t=>this._handleFocusin(t))),N.on(document,Zi,(t=>this._handleKeydown(t))),this._isActive=!0)}deactivate(){this._isActive&&(this._isActive=!1,N.off(document,Gi))}_handleFocusin(t){const{trapElement:e}=this._config;if(t.target===document||t.target===e||e.contains(t.target))return;const i=z.focusableChildren(e);0===i.length?e.focus():this._lastTabNavDirection===tn?i[i.length-1].focus():i[0].focus()}_handleKeydown(t){"Tab"===t.key&&(this._lastTabNavDirection=t.shiftKey?tn:"forward")}}const on=".fixed-top, .fixed-bottom, .is-fixed, .sticky-top",rn=".sticky-top",an="padding-right",ln="margin-right";class cn{constructor(){this._element=document.body}getWidth(){const t=document.documentElement.clientWidth;return Math.abs(window.innerWidth-t)}hide(){const t=this.getWidth();this._disableOverFlow(),this._setElementAttributes(this._element,an,(e=>e+t)),this._setElementAttributes(on,an,(e=>e+t)),this._setElementAttributes(rn,ln,(e=>e-t))}reset(){this._resetElementAttributes(this._element,"overflow"),this._resetElementAttributes(this._element,an),this._resetElementAttributes(on,an),this._resetElementAttributes(rn,ln)}isOverflowing(){return this.getWidth()>0}_disableOverFlow(){this._saveInitialAttribute(this._element,"overflow"),this._element.style.overflow="hidden"}_setElementAttributes(t,e,i){const n=this.getWidth();this._applyManipulationCallback(t,(t=>{if(t!==this._element&&window.innerWidth>t.clientWidth+n)return;this._saveInitialAttribute(t,e);const s=window.getComputedStyle(t).getPropertyValue(e);t.style.setProperty(e,`${i(Number.parseFloat(s))}px`)}))}_saveInitialAttribute(t,e){const i=t.style.getPropertyValue(e);i&&F.setDataAttribute(t,e,i)}_resetElementAttributes(t,e){this._applyManipulationCallback(t,(t=>{const i=F.getDataAttribute(t,e);null!==i?(F.removeDataAttribute(t,e),t.style.setProperty(e,i)):t.style.removeProperty(e)}))}_applyManipulationCallback(t,e){if(o(t))e(t);else for(const i of z.find(t,this._element))e(i)}}const hn=".bs.modal",dn=`hide${hn}`,un=`hidePrevented${hn}`,fn=`hidden${hn}`,pn=`show${hn}`,mn=`shown${hn}`,gn=`resize${hn}`,_n=`click.dismiss${hn}`,bn=`mousedown.dismiss${hn}`,vn=`keydown.dismiss${hn}`,yn=`click${hn}.data-api`,wn="modal-open",An="show",En="modal-static",Tn={backdrop:!0,focus:!0,keyboard:!0},Cn={backdrop:"(boolean|string)",focus:"boolean",keyboard:"boolean"};class On extends W{constructor(t,e){super(t,e),this._dialog=z.findOne(".modal-dialog",this._element),this._backdrop=this._initializeBackDrop(),this._focustrap=this._initializeFocusTrap(),this._isShown=!1,this._isTransitioning=!1,this._scrollBar=new cn,this._addEventListeners()}static get Default(){return Tn}static get DefaultType(){return Cn}static get NAME(){return"modal"}toggle(t){return this._isShown?this.hide():this.show(t)}show(t){this._isShown||this._isTransitioning||N.trigger(this._element,pn,{relatedTarget:t}).defaultPrevented||(this._isShown=!0,this._isTransitioning=!0,this._scrollBar.hide(),document.body.classList.add(wn),this._adjustDialog(),this._backdrop.show((()=>this._showElement(t))))}hide(){this._isShown&&!this._isTransitioning&&(N.trigger(this._element,dn).defaultPrevented||(this._isShown=!1,this._isTransitioning=!0,this._focustrap.deactivate(),this._element.classList.remove(An),this._queueCallback((()=>this._hideModal()),this._element,this._isAnimated())))}dispose(){N.off(window,hn),N.off(this._dialog,hn),this._backdrop.dispose(),this._focustrap.deactivate(),super.dispose()}handleUpdate(){this._adjustDialog()}_initializeBackDrop(){return new Ui({isVisible:Boolean(this._config.backdrop),isAnimated:this._isAnimated()})}_initializeFocusTrap(){return new sn({trapElement:this._element})}_showElement(t){document.body.contains(this._element)||document.body.append(this._element),this._element.style.display="block",this._element.removeAttribute("aria-hidden"),this._element.setAttribute("aria-modal",!0),this._element.setAttribute("role","dialog"),this._element.scrollTop=0;const e=z.findOne(".modal-body",this._dialog);e&&(e.scrollTop=0),d(this._element),this._element.classList.add(An),this._queueCallback((()=>{this._config.focus&&this._focustrap.activate(),this._isTransitioning=!1,N.trigger(this._element,mn,{relatedTarget:t})}),this._dialog,this._isAnimated())}_addEventListeners(){N.on(this._element,vn,(t=>{"Escape"===t.key&&(this._config.keyboard?this.hide():this._triggerBackdropTransition())})),N.on(window,gn,(()=>{this._isShown&&!this._isTransitioning&&this._adjustDialog()})),N.on(this._element,bn,(t=>{N.one(this._element,_n,(e=>{this._element===t.target&&this._element===e.target&&("static"!==this._config.backdrop?this._config.backdrop&&this.hide():this._triggerBackdropTransition())}))}))}_hideModal(){this._element.style.display="none",this._element.setAttribute("aria-hidden",!0),this._element.removeAttribute("aria-modal"),this._element.removeAttribute("role"),this._isTransitioning=!1,this._backdrop.hide((()=>{document.body.classList.remove(wn),this._resetAdjustments(),this._scrollBar.reset(),N.trigger(this._element,fn)}))}_isAnimated(){return this._element.classList.contains("fade")}_triggerBackdropTransition(){if(N.trigger(this._element,un).defaultPrevented)return;const t=this._element.scrollHeight>document.documentElement.clientHeight,e=this._element.style.overflowY;"hidden"===e||this._element.classList.contains(En)||(t||(this._element.style.overflowY="hidden"),this._element.classList.add(En),this._queueCallback((()=>{this._element.classList.remove(En),this._queueCallback((()=>{this._element.style.overflowY=e}),this._dialog)}),this._dialog),this._element.focus())}_adjustDialog(){const t=this._element.scrollHeight>document.documentElement.clientHeight,e=this._scrollBar.getWidth(),i=e>0;if(i&&!t){const t=p()?"paddingLeft":"paddingRight";this._element.style[t]=`${e}px`}if(!i&&t){const t=p()?"paddingRight":"paddingLeft";this._element.style[t]=`${e}px`}}_resetAdjustments(){this._element.style.paddingLeft="",this._element.style.paddingRight=""}static jQueryInterface(t,e){return this.each((function(){const i=On.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===i[t])throw new TypeError(`No method named "${t}"`);i[t](e)}}))}}N.on(document,yn,'[data-bs-toggle="modal"]',(function(t){const e=z.getElementFromSelector(this);["A","AREA"].includes(this.tagName)&&t.preventDefault(),N.one(e,pn,(t=>{t.defaultPrevented||N.one(e,fn,(()=>{a(this)&&this.focus()}))}));const i=z.findOne(".modal.show");i&&On.getInstance(i).hide(),On.getOrCreateInstance(e).toggle(this)})),R(On),m(On);const xn=".bs.offcanvas",kn=".data-api",Ln=`load${xn}${kn}`,Sn="show",Dn="showing",$n="hiding",In=".offcanvas.show",Nn=`show${xn}`,Pn=`shown${xn}`,Mn=`hide${xn}`,jn=`hidePrevented${xn}`,Fn=`hidden${xn}`,Hn=`resize${xn}`,Wn=`click${xn}${kn}`,Bn=`keydown.dismiss${xn}`,zn={backdrop:!0,keyboard:!0,scroll:!1},Rn={backdrop:"(boolean|string)",keyboard:"boolean",scroll:"boolean"};class qn extends W{constructor(t,e){super(t,e),this._isShown=!1,this._backdrop=this._initializeBackDrop(),this._focustrap=this._initializeFocusTrap(),this._addEventListeners()}static get Default(){return zn}static get DefaultType(){return Rn}static get NAME(){return"offcanvas"}toggle(t){return this._isShown?this.hide():this.show(t)}show(t){this._isShown||N.trigger(this._element,Nn,{relatedTarget:t}).defaultPrevented||(this._isShown=!0,this._backdrop.show(),this._config.scroll||(new cn).hide(),this._element.setAttribute("aria-modal",!0),this._element.setAttribute("role","dialog"),this._element.classList.add(Dn),this._queueCallback((()=>{this._config.scroll&&!this._config.backdrop||this._focustrap.activate(),this._element.classList.add(Sn),this._element.classList.remove(Dn),N.trigger(this._element,Pn,{relatedTarget:t})}),this._element,!0))}hide(){this._isShown&&(N.trigger(this._element,Mn).defaultPrevented||(this._focustrap.deactivate(),this._element.blur(),this._isShown=!1,this._element.classList.add($n),this._backdrop.hide(),this._queueCallback((()=>{this._element.classList.remove(Sn,$n),this._element.removeAttribute("aria-modal"),this._element.removeAttribute("role"),this._config.scroll||(new cn).reset(),N.trigger(this._element,Fn)}),this._element,!0)))}dispose(){this._backdrop.dispose(),this._focustrap.deactivate(),super.dispose()}_initializeBackDrop(){const t=Boolean(this._config.backdrop);return new Ui({className:"offcanvas-backdrop",isVisible:t,isAnimated:!0,rootElement:this._element.parentNode,clickCallback:t?()=>{"static"!==this._config.backdrop?this.hide():N.trigger(this._element,jn)}:null})}_initializeFocusTrap(){return new sn({trapElement:this._element})}_addEventListeners(){N.on(this._element,Bn,(t=>{"Escape"===t.key&&(this._config.keyboard?this.hide():N.trigger(this._element,jn))}))}static jQueryInterface(t){return this.each((function(){const e=qn.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===e[t]||t.startsWith("_")||"constructor"===t)throw new TypeError(`No method named "${t}"`);e[t](this)}}))}}N.on(document,Wn,'[data-bs-toggle="offcanvas"]',(function(t){const e=z.getElementFromSelector(this);if(["A","AREA"].includes(this.tagName)&&t.preventDefault(),l(this))return;N.one(e,Fn,(()=>{a(this)&&this.focus()}));const i=z.findOne(In);i&&i!==e&&qn.getInstance(i).hide(),qn.getOrCreateInstance(e).toggle(this)})),N.on(window,Ln,(()=>{for(const t of z.find(In))qn.getOrCreateInstance(t).show()})),N.on(window,Hn,(()=>{for(const t of z.find("[aria-modal][class*=show][class*=offcanvas-]"))"fixed"!==getComputedStyle(t).position&&qn.getOrCreateInstance(t).hide()})),R(qn),m(qn);const Vn={"*":["class","dir","id","lang","role",/^aria-[\w-]*$/i],a:["target","href","title","rel"],area:[],b:[],br:[],col:[],code:[],div:[],em:[],hr:[],h1:[],h2:[],h3:[],h4:[],h5:[],h6:[],i:[],img:["src","srcset","alt","title","width","height"],li:[],ol:[],p:[],pre:[],s:[],small:[],span:[],sub:[],sup:[],strong:[],u:[],ul:[]},Kn=new Set(["background","cite","href","itemtype","longdesc","poster","src","xlink:href"]),Qn=/^(?!javascript:)(?:[a-z0-9+.-]+:|[^&:/?#]*(?:[/?#]|$))/i,Xn=(t,e)=>{const i=t.nodeName.toLowerCase();return e.includes(i)?!Kn.has(i)||Boolean(Qn.test(t.nodeValue)):e.filter((t=>t instanceof RegExp)).some((t=>t.test(i)))},Yn={allowList:Vn,content:{},extraClass:"",html:!1,sanitize:!0,sanitizeFn:null,template:"<div></div>"},Un={allowList:"object",content:"object",extraClass:"(string|function)",html:"boolean",sanitize:"boolean",sanitizeFn:"(null|function)",template:"string"},Gn={entry:"(string|element|function|null)",selector:"(string|element)"};class Jn extends H{constructor(t){super(),this._config=this._getConfig(t)}static get Default(){return Yn}static get DefaultType(){return Un}static get NAME(){return"TemplateFactory"}getContent(){return Object.values(this._config.content).map((t=>this._resolvePossibleFunction(t))).filter(Boolean)}hasContent(){return this.getContent().length>0}changeContent(t){return this._checkContent(t),this._config.content={...this._config.content,...t},this}toHtml(){const t=document.createElement("div");t.innerHTML=this._maybeSanitize(this._config.template);for(const[e,i]of Object.entries(this._config.content))this._setContent(t,i,e);const e=t.children[0],i=this._resolvePossibleFunction(this._config.extraClass);return i&&e.classList.add(...i.split(" ")),e}_typeCheckConfig(t){super._typeCheckConfig(t),this._checkContent(t.content)}_checkContent(t){for(const[e,i]of Object.entries(t))super._typeCheckConfig({selector:e,entry:i},Gn)}_setContent(t,e,i){const n=z.findOne(i,t);n&&((e=this._resolvePossibleFunction(e))?o(e)?this._putElementInTemplate(r(e),n):this._config.html?n.innerHTML=this._maybeSanitize(e):n.textContent=e:n.remove())}_maybeSanitize(t){return this._config.sanitize?function(t,e,i){if(!t.length)return t;if(i&&"function"==typeof i)return i(t);const n=(new window.DOMParser).parseFromString(t,"text/html"),s=[].concat(...n.body.querySelectorAll("*"));for(const t of s){const i=t.nodeName.toLowerCase();if(!Object.keys(e).includes(i)){t.remove();continue}const n=[].concat(...t.attributes),s=[].concat(e["*"]||[],e[i]||[]);for(const e of n)Xn(e,s)||t.removeAttribute(e.nodeName)}return n.body.innerHTML}(t,this._config.allowList,this._config.sanitizeFn):t}_resolvePossibleFunction(t){return g(t,[this])}_putElementInTemplate(t,e){if(this._config.html)return e.innerHTML="",void e.append(t);e.textContent=t.textContent}}const Zn=new Set(["sanitize","allowList","sanitizeFn"]),ts="fade",es="show",is=".modal",ns="hide.bs.modal",ss="hover",os="focus",rs={AUTO:"auto",TOP:"top",RIGHT:p()?"left":"right",BOTTOM:"bottom",LEFT:p()?"right":"left"},as={allowList:Vn,animation:!0,boundary:"clippingParents",container:!1,customClass:"",delay:0,fallbackPlacements:["top","right","bottom","left"],html:!1,offset:[0,6],placement:"top",popperConfig:null,sanitize:!0,sanitizeFn:null,selector:!1,template:'<div class="tooltip" role="tooltip"><div class="tooltip-arrow"></div><div class="tooltip-inner"></div></div>',title:"",trigger:"hover focus"},ls={allowList:"object",animation:"boolean",boundary:"(string|element)",container:"(string|element|boolean)",customClass:"(string|function)",delay:"(number|object)",fallbackPlacements:"array",html:"boolean",offset:"(array|string|function)",placement:"(string|function)",popperConfig:"(null|object|function)",sanitize:"boolean",sanitizeFn:"(null|function)",selector:"(string|boolean)",template:"string",title:"(string|element|function)",trigger:"string"};class cs extends W{constructor(t,e){if(void 0===vi)throw new TypeError("Bootstrap's tooltips require Popper (https://popper.js.org)");super(t,e),this._isEnabled=!0,this._timeout=0,this._isHovered=null,this._activeTrigger={},this._popper=null,this._templateFactory=null,this._newContent=null,this.tip=null,this._setListeners(),this._config.selector||this._fixTitle()}static get Default(){return as}static get DefaultType(){return ls}static get NAME(){return"tooltip"}enable(){this._isEnabled=!0}disable(){this._isEnabled=!1}toggleEnabled(){this._isEnabled=!this._isEnabled}toggle(){this._isEnabled&&(this._activeTrigger.click=!this._activeTrigger.click,this._isShown()?this._leave():this._enter())}dispose(){clearTimeout(this._timeout),N.off(this._element.closest(is),ns,this._hideModalHandler),this._element.getAttribute("data-bs-original-title")&&this._element.setAttribute("title",this._element.getAttribute("data-bs-original-title")),this._disposePopper(),super.dispose()}show(){if("none"===this._element.style.display)throw new Error("Please use show on visible elements");if(!this._isWithContent()||!this._isEnabled)return;const t=N.trigger(this._element,this.constructor.eventName("show")),e=(c(this._element)||this._element.ownerDocument.documentElement).contains(this._element);if(t.defaultPrevented||!e)return;this._disposePopper();const i=this._getTipElement();this._element.setAttribute("aria-describedby",i.getAttribute("id"));const{container:n}=this._config;if(this._element.ownerDocument.documentElement.contains(this.tip)||(n.append(i),N.trigger(this._element,this.constructor.eventName("inserted"))),this._popper=this._createPopper(i),i.classList.add(es),"ontouchstart"in document.documentElement)for(const t of[].concat(...document.body.children))N.on(t,"mouseover",h);this._queueCallback((()=>{N.trigger(this._element,this.constructor.eventName("shown")),!1===this._isHovered&&this._leave(),this._isHovered=!1}),this.tip,this._isAnimated())}hide(){if(this._isShown()&&!N.trigger(this._element,this.constructor.eventName("hide")).defaultPrevented){if(this._getTipElement().classList.remove(es),"ontouchstart"in document.documentElement)for(const t of[].concat(...document.body.children))N.off(t,"mouseover",h);this._activeTrigger.click=!1,this._activeTrigger[os]=!1,this._activeTrigger[ss]=!1,this._isHovered=null,this._queueCallback((()=>{this._isWithActiveTrigger()||(this._isHovered||this._disposePopper(),this._element.removeAttribute("aria-describedby"),N.trigger(this._element,this.constructor.eventName("hidden")))}),this.tip,this._isAnimated())}}update(){this._popper&&this._popper.update()}_isWithContent(){return Boolean(this._getTitle())}_getTipElement(){return this.tip||(this.tip=this._createTipElement(this._newContent||this._getContentForTemplate())),this.tip}_createTipElement(t){const e=this._getTemplateFactory(t).toHtml();if(!e)return null;e.classList.remove(ts,es),e.classList.add(`bs-${this.constructor.NAME}-auto`);const i=(t=>{do{t+=Math.floor(1e6*Math.random())}while(document.getElementById(t));return t})(this.constructor.NAME).toString();return e.setAttribute("id",i),this._isAnimated()&&e.classList.add(ts),e}setContent(t){this._newContent=t,this._isShown()&&(this._disposePopper(),this.show())}_getTemplateFactory(t){return this._templateFactory?this._templateFactory.changeContent(t):this._templateFactory=new Jn({...this._config,content:t,extraClass:this._resolvePossibleFunction(this._config.customClass)}),this._templateFactory}_getContentForTemplate(){return{".tooltip-inner":this._getTitle()}}_getTitle(){return this._resolvePossibleFunction(this._config.title)||this._element.getAttribute("data-bs-original-title")}_initializeOnDelegatedTarget(t){return this.constructor.getOrCreateInstance(t.delegateTarget,this._getDelegateConfig())}_isAnimated(){return this._config.animation||this.tip&&this.tip.classList.contains(ts)}_isShown(){return this.tip&&this.tip.classList.contains(es)}_createPopper(t){const e=g(this._config.placement,[this,t,this._element]),i=rs[e.toUpperCase()];return bi(this._element,t,this._getPopperConfig(i))}_getOffset(){const{offset:t}=this._config;return"string"==typeof t?t.split(",").map((t=>Number.parseInt(t,10))):"function"==typeof t?e=>t(e,this._element):t}_resolvePossibleFunction(t){return g(t,[this._element])}_getPopperConfig(t){const e={placement:t,modifiers:[{name:"flip",options:{fallbackPlacements:this._config.fallbackPlacements}},{name:"offset",options:{offset:this._getOffset()}},{name:"preventOverflow",options:{boundary:this._config.boundary}},{name:"arrow",options:{element:`.${this.constructor.NAME}-arrow`}},{name:"preSetPlacement",enabled:!0,phase:"beforeMain",fn:t=>{this._getTipElement().setAttribute("data-popper-placement",t.state.placement)}}]};return{...e,...g(this._config.popperConfig,[e])}}_setListeners(){const t=this._config.trigger.split(" ");for(const e of t)if("click"===e)N.on(this._element,this.constructor.eventName("click"),this._config.selector,(t=>{this._initializeOnDelegatedTarget(t).toggle()}));else if("manual"!==e){const t=e===ss?this.constructor.eventName("mouseenter"):this.constructor.eventName("focusin"),i=e===ss?this.constructor.eventName("mouseleave"):this.constructor.eventName("focusout");N.on(this._element,t,this._config.selector,(t=>{const e=this._initializeOnDelegatedTarget(t);e._activeTrigger["focusin"===t.type?os:ss]=!0,e._enter()})),N.on(this._element,i,this._config.selector,(t=>{const e=this._initializeOnDelegatedTarget(t);e._activeTrigger["focusout"===t.type?os:ss]=e._element.contains(t.relatedTarget),e._leave()}))}this._hideModalHandler=()=>{this._element&&this.hide()},N.on(this._element.closest(is),ns,this._hideModalHandler)}_fixTitle(){const t=this._element.getAttribute("title");t&&(this._element.getAttribute("aria-label")||this._element.textContent.trim()||this._element.setAttribute("aria-label",t),this._element.setAttribute("data-bs-original-title",t),this._element.removeAttribute("title"))}_enter(){this._isShown()||this._isHovered?this._isHovered=!0:(this._isHovered=!0,this._setTimeout((()=>{this._isHovered&&this.show()}),this._config.delay.show))}_leave(){this._isWithActiveTrigger()||(this._isHovered=!1,this._setTimeout((()=>{this._isHovered||this.hide()}),this._config.delay.hide))}_setTimeout(t,e){clearTimeout(this._timeout),this._timeout=setTimeout(t,e)}_isWithActiveTrigger(){return Object.values(this._activeTrigger).includes(!0)}_getConfig(t){const e=F.getDataAttributes(this._element);for(const t of Object.keys(e))Zn.has(t)&&delete e[t];return t={...e,..."object"==typeof t&&t?t:{}},t=this._mergeConfigObj(t),t=this._configAfterMerge(t),this._typeCheckConfig(t),t}_configAfterMerge(t){return t.container=!1===t.container?document.body:r(t.container),"number"==typeof t.delay&&(t.delay={show:t.delay,hide:t.delay}),"number"==typeof t.title&&(t.title=t.title.toString()),"number"==typeof t.content&&(t.content=t.content.toString()),t}_getDelegateConfig(){const t={};for(const[e,i]of Object.entries(this._config))this.constructor.Default[e]!==i&&(t[e]=i);return t.selector=!1,t.trigger="manual",t}_disposePopper(){this._popper&&(this._popper.destroy(),this._popper=null),this.tip&&(this.tip.remove(),this.tip=null)}static jQueryInterface(t){return this.each((function(){const e=cs.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===e[t])throw new TypeError(`No method named "${t}"`);e[t]()}}))}}m(cs);const hs={...cs.Default,content:"",offset:[0,8],placement:"right",template:'<div class="popover" role="tooltip"><div class="popover-arrow"></div><h3 class="popover-header"></h3><div class="popover-body"></div></div>',trigger:"click"},ds={...cs.DefaultType,content:"(null|string|element|function)"};class us extends cs{static get Default(){return hs}static get DefaultType(){return ds}static get NAME(){return"popover"}_isWithContent(){return this._getTitle()||this._getContent()}_getContentForTemplate(){return{".popover-header":this._getTitle(),".popover-body":this._getContent()}}_getContent(){return this._resolvePossibleFunction(this._config.content)}static jQueryInterface(t){return this.each((function(){const e=us.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===e[t])throw new TypeError(`No method named "${t}"`);e[t]()}}))}}m(us);const fs=".bs.scrollspy",ps=`activate${fs}`,ms=`click${fs}`,gs=`load${fs}.data-api`,_s="active",bs="[href]",vs=".nav-link",ys=`${vs}, .nav-item > ${vs}, .list-group-item`,ws={offset:null,rootMargin:"0px 0px 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t){if(!o.isIntersecting){this._activeTarget=null,this._clearActiveClass(e(o));continue}const t=o.target.offsetTop>=this._previousScrollData.visibleEntryTop;if(s&&t){if(i(o),!n)return}else s||t||i(o)}}_initializeTargetsAndObservables(){this._targetLinks=new Map,this._observableSections=new Map;const t=z.find(bs,this._config.target);for(const e of t){if(!e.hash||l(e))continue;const t=z.findOne(decodeURI(e.hash),this._element);a(t)&&(this._targetLinks.set(decodeURI(e.hash),e),this._observableSections.set(e.hash,t))}}_process(t){this._activeTarget!==t&&(this._clearActiveClass(this._config.target),this._activeTarget=t,t.classList.add(_s),this._activateParents(t),N.trigger(this._element,ps,{relatedTarget:t}))}_activateParents(t){if(t.classList.contains("dropdown-item"))z.findOne(".dropdown-toggle",t.closest(".dropdown")).classList.add(_s);else for(const e of z.parents(t,".nav, .list-group"))for(const t of z.prev(e,ys))t.classList.add(_s)}_clearActiveClass(t){t.classList.remove(_s);const e=z.find(`${bs}.${_s}`,t);for(const t of e)t.classList.remove(_s)}static jQueryInterface(t){return this.each((function(){const e=Es.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===e[t]||t.startsWith("_")||"constructor"===t)throw new TypeError(`No method named "${t}"`);e[t]()}}))}}N.on(window,gs,(()=>{for(const t of z.find('[data-bs-spy="scroll"]'))Es.getOrCreateInstance(t)})),m(Es);const Ts=".bs.tab",Cs=`hide${Ts}`,Os=`hidden${Ts}`,xs=`show${Ts}`,ks=`shown${Ts}`,Ls=`click${Ts}`,Ss=`keydown${Ts}`,Ds=`load${Ts}`,$s="ArrowLeft",Is="ArrowRight",Ns="ArrowUp",Ps="ArrowDown",Ms="Home",js="End",Fs="active",Hs="fade",Ws="show",Bs=":not(.dropdown-toggle)",zs='[data-bs-toggle="tab"], [data-bs-toggle="pill"], [data-bs-toggle="list"]',Rs=`.nav-link${Bs}, .list-group-item${Bs}, [role="tab"]${Bs}, ${zs}`,qs=`.${Fs}[data-bs-toggle="tab"], .${Fs}[data-bs-toggle="pill"], .${Fs}[data-bs-toggle="list"]`;class Vs extends W{constructor(t){super(t),this._parent=this._element.closest('.list-group, .nav, [role="tablist"]'),this._parent&&(this._setInitialAttributes(this._parent,this._getChildren()),N.on(this._element,Ss,(t=>this._keydown(t))))}static get NAME(){return"tab"}show(){const t=this._element;if(this._elemIsActive(t))return;const e=this._getActiveElem(),i=e?N.trigger(e,Cs,{relatedTarget:t}):null;N.trigger(t,xs,{relatedTarget:e}).defaultPrevented||i&&i.defaultPrevented||(this._deactivate(e,t),this._activate(t,e))}_activate(t,e){t&&(t.classList.add(Fs),this._activate(z.getElementFromSelector(t)),this._queueCallback((()=>{"tab"===t.getAttribute("role")?(t.removeAttribute("tabindex"),t.setAttribute("aria-selected",!0),this._toggleDropDown(t,!0),N.trigger(t,ks,{relatedTarget:e})):t.classList.add(Ws)}),t,t.classList.contains(Hs)))}_deactivate(t,e){t&&(t.classList.remove(Fs),t.blur(),this._deactivate(z.getElementFromSelector(t)),this._queueCallback((()=>{"tab"===t.getAttribute("role")?(t.setAttribute("aria-selected",!1),t.setAttribute("tabindex","-1"),this._toggleDropDown(t,!1),N.trigger(t,Os,{relatedTarget:e})):t.classList.remove(Ws)}),t,t.classList.contains(Hs)))}_keydown(t){if(![$s,Is,Ns,Ps,Ms,js].includes(t.key))return;t.stopPropagation(),t.preventDefault();const e=this._getChildren().filter((t=>!l(t)));let i;if([Ms,js].includes(t.key))i=e[t.key===Ms?0:e.length-1];else{const n=[Is,Ps].includes(t.key);i=b(e,t.target,n,!0)}i&&(i.focus({preventScroll:!0}),Vs.getOrCreateInstance(i).show())}_getChildren(){return z.find(Rs,this._parent)}_getActiveElem(){return this._getChildren().find((t=>this._elemIsActive(t)))||null}_setInitialAttributes(t,e){this._setAttributeIfNotExists(t,"role","tablist");for(const t of e)this._setInitialAttributesOnChild(t)}_setInitialAttributesOnChild(t){t=this._getInnerElement(t);const e=this._elemIsActive(t),i=this._getOuterElement(t);t.setAttribute("aria-selected",e),i!==t&&this._setAttributeIfNotExists(i,"role","presentation"),e||t.setAttribute("tabindex","-1"),this._setAttributeIfNotExists(t,"role","tab"),this._setInitialAttributesOnTargetPanel(t)}_setInitialAttributesOnTargetPanel(t){const e=z.getElementFromSelector(t);e&&(this._setAttributeIfNotExists(e,"role","tabpanel"),t.id&&this._setAttributeIfNotExists(e,"aria-labelledby",`${t.id}`))}_toggleDropDown(t,e){const i=this._getOuterElement(t);if(!i.classList.contains("dropdown"))return;const n=(t,n)=>{const s=z.findOne(t,i);s&&s.classList.toggle(n,e)};n(".dropdown-toggle",Fs),n(".dropdown-menu",Ws),i.setAttribute("aria-expanded",e)}_setAttributeIfNotExists(t,e,i){t.hasAttribute(e)||t.setAttribute(e,i)}_elemIsActive(t){return t.classList.contains(Fs)}_getInnerElement(t){return t.matches(Rs)?t:z.findOne(Rs,t)}_getOuterElement(t){return t.closest(".nav-item, .list-group-item")||t}static jQueryInterface(t){return this.each((function(){const e=Vs.getOrCreateInstance(this);if("string"==typeof t){if(void 0===e[t]||t.startsWith("_")||"constructor"===t)throw new TypeError(`No method named 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* --------------------------------------------------------------------------\n * Bootstrap dom/data.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\n/**\n * Constants\n */\n\nconst elementMap = new Map()\n\nexport default {\n  set(element, key, instance) {\n    if (!elementMap.has(element)) {\n      elementMap.set(element, new Map())\n    }\n\n    const instanceMap = elementMap.get(element)\n\n    // make it clear we only want one instance per element\n    // can be removed later when multiple key/instances are fine to be used\n    if (!instanceMap.has(key) && instanceMap.size !== 0) {\n      // eslint-disable-next-line no-console\n      console.error(`Bootstrap doesn't allow more than one instance per element. Bound instance: ${Array.from(instanceMap.keys())[0]}.`)\n      return\n    }\n\n    instanceMap.set(key, instance)\n  },\n\n  get(element, key) {\n    if (elementMap.has(element)) {\n      return elementMap.get(element).get(key) || null\n    }\n\n    return null\n  },\n\n  remove(element, key) {\n    if (!elementMap.has(element)) {\n      return\n    }\n\n    const instanceMap = elementMap.get(element)\n\n    instanceMap.delete(key)\n\n    // free up element references if there are no instances left for an element\n    if (instanceMap.size === 0) {\n      elementMap.delete(element)\n    }\n  }\n}\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap util/index.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nconst MAX_UID = 1_000_000\nconst MILLISECONDS_MULTIPLIER = 1000\nconst TRANSITION_END = 'transitionend'\n\n/**\n * Properly escape IDs selectors to handle weird IDs\n * @param {string} selector\n * @returns {string}\n */\nconst parseSelector = selector => {\n  if (selector && window.CSS && window.CSS.escape) {\n    // document.querySelector needs escaping to handle IDs (html5+) containing for instance /\n    selector = selector.replace(/#([^\\s\"#']+)/g, (match, id) => `#${CSS.escape(id)}`)\n  }\n\n  return selector\n}\n\n// Shout-out Angus Croll (https://goo.gl/pxwQGp)\nconst toType = object => {\n  if (object === null || object === undefined) {\n    return `${object}`\n  }\n\n  return Object.prototype.toString.call(object).match(/\\s([a-z]+)/i)[1].toLowerCase()\n}\n\n/**\n * Public Util API\n */\n\nconst getUID = prefix => {\n  do {\n    prefix += Math.floor(Math.random() * MAX_UID)\n  } while (document.getElementById(prefix))\n\n  return prefix\n}\n\nconst getTransitionDurationFromElement = element => {\n  if (!element) {\n    return 0\n  }\n\n  // Get transition-duration of the element\n  let { transitionDuration, transitionDelay } = window.getComputedStyle(element)\n\n  const floatTransitionDuration = Number.parseFloat(transitionDuration)\n  const floatTransitionDelay = Number.parseFloat(transitionDelay)\n\n  // Return 0 if element or transition duration is not found\n  if (!floatTransitionDuration && !floatTransitionDelay) {\n    return 0\n  }\n\n  // If multiple durations are defined, take the first\n  transitionDuration = transitionDuration.split(',')[0]\n  transitionDelay = transitionDelay.split(',')[0]\n\n  return (Number.parseFloat(transitionDuration) + Number.parseFloat(transitionDelay)) * MILLISECONDS_MULTIPLIER\n}\n\nconst triggerTransitionEnd = element => {\n  element.dispatchEvent(new Event(TRANSITION_END))\n}\n\nconst isElement = object => {\n  if (!object || typeof object !== 'object') {\n    return false\n  }\n\n  if (typeof object.jquery !== 'undefined') {\n    object = object[0]\n  }\n\n  return typeof object.nodeType !== 'undefined'\n}\n\nconst getElement = object => {\n  // it's a jQuery object or a node element\n  if (isElement(object)) {\n    return object.jquery ? object[0] : object\n  }\n\n  if (typeof object === 'string' && object.length > 0) {\n    return document.querySelector(parseSelector(object))\n  }\n\n  return null\n}\n\nconst isVisible = element => {\n  if (!isElement(element) || element.getClientRects().length === 0) {\n    return false\n  }\n\n  const elementIsVisible = getComputedStyle(element).getPropertyValue('visibility') === 'visible'\n  // Handle `details` element as its content may falsie appear visible when it is closed\n  const closedDetails = element.closest('details:not([open])')\n\n  if (!closedDetails) {\n    return elementIsVisible\n  }\n\n  if (closedDetails !== element) {\n    const summary = element.closest('summary')\n    if (summary && summary.parentNode !== closedDetails) {\n      return false\n    }\n\n    if (summary === null) {\n      return false\n    }\n  }\n\n  return elementIsVisible\n}\n\nconst isDisabled = element => {\n  if (!element || element.nodeType !== Node.ELEMENT_NODE) {\n    return true\n  }\n\n  if (element.classList.contains('disabled')) {\n    return true\n  }\n\n  if (typeof element.disabled !== 'undefined') {\n    return element.disabled\n  }\n\n  return element.hasAttribute('disabled') && element.getAttribute('disabled') !== 'false'\n}\n\nconst findShadowRoot = element => {\n  if (!document.documentElement.attachShadow) {\n    return null\n  }\n\n  // Can find the shadow root otherwise it'll return the document\n  if (typeof element.getRootNode === 'function') {\n    const root = element.getRootNode()\n    return root instanceof ShadowRoot ? root : null\n  }\n\n  if (element instanceof ShadowRoot) {\n    return element\n  }\n\n  // when we don't find a shadow root\n  if (!element.parentNode) {\n    return null\n  }\n\n  return findShadowRoot(element.parentNode)\n}\n\nconst noop = () => {}\n\n/**\n * Trick to restart an element's animation\n *\n * @param {HTMLElement} element\n * @return void\n *\n * @see https://www.charistheo.io/blog/2021/02/restart-a-css-animation-with-javascript/#restarting-a-css-animation\n */\nconst reflow = element => {\n  element.offsetHeight // eslint-disable-line no-unused-expressions\n}\n\nconst getjQuery = () => {\n  if (window.jQuery && !document.body.hasAttribute('data-bs-no-jquery')) {\n    return window.jQuery\n  }\n\n  return null\n}\n\nconst DOMContentLoadedCallbacks = []\n\nconst onDOMContentLoaded = callback => {\n  if (document.readyState === 'loading') {\n    // add listener on the first call when the document is in loading state\n    if (!DOMContentLoadedCallbacks.length) {\n      document.addEventListener('DOMContentLoaded', () => {\n        for (const callback of DOMContentLoadedCallbacks) {\n          callback()\n        }\n      })\n    }\n\n    DOMContentLoadedCallbacks.push(callback)\n  } else {\n    callback()\n  }\n}\n\nconst isRTL = () => document.documentElement.dir === 'rtl'\n\nconst defineJQueryPlugin = plugin => {\n  onDOMContentLoaded(() => {\n    const $ = getjQuery()\n    /* istanbul ignore if */\n    if ($) {\n      const name = plugin.NAME\n      const JQUERY_NO_CONFLICT = $.fn[name]\n      $.fn[name] = plugin.jQueryInterface\n      $.fn[name].Constructor = plugin\n      $.fn[name].noConflict = () => {\n        $.fn[name] = JQUERY_NO_CONFLICT\n        return plugin.jQueryInterface\n      }\n    }\n  })\n}\n\nconst execute = (possibleCallback, args = [], defaultValue = possibleCallback) => {\n  return typeof possibleCallback === 'function' ? possibleCallback(...args) : defaultValue\n}\n\nconst executeAfterTransition = (callback, transitionElement, waitForTransition = true) => {\n  if (!waitForTransition) {\n    execute(callback)\n    return\n  }\n\n  const durationPadding = 5\n  const emulatedDuration = getTransitionDurationFromElement(transitionElement) + durationPadding\n\n  let called = false\n\n  const handler = ({ target }) => {\n    if (target !== transitionElement) {\n      return\n    }\n\n    called = true\n    transitionElement.removeEventListener(TRANSITION_END, handler)\n    execute(callback)\n  }\n\n  transitionElement.addEventListener(TRANSITION_END, handler)\n  setTimeout(() => {\n    if (!called) {\n      triggerTransitionEnd(transitionElement)\n    }\n  }, emulatedDuration)\n}\n\n/**\n * Return the previous/next element of a list.\n *\n * @param {array} list    The list of elements\n * @param activeElement   The active element\n * @param shouldGetNext   Choose to get next or previous element\n * @param isCycleAllowed\n * @return {Element|elem} The proper element\n */\nconst getNextActiveElement = (list, activeElement, shouldGetNext, isCycleAllowed) => {\n  const listLength = list.length\n  let index = list.indexOf(activeElement)\n\n  // if the element does not exist in the list return an element\n  // depending on the direction and if cycle is allowed\n  if (index === -1) {\n    return !shouldGetNext && isCycleAllowed ? list[listLength - 1] : list[0]\n  }\n\n  index += shouldGetNext ? 1 : -1\n\n  if (isCycleAllowed) {\n    index = (index + listLength) % listLength\n  }\n\n  return list[Math.max(0, Math.min(index, listLength - 1))]\n}\n\nexport {\n  defineJQueryPlugin,\n  execute,\n  executeAfterTransition,\n  findShadowRoot,\n  getElement,\n  getjQuery,\n  getNextActiveElement,\n  getTransitionDurationFromElement,\n  getUID,\n  isDisabled,\n  isElement,\n  isRTL,\n  isVisible,\n  noop,\n  onDOMContentLoaded,\n  parseSelector,\n  reflow,\n  triggerTransitionEnd,\n  toType\n}\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap dom/event-handler.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport { getjQuery } from '../util/index.js'\n\n/**\n * Constants\n */\n\nconst namespaceRegex = /[^.]*(?=\\..*)\\.|.*/\nconst stripNameRegex = /\\..*/\nconst stripUidRegex = /::\\d+$/\nconst eventRegistry = {} // Events storage\nlet uidEvent = 1\nconst customEvents = {\n  mouseenter: 'mouseover',\n  mouseleave: 'mouseout'\n}\n\nconst nativeEvents = new Set([\n  'click',\n  'dblclick',\n  'mouseup',\n  'mousedown',\n  'contextmenu',\n  'mousewheel',\n  'DOMMouseScroll',\n  'mouseover',\n  'mouseout',\n  'mousemove',\n  'selectstart',\n  'selectend',\n  'keydown',\n  'keypress',\n  'keyup',\n  'orientationchange',\n  'touchstart',\n  'touchmove',\n  'touchend',\n  'touchcancel',\n  'pointerdown',\n  'pointermove',\n  'pointerup',\n  'pointerleave',\n  'pointercancel',\n  'gesturestart',\n  'gesturechange',\n  'gestureend',\n  'focus',\n  'blur',\n  'change',\n  'reset',\n  'select',\n  'submit',\n  'focusin',\n  'focusout',\n  'load',\n  'unload',\n  'beforeunload',\n  'resize',\n  'move',\n  'DOMContentLoaded',\n  'readystatechange',\n  'error',\n  'abort',\n  'scroll'\n])\n\n/**\n * Private methods\n */\n\nfunction makeEventUid(element, uid) {\n  return (uid && `${uid}::${uidEvent++}`) || element.uidEvent || uidEvent++\n}\n\nfunction getElementEvents(element) {\n  const uid = makeEventUid(element)\n\n  element.uidEvent = uid\n  eventRegistry[uid] = eventRegistry[uid] || {}\n\n  return eventRegistry[uid]\n}\n\nfunction bootstrapHandler(element, fn) {\n  return function handler(event) {\n    hydrateObj(event, { delegateTarget: element })\n\n    if (handler.oneOff) {\n      EventHandler.off(element, event.type, fn)\n    }\n\n    return fn.apply(element, [event])\n  }\n}\n\nfunction bootstrapDelegationHandler(element, selector, fn) {\n  return function handler(event) {\n    const domElements = element.querySelectorAll(selector)\n\n    for (let { target } = event; target && target !== this; target = target.parentNode) {\n      for (const domElement of domElements) {\n        if (domElement !== target) {\n          continue\n        }\n\n        hydrateObj(event, { delegateTarget: target })\n\n        if (handler.oneOff) {\n          EventHandler.off(element, event.type, selector, fn)\n        }\n\n        return fn.apply(target, [event])\n      }\n    }\n  }\n}\n\nfunction findHandler(events, callable, delegationSelector = null) {\n  return Object.values(events)\n    .find(event => event.callable === callable && event.delegationSelector === delegationSelector)\n}\n\nfunction normalizeParameters(originalTypeEvent, handler, delegationFunction) {\n  const isDelegated = typeof handler === 'string'\n  // TODO: tooltip passes `false` instead of selector, so we need to check\n  const callable = isDelegated ? delegationFunction : (handler || delegationFunction)\n  let typeEvent = getTypeEvent(originalTypeEvent)\n\n  if (!nativeEvents.has(typeEvent)) {\n    typeEvent = originalTypeEvent\n  }\n\n  return [isDelegated, callable, typeEvent]\n}\n\nfunction addHandler(element, originalTypeEvent, handler, delegationFunction, oneOff) {\n  if (typeof originalTypeEvent !== 'string' || !element) {\n    return\n  }\n\n  let [isDelegated, callable, typeEvent] = normalizeParameters(originalTypeEvent, handler, delegationFunction)\n\n  // in case of mouseenter or mouseleave wrap the handler within a function that checks for its DOM position\n  // this prevents the handler from being dispatched the same way as mouseover or mouseout does\n  if (originalTypeEvent in customEvents) {\n    const wrapFunction = fn => {\n      return function (event) {\n        if (!event.relatedTarget || (event.relatedTarget !== event.delegateTarget && !event.delegateTarget.contains(event.relatedTarget))) {\n          return fn.call(this, event)\n        }\n      }\n    }\n\n    callable = wrapFunction(callable)\n  }\n\n  const events = getElementEvents(element)\n  const handlers = events[typeEvent] || (events[typeEvent] = {})\n  const previousFunction = findHandler(handlers, callable, isDelegated ? handler : null)\n\n  if (previousFunction) {\n    previousFunction.oneOff = previousFunction.oneOff && oneOff\n\n    return\n  }\n\n  const uid = makeEventUid(callable, originalTypeEvent.replace(namespaceRegex, ''))\n  const fn = isDelegated ?\n    bootstrapDelegationHandler(element, handler, callable) :\n    bootstrapHandler(element, callable)\n\n  fn.delegationSelector = isDelegated ? handler : null\n  fn.callable = callable\n  fn.oneOff = oneOff\n  fn.uidEvent = uid\n  handlers[uid] = fn\n\n  element.addEventListener(typeEvent, fn, isDelegated)\n}\n\nfunction removeHandler(element, events, typeEvent, handler, delegationSelector) {\n  const fn = findHandler(events[typeEvent], handler, delegationSelector)\n\n  if (!fn) {\n    return\n  }\n\n  element.removeEventListener(typeEvent, fn, Boolean(delegationSelector))\n  delete events[typeEvent][fn.uidEvent]\n}\n\nfunction removeNamespacedHandlers(element, events, typeEvent, namespace) {\n  const storeElementEvent = events[typeEvent] || {}\n\n  for (const [handlerKey, event] of Object.entries(storeElementEvent)) {\n    if (handlerKey.includes(namespace)) {\n      removeHandler(element, events, typeEvent, event.callable, event.delegationSelector)\n    }\n  }\n}\n\nfunction getTypeEvent(event) {\n  // allow to get the native events from namespaced events ('click.bs.button' --> 'click')\n  event = event.replace(stripNameRegex, '')\n  return customEvents[event] || event\n}\n\nconst EventHandler = {\n  on(element, event, handler, delegationFunction) {\n    addHandler(element, event, handler, delegationFunction, false)\n  },\n\n  one(element, event, handler, delegationFunction) {\n    addHandler(element, event, handler, delegationFunction, true)\n  },\n\n  off(element, originalTypeEvent, handler, delegationFunction) {\n    if (typeof originalTypeEvent !== 'string' || !element) {\n      return\n    }\n\n    const [isDelegated, callable, typeEvent] = normalizeParameters(originalTypeEvent, handler, delegationFunction)\n    const inNamespace = typeEvent !== originalTypeEvent\n    const events = getElementEvents(element)\n    const storeElementEvent = events[typeEvent] || {}\n    const isNamespace = originalTypeEvent.startsWith('.')\n\n    if (typeof callable !== 'undefined') {\n      // Simplest case: handler is passed, remove that listener ONLY.\n      if (!Object.keys(storeElementEvent).length) {\n        return\n      }\n\n      removeHandler(element, events, typeEvent, callable, isDelegated ? handler : null)\n      return\n    }\n\n    if (isNamespace) {\n      for (const elementEvent of Object.keys(events)) {\n        removeNamespacedHandlers(element, events, elementEvent, originalTypeEvent.slice(1))\n      }\n    }\n\n    for (const [keyHandlers, event] of Object.entries(storeElementEvent)) {\n      const handlerKey = keyHandlers.replace(stripUidRegex, '')\n\n      if (!inNamespace || originalTypeEvent.includes(handlerKey)) {\n        removeHandler(element, events, typeEvent, event.callable, event.delegationSelector)\n      }\n    }\n  },\n\n  trigger(element, event, args) {\n    if (typeof event !== 'string' || !element) {\n      return null\n    }\n\n    const $ = getjQuery()\n    const typeEvent = getTypeEvent(event)\n    const inNamespace = event !== typeEvent\n\n    let jQueryEvent = null\n    let bubbles = true\n    let nativeDispatch = true\n    let defaultPrevented = false\n\n    if (inNamespace && $) {\n      jQueryEvent = $.Event(event, args)\n\n      $(element).trigger(jQueryEvent)\n      bubbles = !jQueryEvent.isPropagationStopped()\n      nativeDispatch = !jQueryEvent.isImmediatePropagationStopped()\n      defaultPrevented = jQueryEvent.isDefaultPrevented()\n    }\n\n    const evt = hydrateObj(new Event(event, { bubbles, cancelable: true }), args)\n\n    if (defaultPrevented) {\n      evt.preventDefault()\n    }\n\n    if (nativeDispatch) {\n      element.dispatchEvent(evt)\n    }\n\n    if (evt.defaultPrevented && jQueryEvent) {\n      jQueryEvent.preventDefault()\n    }\n\n    return evt\n  }\n}\n\nfunction hydrateObj(obj, meta = {}) {\n  for (const [key, value] of Object.entries(meta)) {\n    try {\n      obj[key] = value\n    } catch {\n      Object.defineProperty(obj, key, {\n        configurable: true,\n        get() {\n          return value\n        }\n      })\n    }\n  }\n\n  return obj\n}\n\nexport default EventHandler\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap dom/manipulator.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nfunction normalizeData(value) {\n  if (value === 'true') {\n    return true\n  }\n\n  if (value === 'false') {\n    return false\n  }\n\n  if (value === Number(value).toString()) {\n    return Number(value)\n  }\n\n  if (value === '' || value === 'null') {\n    return null\n  }\n\n  if (typeof value !== 'string') {\n    return value\n  }\n\n  try {\n    return JSON.parse(decodeURIComponent(value))\n  } catch {\n    return value\n  }\n}\n\nfunction normalizeDataKey(key) {\n  return key.replace(/[A-Z]/g, chr => `-${chr.toLowerCase()}`)\n}\n\nconst Manipulator = {\n  setDataAttribute(element, key, value) {\n    element.setAttribute(`data-bs-${normalizeDataKey(key)}`, value)\n  },\n\n  removeDataAttribute(element, key) {\n    element.removeAttribute(`data-bs-${normalizeDataKey(key)}`)\n  },\n\n  getDataAttributes(element) {\n    if (!element) {\n      return {}\n    }\n\n    const attributes = {}\n    const bsKeys = Object.keys(element.dataset).filter(key => key.startsWith('bs') && !key.startsWith('bsConfig'))\n\n    for (const key of bsKeys) {\n      let pureKey = key.replace(/^bs/, '')\n      pureKey = pureKey.charAt(0).toLowerCase() + pureKey.slice(1, pureKey.length)\n      attributes[pureKey] = normalizeData(element.dataset[key])\n    }\n\n    return attributes\n  },\n\n  getDataAttribute(element, key) {\n    return normalizeData(element.getAttribute(`data-bs-${normalizeDataKey(key)}`))\n  }\n}\n\nexport default Manipulator\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap util/config.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport Manipulator from '../dom/manipulator.js'\nimport { isElement, toType } from './index.js'\n\n/**\n * Class definition\n */\n\nclass Config {\n  // Getters\n  static get Default() {\n    return {}\n  }\n\n  static get DefaultType() {\n    return {}\n  }\n\n  static get NAME() {\n    throw new Error('You have to implement the static method \"NAME\", for each component!')\n  }\n\n  _getConfig(config) {\n    config = this._mergeConfigObj(config)\n    config = this._configAfterMerge(config)\n    this._typeCheckConfig(config)\n    return config\n  }\n\n  _configAfterMerge(config) {\n    return config\n  }\n\n  _mergeConfigObj(config, element) {\n    const jsonConfig = isElement(element) ? Manipulator.getDataAttribute(element, 'config') : {} // try to parse\n\n    return {\n      ...this.constructor.Default,\n      ...(typeof jsonConfig === 'object' ? jsonConfig : {}),\n      ...(isElement(element) ? Manipulator.getDataAttributes(element) : {}),\n      ...(typeof config === 'object' ? config : {})\n    }\n  }\n\n  _typeCheckConfig(config, configTypes = this.constructor.DefaultType) {\n    for (const [property, expectedTypes] of Object.entries(configTypes)) {\n      const value = config[property]\n      const valueType = isElement(value) ? 'element' : toType(value)\n\n      if (!new RegExp(expectedTypes).test(valueType)) {\n        throw new TypeError(\n          `${this.constructor.NAME.toUpperCase()}: Option \"${property}\" provided type \"${valueType}\" but expected type \"${expectedTypes}\".`\n        )\n      }\n    }\n  }\n}\n\nexport default Config\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap base-component.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport Data from './dom/data.js'\nimport EventHandler from './dom/event-handler.js'\nimport Config from './util/config.js'\nimport { executeAfterTransition, getElement } from './util/index.js'\n\n/**\n * Constants\n */\n\nconst VERSION = '5.3.1'\n\n/**\n * Class definition\n */\n\nclass BaseComponent extends Config {\n  constructor(element, config) {\n    super()\n\n    element = getElement(element)\n    if (!element) {\n      return\n    }\n\n    this._element = element\n    this._config = this._getConfig(config)\n\n    Data.set(this._element, this.constructor.DATA_KEY, this)\n  }\n\n  // Public\n  dispose() {\n    Data.remove(this._element, this.constructor.DATA_KEY)\n    EventHandler.off(this._element, this.constructor.EVENT_KEY)\n\n    for (const propertyName of Object.getOwnPropertyNames(this)) {\n      this[propertyName] = null\n    }\n  }\n\n  _queueCallback(callback, element, isAnimated = true) {\n    executeAfterTransition(callback, element, isAnimated)\n  }\n\n  _getConfig(config) {\n    config = this._mergeConfigObj(config, this._element)\n    config = this._configAfterMerge(config)\n    this._typeCheckConfig(config)\n    return config\n  }\n\n  // Static\n  static getInstance(element) {\n    return Data.get(getElement(element), this.DATA_KEY)\n  }\n\n  static getOrCreateInstance(element, config = {}) {\n    return this.getInstance(element) || new this(element, typeof config === 'object' ? config : null)\n  }\n\n  static get VERSION() {\n    return VERSION\n  }\n\n  static get DATA_KEY() {\n    return `bs.${this.NAME}`\n  }\n\n  static get EVENT_KEY() {\n    return `.${this.DATA_KEY}`\n  }\n\n  static eventName(name) {\n    return `${name}${this.EVENT_KEY}`\n  }\n}\n\nexport default BaseComponent\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap dom/selector-engine.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport { isDisabled, isVisible, parseSelector } from '../util/index.js'\n\nconst getSelector = element => {\n  let selector = element.getAttribute('data-bs-target')\n\n  if (!selector || selector === '#') {\n    let hrefAttribute = element.getAttribute('href')\n\n    // The only valid content that could double as a selector are IDs or classes,\n    // so everything starting with `#` or `.`. If a \"real\" URL is used as the selector,\n    // `document.querySelector` will rightfully complain it is invalid.\n    // See https://github.com/twbs/bootstrap/issues/32273\n    if (!hrefAttribute || (!hrefAttribute.includes('#') && !hrefAttribute.startsWith('.'))) {\n      return null\n    }\n\n    // Just in case some CMS puts out a full URL with the anchor appended\n    if (hrefAttribute.includes('#') && !hrefAttribute.startsWith('#')) {\n      hrefAttribute = `#${hrefAttribute.split('#')[1]}`\n    }\n\n    selector = hrefAttribute && hrefAttribute !== '#' ? hrefAttribute.trim() : null\n  }\n\n  return parseSelector(selector)\n}\n\nconst SelectorEngine = {\n  find(selector, element = document.documentElement) {\n    return [].concat(...Element.prototype.querySelectorAll.call(element, selector))\n  },\n\n  findOne(selector, element = document.documentElement) {\n    return Element.prototype.querySelector.call(element, selector)\n  },\n\n  children(element, selector) {\n    return [].concat(...element.children).filter(child => child.matches(selector))\n  },\n\n  parents(element, selector) {\n    const parents = []\n    let ancestor = element.parentNode.closest(selector)\n\n    while (ancestor) {\n      parents.push(ancestor)\n      ancestor = ancestor.parentNode.closest(selector)\n    }\n\n    return parents\n  },\n\n  prev(element, selector) {\n    let previous = element.previousElementSibling\n\n    while (previous) {\n      if (previous.matches(selector)) {\n        return [previous]\n      }\n\n      previous = previous.previousElementSibling\n    }\n\n    return []\n  },\n  // TODO: this is now unused; remove later along with prev()\n  next(element, selector) {\n    let next = element.nextElementSibling\n\n    while (next) {\n      if (next.matches(selector)) {\n        return [next]\n      }\n\n      next = next.nextElementSibling\n    }\n\n    return []\n  },\n\n  focusableChildren(element) {\n    const focusables = [\n      'a',\n      'button',\n      'input',\n      'textarea',\n      'select',\n      'details',\n      '[tabindex]',\n      '[contenteditable=\"true\"]'\n    ].map(selector => `${selector}:not([tabindex^=\"-\"])`).join(',')\n\n    return this.find(focusables, element).filter(el => !isDisabled(el) && isVisible(el))\n  },\n\n  getSelectorFromElement(element) {\n    const selector = getSelector(element)\n\n    if (selector) {\n      return SelectorEngine.findOne(selector) ? selector : null\n    }\n\n    return null\n  },\n\n  getElementFromSelector(element) {\n    const selector = getSelector(element)\n\n    return selector ? SelectorEngine.findOne(selector) : null\n  },\n\n  getMultipleElementsFromSelector(element) {\n    const selector = getSelector(element)\n\n    return selector ? SelectorEngine.find(selector) : []\n  }\n}\n\nexport default SelectorEngine\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap util/component-functions.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport EventHandler from '../dom/event-handler.js'\nimport SelectorEngine from '../dom/selector-engine.js'\nimport { isDisabled } from './index.js'\n\nconst enableDismissTrigger = (component, method = 'hide') => {\n  const clickEvent = `click.dismiss${component.EVENT_KEY}`\n  const name = component.NAME\n\n  EventHandler.on(document, clickEvent, `[data-bs-dismiss=\"${name}\"]`, function (event) {\n    if (['A', 'AREA'].includes(this.tagName)) {\n      event.preventDefault()\n    }\n\n    if (isDisabled(this)) {\n      return\n    }\n\n    const target = SelectorEngine.getElementFromSelector(this) || this.closest(`.${name}`)\n    const instance = component.getOrCreateInstance(target)\n\n    // Method argument is left, for Alert and only, as it doesn't implement the 'hide' method\n    instance[method]()\n  })\n}\n\nexport {\n  enableDismissTrigger\n}\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap alert.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport BaseComponent from './base-component.js'\nimport EventHandler from './dom/event-handler.js'\nimport { enableDismissTrigger } from './util/component-functions.js'\nimport { defineJQueryPlugin } from './util/index.js'\n\n/**\n * Constants\n */\n\nconst NAME = 'alert'\nconst DATA_KEY = 'bs.alert'\nconst EVENT_KEY = `.${DATA_KEY}`\n\nconst EVENT_CLOSE = `close${EVENT_KEY}`\nconst EVENT_CLOSED = `closed${EVENT_KEY}`\nconst CLASS_NAME_FADE = 'fade'\nconst CLASS_NAME_SHOW = 'show'\n\n/**\n * Class definition\n */\n\nclass Alert extends BaseComponent {\n  // Getters\n  static get NAME() {\n    return NAME\n  }\n\n  // Public\n  close() {\n    const closeEvent = EventHandler.trigger(this._element, EVENT_CLOSE)\n\n    if (closeEvent.defaultPrevented) {\n      return\n    }\n\n    this._element.classList.remove(CLASS_NAME_SHOW)\n\n    const isAnimated = this._element.classList.contains(CLASS_NAME_FADE)\n    this._queueCallback(() => this._destroyElement(), this._element, isAnimated)\n  }\n\n  // Private\n  _destroyElement() {\n    this._element.remove()\n    EventHandler.trigger(this._element, EVENT_CLOSED)\n    this.dispose()\n  }\n\n  // Static\n  static jQueryInterface(config) {\n    return this.each(function () {\n      const data = Alert.getOrCreateInstance(this)\n\n      if (typeof config !== 'string') {\n        return\n      }\n\n      if (data[config] === undefined || config.startsWith('_') || config === 'constructor') {\n        throw new TypeError(`No method named \"${config}\"`)\n      }\n\n      data[config](this)\n    })\n  }\n}\n\n/**\n * Data API implementation\n */\n\nenableDismissTrigger(Alert, 'close')\n\n/**\n * jQuery\n */\n\ndefineJQueryPlugin(Alert)\n\nexport default Alert\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap button.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport BaseComponent from './base-component.js'\nimport EventHandler from './dom/event-handler.js'\nimport { defineJQueryPlugin } from './util/index.js'\n\n/**\n * Constants\n */\n\nconst NAME = 'button'\nconst DATA_KEY = 'bs.button'\nconst EVENT_KEY = `.${DATA_KEY}`\nconst DATA_API_KEY = '.data-api'\n\nconst CLASS_NAME_ACTIVE = 'active'\nconst SELECTOR_DATA_TOGGLE = '[data-bs-toggle=\"button\"]'\nconst EVENT_CLICK_DATA_API = `click${EVENT_KEY}${DATA_API_KEY}`\n\n/**\n * Class definition\n */\n\nclass Button extends BaseComponent {\n  // Getters\n  static get NAME() {\n    return NAME\n  }\n\n  // Public\n  toggle() {\n    // Toggle class and sync the `aria-pressed` attribute with the return value of the `.toggle()` method\n    this._element.setAttribute('aria-pressed', this._element.classList.toggle(CLASS_NAME_ACTIVE))\n  }\n\n  // Static\n  static jQueryInterface(config) {\n    return this.each(function () {\n      const data = Button.getOrCreateInstance(this)\n\n      if (config === 'toggle') {\n        data[config]()\n      }\n    })\n  }\n}\n\n/**\n * Data API implementation\n */\n\nEventHandler.on(document, EVENT_CLICK_DATA_API, SELECTOR_DATA_TOGGLE, event => {\n  event.preventDefault()\n\n  const button = event.target.closest(SELECTOR_DATA_TOGGLE)\n  const data = Button.getOrCreateInstance(button)\n\n  data.toggle()\n})\n\n/**\n * jQuery\n */\n\ndefineJQueryPlugin(Button)\n\nexport default Button\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap util/swipe.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport EventHandler from '../dom/event-handler.js'\nimport Config from './config.js'\nimport { execute } from './index.js'\n\n/**\n * Constants\n */\n\nconst NAME = 'swipe'\nconst EVENT_KEY = '.bs.swipe'\nconst EVENT_TOUCHSTART = `touchstart${EVENT_KEY}`\nconst EVENT_TOUCHMOVE = `touchmove${EVENT_KEY}`\nconst EVENT_TOUCHEND = `touchend${EVENT_KEY}`\nconst EVENT_POINTERDOWN = `pointerdown${EVENT_KEY}`\nconst EVENT_POINTERUP = `pointerup${EVENT_KEY}`\nconst POINTER_TYPE_TOUCH = 'touch'\nconst POINTER_TYPE_PEN = 'pen'\nconst CLASS_NAME_POINTER_EVENT = 'pointer-event'\nconst SWIPE_THRESHOLD = 40\n\nconst Default = {\n  endCallback: null,\n  leftCallback: null,\n  rightCallback: null\n}\n\nconst DefaultType = {\n  endCallback: '(function|null)',\n  leftCallback: '(function|null)',\n  rightCallback: '(function|null)'\n}\n\n/**\n * Class definition\n */\n\nclass Swipe extends Config {\n  constructor(element, config) {\n    super()\n    this._element = element\n\n    if (!element || !Swipe.isSupported()) {\n      return\n    }\n\n    this._config = this._getConfig(config)\n    this._deltaX = 0\n    this._supportPointerEvents = Boolean(window.PointerEvent)\n    this._initEvents()\n  }\n\n  // Getters\n  static get Default() {\n    return Default\n  }\n\n  static get DefaultType() {\n    return DefaultType\n  }\n\n  static get NAME() {\n    return NAME\n  }\n\n  // Public\n  dispose() {\n    EventHandler.off(this._element, EVENT_KEY)\n  }\n\n  // Private\n  _start(event) {\n    if (!this._supportPointerEvents) {\n      this._deltaX = event.touches[0].clientX\n\n      return\n    }\n\n    if (this._eventIsPointerPenTouch(event)) {\n      this._deltaX = event.clientX\n    }\n  }\n\n  _end(event) {\n    if (this._eventIsPointerPenTouch(event)) {\n      this._deltaX = event.clientX - this._deltaX\n    }\n\n    this._handleSwipe()\n    execute(this._config.endCallback)\n  }\n\n  _move(event) {\n    this._deltaX = event.touches && event.touches.length > 1 ?\n      0 :\n      event.touches[0].clientX - this._deltaX\n  }\n\n  _handleSwipe() {\n    const absDeltaX = Math.abs(this._deltaX)\n\n    if (absDeltaX <= SWIPE_THRESHOLD) {\n      return\n    }\n\n    const direction = absDeltaX / this._deltaX\n\n    this._deltaX = 0\n\n    if (!direction) {\n      return\n    }\n\n    execute(direction > 0 ? this._config.rightCallback : this._config.leftCallback)\n  }\n\n  _initEvents() {\n    if (this._supportPointerEvents) {\n      EventHandler.on(this._element, EVENT_POINTERDOWN, event => this._start(event))\n      EventHandler.on(this._element, EVENT_POINTERUP, event => this._end(event))\n\n      this._element.classList.add(CLASS_NAME_POINTER_EVENT)\n    } else {\n      EventHandler.on(this._element, EVENT_TOUCHSTART, event => this._start(event))\n      EventHandler.on(this._element, EVENT_TOUCHMOVE, event => this._move(event))\n      EventHandler.on(this._element, EVENT_TOUCHEND, event => this._end(event))\n    }\n  }\n\n  _eventIsPointerPenTouch(event) {\n    return this._supportPointerEvents && (event.pointerType === POINTER_TYPE_PEN || event.pointerType === POINTER_TYPE_TOUCH)\n  }\n\n  // Static\n  static isSupported() {\n    return 'ontouchstart' in document.documentElement || navigator.maxTouchPoints > 0\n  }\n}\n\nexport default Swipe\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap carousel.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport BaseComponent from './base-component.js'\nimport EventHandler from './dom/event-handler.js'\nimport Manipulator from './dom/manipulator.js'\nimport SelectorEngine from './dom/selector-engine.js'\nimport {\n  defineJQueryPlugin,\n  getNextActiveElement,\n  isRTL,\n  isVisible,\n  reflow,\n  triggerTransitionEnd\n} from './util/index.js'\nimport Swipe from './util/swipe.js'\n\n/**\n * Constants\n */\n\nconst NAME = 'carousel'\nconst DATA_KEY = 'bs.carousel'\nconst EVENT_KEY = `.${DATA_KEY}`\nconst DATA_API_KEY = '.data-api'\n\nconst ARROW_LEFT_KEY = 'ArrowLeft'\nconst ARROW_RIGHT_KEY = 'ArrowRight'\nconst TOUCHEVENT_COMPAT_WAIT = 500 // Time for mouse compat events to fire after touch\n\nconst ORDER_NEXT = 'next'\nconst ORDER_PREV = 'prev'\nconst DIRECTION_LEFT = 'left'\nconst DIRECTION_RIGHT = 'right'\n\nconst EVENT_SLIDE = `slide${EVENT_KEY}`\nconst EVENT_SLID = `slid${EVENT_KEY}`\nconst EVENT_KEYDOWN = `keydown${EVENT_KEY}`\nconst EVENT_MOUSEENTER = `mouseenter${EVENT_KEY}`\nconst EVENT_MOUSELEAVE = `mouseleave${EVENT_KEY}`\nconst EVENT_DRAG_START = `dragstart${EVENT_KEY}`\nconst EVENT_LOAD_DATA_API = `load${EVENT_KEY}${DATA_API_KEY}`\nconst EVENT_CLICK_DATA_API = `click${EVENT_KEY}${DATA_API_KEY}`\n\nconst CLASS_NAME_CAROUSEL = 'carousel'\nconst CLASS_NAME_ACTIVE = 'active'\nconst CLASS_NAME_SLIDE = 'slide'\nconst CLASS_NAME_END = 'carousel-item-end'\nconst CLASS_NAME_START = 'carousel-item-start'\nconst CLASS_NAME_NEXT = 'carousel-item-next'\nconst CLASS_NAME_PREV = 'carousel-item-prev'\n\nconst SELECTOR_ACTIVE = '.active'\nconst SELECTOR_ITEM = '.carousel-item'\nconst SELECTOR_ACTIVE_ITEM = SELECTOR_ACTIVE + SELECTOR_ITEM\nconst SELECTOR_ITEM_IMG = '.carousel-item img'\nconst SELECTOR_INDICATORS = '.carousel-indicators'\nconst SELECTOR_DATA_SLIDE = '[data-bs-slide], [data-bs-slide-to]'\nconst SELECTOR_DATA_RIDE = '[data-bs-ride=\"carousel\"]'\n\nconst KEY_TO_DIRECTION = {\n  [ARROW_LEFT_KEY]: DIRECTION_RIGHT,\n  [ARROW_RIGHT_KEY]: DIRECTION_LEFT\n}\n\nconst Default = {\n  interval: 5000,\n  keyboard: true,\n  pause: 'hover',\n  ride: false,\n  touch: true,\n  wrap: true\n}\n\nconst DefaultType = {\n  interval: '(number|boolean)', // TODO:v6 remove boolean support\n  keyboard: 'boolean',\n  pause: '(string|boolean)',\n  ride: '(boolean|string)',\n  touch: 'boolean',\n  wrap: 'boolean'\n}\n\n/**\n * Class definition\n */\n\nclass Carousel extends BaseComponent {\n  constructor(element, config) {\n    super(element, config)\n\n    this._interval = null\n    this._activeElement = null\n    this._isSliding = false\n    this.touchTimeout = null\n    this._swipeHelper = null\n\n    this._indicatorsElement = SelectorEngine.findOne(SELECTOR_INDICATORS, this._element)\n    this._addEventListeners()\n\n    if (this._config.ride === CLASS_NAME_CAROUSEL) {\n      this.cycle()\n    }\n  }\n\n  // Getters\n  static get Default() {\n    return Default\n  }\n\n  static get DefaultType() {\n    return DefaultType\n  }\n\n  static get NAME() {\n    return NAME\n  }\n\n  // Public\n  next() {\n    this._slide(ORDER_NEXT)\n  }\n\n  nextWhenVisible() {\n    // FIXME TODO use `document.visibilityState`\n    // Don't call next when the page isn't visible\n    // or the carousel or its parent isn't visible\n    if (!document.hidden && isVisible(this._element)) {\n      this.next()\n    }\n  }\n\n  prev() {\n    this._slide(ORDER_PREV)\n  }\n\n  pause() {\n    if (this._isSliding) {\n      triggerTransitionEnd(this._element)\n    }\n\n    this._clearInterval()\n  }\n\n  cycle() {\n    this._clearInterval()\n    this._updateInterval()\n\n    this._interval = setInterval(() => this.nextWhenVisible(), this._config.interval)\n  }\n\n  _maybeEnableCycle() {\n    if (!this._config.ride) {\n      return\n    }\n\n    if (this._isSliding) {\n      EventHandler.one(this._element, EVENT_SLID, () => this.cycle())\n      return\n    }\n\n    this.cycle()\n  }\n\n  to(index) {\n    const items = this._getItems()\n    if (index > items.length - 1 || index < 0) {\n      return\n    }\n\n    if (this._isSliding) {\n      EventHandler.one(this._element, EVENT_SLID, () => this.to(index))\n      return\n    }\n\n    const activeIndex = this._getItemIndex(this._getActive())\n    if (activeIndex === index) {\n      return\n    }\n\n    const order = index > activeIndex ? ORDER_NEXT : ORDER_PREV\n\n    this._slide(order, items[index])\n  }\n\n  dispose() {\n    if (this._swipeHelper) {\n      this._swipeHelper.dispose()\n    }\n\n    super.dispose()\n  }\n\n  // Private\n  _configAfterMerge(config) {\n    config.defaultInterval = config.interval\n    return config\n  }\n\n  _addEventListeners() {\n    if (this._config.keyboard) {\n      EventHandler.on(this._element, EVENT_KEYDOWN, event => this._keydown(event))\n    }\n\n    if (this._config.pause === 'hover') {\n      EventHandler.on(this._element, EVENT_MOUSEENTER, () => this.pause())\n      EventHandler.on(this._element, EVENT_MOUSELEAVE, () => this._maybeEnableCycle())\n    }\n\n    if (this._config.touch && Swipe.isSupported()) {\n      this._addTouchEventListeners()\n    }\n  }\n\n  _addTouchEventListeners() {\n    for (const img of SelectorEngine.find(SELECTOR_ITEM_IMG, this._element)) {\n      EventHandler.on(img, EVENT_DRAG_START, event => event.preventDefault())\n    }\n\n    const endCallBack = () => {\n      if (this._config.pause !== 'hover') {\n        return\n      }\n\n      // If it's a touch-enabled device, mouseenter/leave are fired as\n      // part of the mouse compatibility events on first tap - the carousel\n      // would stop cycling until user tapped out of it;\n      // here, we listen for touchend, explicitly pause the carousel\n      // (as if it's the second time we tap on it, mouseenter compat event\n      // is NOT fired) and after a timeout (to allow for mouse compatibility\n      // events to fire) we explicitly restart cycling\n\n      this.pause()\n      if (this.touchTimeout) {\n        clearTimeout(this.touchTimeout)\n      }\n\n      this.touchTimeout = setTimeout(() => this._maybeEnableCycle(), TOUCHEVENT_COMPAT_WAIT + this._config.interval)\n    }\n\n    const swipeConfig = {\n      leftCallback: () => this._slide(this._directionToOrder(DIRECTION_LEFT)),\n      rightCallback: () => this._slide(this._directionToOrder(DIRECTION_RIGHT)),\n      endCallback: endCallBack\n    }\n\n    this._swipeHelper = new Swipe(this._element, swipeConfig)\n  }\n\n  _keydown(event) {\n    if (/input|textarea/i.test(event.target.tagName)) {\n      return\n    }\n\n    const direction = KEY_TO_DIRECTION[event.key]\n    if (direction) {\n      event.preventDefault()\n      this._slide(this._directionToOrder(direction))\n    }\n  }\n\n  _getItemIndex(element) {\n    return this._getItems().indexOf(element)\n  }\n\n  _setActiveIndicatorElement(index) {\n    if (!this._indicatorsElement) {\n      return\n    }\n\n    const activeIndicator = SelectorEngine.findOne(SELECTOR_ACTIVE, this._indicatorsElement)\n\n    activeIndicator.classList.remove(CLASS_NAME_ACTIVE)\n    activeIndicator.removeAttribute('aria-current')\n\n    const newActiveIndicator = SelectorEngine.findOne(`[data-bs-slide-to=\"${index}\"]`, this._indicatorsElement)\n\n    if (newActiveIndicator) {\n      newActiveIndicator.classList.add(CLASS_NAME_ACTIVE)\n      newActiveIndicator.setAttribute('aria-current', 'true')\n    }\n  }\n\n  _updateInterval() {\n    const element = this._activeElement || this._getActive()\n\n    if (!element) {\n      return\n    }\n\n    const elementInterval = Number.parseInt(element.getAttribute('data-bs-interval'), 10)\n\n    this._config.interval = elementInterval || this._config.defaultInterval\n  }\n\n  _slide(order, element = null) {\n    if (this._isSliding) {\n      return\n    }\n\n    const activeElement = this._getActive()\n    const isNext = order === ORDER_NEXT\n    const nextElement = element || getNextActiveElement(this._getItems(), activeElement, isNext, this._config.wrap)\n\n    if (nextElement === activeElement) {\n      return\n    }\n\n    const nextElementIndex = this._getItemIndex(nextElement)\n\n    const triggerEvent = eventName => {\n      return EventHandler.trigger(this._element, eventName, {\n        relatedTarget: nextElement,\n        direction: this._orderToDirection(order),\n        from: this._getItemIndex(activeElement),\n        to: nextElementIndex\n      })\n    }\n\n    const slideEvent = triggerEvent(EVENT_SLIDE)\n\n    if (slideEvent.defaultPrevented) {\n      return\n    }\n\n    if (!activeElement || !nextElement) {\n      // Some weirdness is happening, so we bail\n      // TODO: change tests that use empty divs to avoid this check\n      return\n    }\n\n    const isCycling = Boolean(this._interval)\n    this.pause()\n\n    this._isSliding = true\n\n    this._setActiveIndicatorElement(nextElementIndex)\n    this._activeElement = nextElement\n\n    const directionalClassName = isNext ? CLASS_NAME_START : CLASS_NAME_END\n    const orderClassName = isNext ? CLASS_NAME_NEXT : CLASS_NAME_PREV\n\n    nextElement.classList.add(orderClassName)\n\n    reflow(nextElement)\n\n    activeElement.classList.add(directionalClassName)\n    nextElement.classList.add(directionalClassName)\n\n    const completeCallBack = () => {\n      nextElement.classList.remove(directionalClassName, orderClassName)\n      nextElement.classList.add(CLASS_NAME_ACTIVE)\n\n      activeElement.classList.remove(CLASS_NAME_ACTIVE, orderClassName, directionalClassName)\n\n      this._isSliding = false\n\n      triggerEvent(EVENT_SLID)\n    }\n\n    this._queueCallback(completeCallBack, activeElement, this._isAnimated())\n\n    if (isCycling) {\n      this.cycle()\n    }\n  }\n\n  _isAnimated() {\n    return this._element.classList.contains(CLASS_NAME_SLIDE)\n  }\n\n  _getActive() {\n    return SelectorEngine.findOne(SELECTOR_ACTIVE_ITEM, this._element)\n  }\n\n  _getItems() {\n    return SelectorEngine.find(SELECTOR_ITEM, this._element)\n  }\n\n  _clearInterval() {\n    if (this._interval) {\n      clearInterval(this._interval)\n      this._interval = null\n    }\n  }\n\n  _directionToOrder(direction) {\n    if (isRTL()) {\n      return direction === DIRECTION_LEFT ? ORDER_PREV : ORDER_NEXT\n    }\n\n    return direction === DIRECTION_LEFT ? ORDER_NEXT : ORDER_PREV\n  }\n\n  _orderToDirection(order) {\n    if (isRTL()) {\n      return order === ORDER_PREV ? DIRECTION_LEFT : DIRECTION_RIGHT\n    }\n\n    return order === ORDER_PREV ? DIRECTION_RIGHT : DIRECTION_LEFT\n  }\n\n  // Static\n  static jQueryInterface(config) {\n    return this.each(function () {\n      const data = Carousel.getOrCreateInstance(this, config)\n\n      if (typeof config === 'number') {\n        data.to(config)\n        return\n      }\n\n      if (typeof config === 'string') {\n        if (data[config] === undefined || config.startsWith('_') || config === 'constructor') {\n          throw new TypeError(`No method named \"${config}\"`)\n        }\n\n        data[config]()\n      }\n    })\n  }\n}\n\n/**\n * Data API implementation\n */\n\nEventHandler.on(document, EVENT_CLICK_DATA_API, SELECTOR_DATA_SLIDE, function (event) {\n  const target = SelectorEngine.getElementFromSelector(this)\n\n  if (!target || !target.classList.contains(CLASS_NAME_CAROUSEL)) {\n    return\n  }\n\n  event.preventDefault()\n\n  const carousel = Carousel.getOrCreateInstance(target)\n  const slideIndex = this.getAttribute('data-bs-slide-to')\n\n  if (slideIndex) {\n    carousel.to(slideIndex)\n    carousel._maybeEnableCycle()\n    return\n  }\n\n  if (Manipulator.getDataAttribute(this, 'slide') === 'next') {\n    carousel.next()\n    carousel._maybeEnableCycle()\n    return\n  }\n\n  carousel.prev()\n  carousel._maybeEnableCycle()\n})\n\nEventHandler.on(window, EVENT_LOAD_DATA_API, () => {\n  const carousels = SelectorEngine.find(SELECTOR_DATA_RIDE)\n\n  for (const carousel of carousels) {\n    Carousel.getOrCreateInstance(carousel)\n  }\n})\n\n/**\n * jQuery\n */\n\ndefineJQueryPlugin(Carousel)\n\nexport default Carousel\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap collapse.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport BaseComponent from './base-component.js'\nimport EventHandler from './dom/event-handler.js'\nimport SelectorEngine from './dom/selector-engine.js'\nimport {\n  defineJQueryPlugin,\n  getElement,\n  reflow\n} from './util/index.js'\n\n/**\n * Constants\n */\n\nconst NAME = 'collapse'\nconst DATA_KEY = 'bs.collapse'\nconst EVENT_KEY = `.${DATA_KEY}`\nconst DATA_API_KEY = '.data-api'\n\nconst EVENT_SHOW = `show${EVENT_KEY}`\nconst EVENT_SHOWN = `shown${EVENT_KEY}`\nconst EVENT_HIDE = `hide${EVENT_KEY}`\nconst EVENT_HIDDEN = `hidden${EVENT_KEY}`\nconst EVENT_CLICK_DATA_API = `click${EVENT_KEY}${DATA_API_KEY}`\n\nconst CLASS_NAME_SHOW = 'show'\nconst CLASS_NAME_COLLAPSE = 'collapse'\nconst CLASS_NAME_COLLAPSING = 'collapsing'\nconst CLASS_NAME_COLLAPSED = 'collapsed'\nconst CLASS_NAME_DEEPER_CHILDREN = `:scope .${CLASS_NAME_COLLAPSE} .${CLASS_NAME_COLLAPSE}`\nconst CLASS_NAME_HORIZONTAL = 'collapse-horizontal'\n\nconst WIDTH = 'width'\nconst HEIGHT = 'height'\n\nconst SELECTOR_ACTIVES = '.collapse.show, .collapse.collapsing'\nconst SELECTOR_DATA_TOGGLE = '[data-bs-toggle=\"collapse\"]'\n\nconst Default = {\n  parent: null,\n  toggle: true\n}\n\nconst DefaultType = {\n  parent: '(null|element)',\n  toggle: 'boolean'\n}\n\n/**\n * Class definition\n */\n\nclass Collapse extends BaseComponent {\n  constructor(element, config) {\n    super(element, config)\n\n    this._isTransitioning = false\n    this._triggerArray = []\n\n    const toggleList = SelectorEngine.find(SELECTOR_DATA_TOGGLE)\n\n    for (const elem of toggleList) {\n      const selector = SelectorEngine.getSelectorFromElement(elem)\n      const filterElement = SelectorEngine.find(selector)\n        .filter(foundElement => foundElement === this._element)\n\n      if (selector !== null && filterElement.length) {\n        this._triggerArray.push(elem)\n      }\n    }\n\n    this._initializeChildren()\n\n    if (!this._config.parent) {\n      this._addAriaAndCollapsedClass(this._triggerArray, this._isShown())\n    }\n\n    if (this._config.toggle) {\n      this.toggle()\n    }\n  }\n\n  // Getters\n  static get Default() {\n    return Default\n  }\n\n  static get DefaultType() {\n    return DefaultType\n  }\n\n  static get NAME() {\n    return NAME\n  }\n\n  // Public\n  toggle() {\n    if (this._isShown()) {\n      this.hide()\n    } else {\n      this.show()\n    }\n  }\n\n  show() {\n    if (this._isTransitioning || this._isShown()) {\n      return\n    }\n\n    let activeChildren = []\n\n    // find active children\n    if (this._config.parent) {\n      activeChildren = this._getFirstLevelChildren(SELECTOR_ACTIVES)\n        .filter(element => element !== this._element)\n        .map(element => Collapse.getOrCreateInstance(element, { toggle: false }))\n    }\n\n    if (activeChildren.length && activeChildren[0]._isTransitioning) {\n      return\n    }\n\n    const startEvent = EventHandler.trigger(this._element, EVENT_SHOW)\n    if (startEvent.defaultPrevented) {\n      return\n    }\n\n    for (const activeInstance of activeChildren) {\n      activeInstance.hide()\n    }\n\n    const dimension = this._getDimension()\n\n    this._element.classList.remove(CLASS_NAME_COLLAPSE)\n    this._element.classList.add(CLASS_NAME_COLLAPSING)\n\n    this._element.style[dimension] = 0\n\n    this._addAriaAndCollapsedClass(this._triggerArray, true)\n    this._isTransitioning = true\n\n    const complete = () => {\n      this._isTransitioning = false\n\n      this._element.classList.remove(CLASS_NAME_COLLAPSING)\n      this._element.classList.add(CLASS_NAME_COLLAPSE, CLASS_NAME_SHOW)\n\n      this._element.style[dimension] = ''\n\n      EventHandler.trigger(this._element, EVENT_SHOWN)\n    }\n\n    const capitalizedDimension = dimension[0].toUpperCase() + dimension.slice(1)\n    const scrollSize = `scroll${capitalizedDimension}`\n\n    this._queueCallback(complete, this._element, true)\n    this._element.style[dimension] = `${this._element[scrollSize]}px`\n  }\n\n  hide() {\n    if (this._isTransitioning || !this._isShown()) {\n      return\n    }\n\n    const startEvent = EventHandler.trigger(this._element, EVENT_HIDE)\n    if (startEvent.defaultPrevented) {\n      return\n    }\n\n    const dimension = this._getDimension()\n\n    this._element.style[dimension] = `${this._element.getBoundingClientRect()[dimension]}px`\n\n    reflow(this._element)\n\n    this._element.classList.add(CLASS_NAME_COLLAPSING)\n    this._element.classList.remove(CLASS_NAME_COLLAPSE, CLASS_NAME_SHOW)\n\n    for (const trigger of this._triggerArray) {\n      const element = SelectorEngine.getElementFromSelector(trigger)\n\n      if (element && !this._isShown(element)) {\n        this._addAriaAndCollapsedClass([trigger], false)\n      }\n    }\n\n    this._isTransitioning = true\n\n    const complete = () => {\n      this._isTransitioning = false\n      this._element.classList.remove(CLASS_NAME_COLLAPSING)\n      this._element.classList.add(CLASS_NAME_COLLAPSE)\n      EventHandler.trigger(this._element, EVENT_HIDDEN)\n    }\n\n    this._element.style[dimension] = ''\n\n    this._queueCallback(complete, this._element, true)\n  }\n\n  _isShown(element = this._element) {\n    return element.classList.contains(CLASS_NAME_SHOW)\n  }\n\n  // Private\n  _configAfterMerge(config) {\n    config.toggle = Boolean(config.toggle) // Coerce string values\n    config.parent = getElement(config.parent)\n    return config\n  }\n\n  _getDimension() {\n    return this._element.classList.contains(CLASS_NAME_HORIZONTAL) ? WIDTH : HEIGHT\n  }\n\n  _initializeChildren() {\n    if (!this._config.parent) {\n      return\n    }\n\n    const children = this._getFirstLevelChildren(SELECTOR_DATA_TOGGLE)\n\n    for (const element of children) {\n      const selected = SelectorEngine.getElementFromSelector(element)\n\n      if (selected) {\n        this._addAriaAndCollapsedClass([element], this._isShown(selected))\n      }\n    }\n  }\n\n  _getFirstLevelChildren(selector) {\n    const children = SelectorEngine.find(CLASS_NAME_DEEPER_CHILDREN, this._config.parent)\n    // remove children if greater depth\n    return SelectorEngine.find(selector, this._config.parent).filter(element => !children.includes(element))\n  }\n\n  _addAriaAndCollapsedClass(triggerArray, isOpen) {\n    if (!triggerArray.length) {\n      return\n    }\n\n    for (const element of triggerArray) {\n      element.classList.toggle(CLASS_NAME_COLLAPSED, !isOpen)\n      element.setAttribute('aria-expanded', isOpen)\n    }\n  }\n\n  // Static\n  static jQueryInterface(config) {\n    const _config = {}\n    if (typeof config === 'string' && /show|hide/.test(config)) {\n      _config.toggle = false\n    }\n\n    return this.each(function () {\n      const data = Collapse.getOrCreateInstance(this, _config)\n\n      if (typeof config === 'string') {\n        if (typeof data[config] === 'undefined') {\n          throw new TypeError(`No method named \"${config}\"`)\n        }\n\n        data[config]()\n      }\n    })\n  }\n}\n\n/**\n * Data API implementation\n */\n\nEventHandler.on(document, EVENT_CLICK_DATA_API, SELECTOR_DATA_TOGGLE, function (event) {\n  // preventDefault only for <a> elements (which change the URL) not inside the collapsible element\n  if (event.target.tagName === 'A' || (event.delegateTarget && event.delegateTarget.tagName === 'A')) {\n    event.preventDefault()\n  }\n\n  for (const element of SelectorEngine.getMultipleElementsFromSelector(this)) {\n    Collapse.getOrCreateInstance(element, { toggle: false }).toggle()\n  }\n})\n\n/**\n * jQuery\n */\n\ndefineJQueryPlugin(Collapse)\n\nexport default Collapse\n","export var top = 'top';\nexport var bottom = 'bottom';\nexport var right = 'right';\nexport var left = 'left';\nexport var auto = 'auto';\nexport var basePlacements = [top, bottom, right, left];\nexport var start = 'start';\nexport var end = 'end';\nexport var clippingParents = 'clippingParents';\nexport var viewport = 'viewport';\nexport var popper = 'popper';\nexport var reference = 'reference';\nexport var variationPlacements = /*#__PURE__*/basePlacements.reduce(function (acc, placement) {\n  return acc.concat([placement + \"-\" + start, placement + \"-\" + end]);\n}, []);\nexport var placements = /*#__PURE__*/[].concat(basePlacements, [auto]).reduce(function (acc, placement) {\n  return acc.concat([placement, placement + \"-\" + start, placement + \"-\" + end]);\n}, []); // modifiers that need to read the DOM\n\nexport var beforeRead = 'beforeRead';\nexport var read = 'read';\nexport var afterRead = 'afterRead'; // pure-logic modifiers\n\nexport var beforeMain = 'beforeMain';\nexport var main = 'main';\nexport var afterMain = 'afterMain'; // modifier with the purpose to write to the DOM (or write into a framework state)\n\nexport var beforeWrite = 'beforeWrite';\nexport var write = 'write';\nexport var afterWrite = 'afterWrite';\nexport var modifierPhases = [beforeRead, read, afterRead, beforeMain, main, afterMain, beforeWrite, write, afterWrite];","export default function getNodeName(element) {\n  return element ? (element.nodeName || '').toLowerCase() : null;\n}","export default function getWindow(node) {\n  if (node == null) {\n    return window;\n  }\n\n  if (node.toString() !== '[object Window]') {\n    var ownerDocument = node.ownerDocument;\n    return ownerDocument ? ownerDocument.defaultView || window : window;\n  }\n\n  return node;\n}","import getWindow from \"./getWindow.js\";\n\nfunction isElement(node) {\n  var OwnElement = getWindow(node).Element;\n  return node instanceof OwnElement || node instanceof Element;\n}\n\nfunction isHTMLElement(node) {\n  var OwnElement = getWindow(node).HTMLElement;\n  return node instanceof OwnElement || node instanceof HTMLElement;\n}\n\nfunction isShadowRoot(node) {\n  // IE 11 has no ShadowRoot\n  if (typeof ShadowRoot === 'undefined') {\n    return false;\n  }\n\n  var OwnElement = getWindow(node).ShadowRoot;\n  return node instanceof OwnElement || node instanceof ShadowRoot;\n}\n\nexport { isElement, isHTMLElement, isShadowRoot };","import getNodeName from \"../dom-utils/getNodeName.js\";\nimport { isHTMLElement } from \"../dom-utils/instanceOf.js\"; // This modifier takes the styles prepared by the `computeStyles` modifier\n// and applies them to the HTMLElements such as popper and arrow\n\nfunction applyStyles(_ref) {\n  var state = _ref.state;\n  Object.keys(state.elements).forEach(function (name) {\n    var style = state.styles[name] || {};\n    var attributes = state.attributes[name] || {};\n    var element = state.elements[name]; // arrow is optional + virtual elements\n\n    if (!isHTMLElement(element) || !getNodeName(element)) {\n      return;\n    } // Flow doesn't support to extend this property, but it's the most\n    // effective way to apply styles to an HTMLElement\n    // $FlowFixMe[cannot-write]\n\n\n    Object.assign(element.style, style);\n    Object.keys(attributes).forEach(function (name) {\n      var value = attributes[name];\n\n      if (value === false) {\n        element.removeAttribute(name);\n      } else {\n        element.setAttribute(name, value === true ? '' : value);\n      }\n    });\n  });\n}\n\nfunction effect(_ref2) {\n  var state = _ref2.state;\n  var initialStyles = {\n    popper: {\n      position: state.options.strategy,\n      left: '0',\n      top: '0',\n      margin: '0'\n    },\n    arrow: {\n      position: 'absolute'\n    },\n    reference: {}\n  };\n  Object.assign(state.elements.popper.style, initialStyles.popper);\n  state.styles = initialStyles;\n\n  if (state.elements.arrow) {\n    Object.assign(state.elements.arrow.style, initialStyles.arrow);\n  }\n\n  return function () {\n    Object.keys(state.elements).forEach(function (name) {\n      var element = state.elements[name];\n      var attributes = state.attributes[name] || {};\n      var styleProperties = Object.keys(state.styles.hasOwnProperty(name) ? state.styles[name] : initialStyles[name]); // Set all values to an empty string to unset them\n\n      var style = styleProperties.reduce(function (style, property) {\n        style[property] = '';\n        return style;\n      }, {}); // arrow is optional + virtual elements\n\n      if (!isHTMLElement(element) || !getNodeName(element)) {\n        return;\n      }\n\n      Object.assign(element.style, style);\n      Object.keys(attributes).forEach(function (attribute) {\n        element.removeAttribute(attribute);\n      });\n    });\n  };\n} // eslint-disable-next-line import/no-unused-modules\n\n\nexport default {\n  name: 'applyStyles',\n  enabled: true,\n  phase: 'write',\n  fn: applyStyles,\n  effect: effect,\n  requires: ['computeStyles']\n};","import { auto } from \"../enums.js\";\nexport default function getBasePlacement(placement) {\n  return placement.split('-')[0];\n}","export var max = Math.max;\nexport var min = Math.min;\nexport var round = Math.round;","export default function getUAString() {\n  var uaData = navigator.userAgentData;\n\n  if (uaData != null && uaData.brands && Array.isArray(uaData.brands)) {\n    return uaData.brands.map(function (item) {\n      return item.brand + \"/\" + item.version;\n    }).join(' ');\n  }\n\n  return navigator.userAgent;\n}","import getUAString from \"../utils/userAgent.js\";\nexport default function isLayoutViewport() {\n  return !/^((?!chrome|android).)*safari/i.test(getUAString());\n}","import { isElement, isHTMLElement } from \"./instanceOf.js\";\nimport { round } from \"../utils/math.js\";\nimport getWindow from \"./getWindow.js\";\nimport isLayoutViewport from \"./isLayoutViewport.js\";\nexport default function getBoundingClientRect(element, includeScale, isFixedStrategy) {\n  if (includeScale === void 0) {\n    includeScale = false;\n  }\n\n  if (isFixedStrategy === void 0) {\n    isFixedStrategy = false;\n  }\n\n  var clientRect = element.getBoundingClientRect();\n  var scaleX = 1;\n  var scaleY = 1;\n\n  if (includeScale && isHTMLElement(element)) {\n    scaleX = element.offsetWidth > 0 ? round(clientRect.width) / element.offsetWidth || 1 : 1;\n    scaleY = element.offsetHeight > 0 ? round(clientRect.height) / element.offsetHeight || 1 : 1;\n  }\n\n  var _ref = isElement(element) ? getWindow(element) : window,\n      visualViewport = _ref.visualViewport;\n\n  var addVisualOffsets = !isLayoutViewport() && isFixedStrategy;\n  var x = (clientRect.left + (addVisualOffsets && visualViewport ? visualViewport.offsetLeft : 0)) / scaleX;\n  var y = (clientRect.top + (addVisualOffsets && visualViewport ? visualViewport.offsetTop : 0)) / scaleY;\n  var width = clientRect.width / scaleX;\n  var height = clientRect.height / scaleY;\n  return {\n    width: width,\n    height: height,\n    top: y,\n    right: x + width,\n    bottom: y + height,\n    left: x,\n    x: x,\n    y: y\n  };\n}","import getBoundingClientRect from \"./getBoundingClientRect.js\"; // Returns the layout rect of an element relative to its offsetParent. Layout\n// means it doesn't take into account transforms.\n\nexport default function getLayoutRect(element) {\n  var clientRect = getBoundingClientRect(element); // Use the clientRect sizes if it's not been transformed.\n  // Fixes https://github.com/popperjs/popper-core/issues/1223\n\n  var width = element.offsetWidth;\n  var height = element.offsetHeight;\n\n  if (Math.abs(clientRect.width - width) <= 1) {\n    width = clientRect.width;\n  }\n\n  if (Math.abs(clientRect.height - height) <= 1) {\n    height = clientRect.height;\n  }\n\n  return {\n    x: element.offsetLeft,\n    y: element.offsetTop,\n    width: width,\n    height: height\n  };\n}","import { isShadowRoot } from \"./instanceOf.js\";\nexport default function contains(parent, child) {\n  var rootNode = child.getRootNode && child.getRootNode(); // First, attempt with faster native method\n\n  if (parent.contains(child)) {\n    return true;\n  } // then fallback to custom implementation with Shadow DOM support\n  else if (rootNode && isShadowRoot(rootNode)) {\n      var next = child;\n\n      do {\n        if (next && parent.isSameNode(next)) {\n          return true;\n        } // $FlowFixMe[prop-missing]: need a better way to handle this...\n\n\n        next = next.parentNode || next.host;\n      } while (next);\n    } // Give up, the result is false\n\n\n  return false;\n}","import getWindow from \"./getWindow.js\";\nexport default function getComputedStyle(element) {\n  return getWindow(element).getComputedStyle(element);\n}","import getNodeName from \"./getNodeName.js\";\nexport default function isTableElement(element) {\n  return ['table', 'td', 'th'].indexOf(getNodeName(element)) >= 0;\n}","import { isElement } from \"./instanceOf.js\";\nexport default function getDocumentElement(element) {\n  // $FlowFixMe[incompatible-return]: assume body is always available\n  return ((isElement(element) ? element.ownerDocument : // $FlowFixMe[prop-missing]\n  element.document) || window.document).documentElement;\n}","import getNodeName from \"./getNodeName.js\";\nimport getDocumentElement from \"./getDocumentElement.js\";\nimport { isShadowRoot } from \"./instanceOf.js\";\nexport default function getParentNode(element) {\n  if (getNodeName(element) === 'html') {\n    return element;\n  }\n\n  return (// this is a quicker (but less type safe) way to save quite some bytes from the bundle\n    // $FlowFixMe[incompatible-return]\n    // $FlowFixMe[prop-missing]\n    element.assignedSlot || // step into the shadow DOM of the parent of a slotted node\n    element.parentNode || ( // DOM Element detected\n    isShadowRoot(element) ? element.host : null) || // ShadowRoot detected\n    // $FlowFixMe[incompatible-call]: HTMLElement is a Node\n    getDocumentElement(element) // fallback\n\n  );\n}","import getWindow from \"./getWindow.js\";\nimport getNodeName from \"./getNodeName.js\";\nimport getComputedStyle from \"./getComputedStyle.js\";\nimport { isHTMLElement, isShadowRoot } from \"./instanceOf.js\";\nimport isTableElement from \"./isTableElement.js\";\nimport getParentNode from \"./getParentNode.js\";\nimport getUAString from \"../utils/userAgent.js\";\n\nfunction getTrueOffsetParent(element) {\n  if (!isHTMLElement(element) || // https://github.com/popperjs/popper-core/issues/837\n  getComputedStyle(element).position === 'fixed') {\n    return null;\n  }\n\n  return element.offsetParent;\n} // `.offsetParent` reports `null` for fixed elements, while absolute elements\n// return the containing block\n\n\nfunction getContainingBlock(element) {\n  var isFirefox = /firefox/i.test(getUAString());\n  var isIE = /Trident/i.test(getUAString());\n\n  if (isIE && isHTMLElement(element)) {\n    // In IE 9, 10 and 11 fixed elements containing block is always established by the viewport\n    var elementCss = getComputedStyle(element);\n\n    if (elementCss.position === 'fixed') {\n      return null;\n    }\n  }\n\n  var currentNode = getParentNode(element);\n\n  if (isShadowRoot(currentNode)) {\n    currentNode = currentNode.host;\n  }\n\n  while (isHTMLElement(currentNode) && ['html', 'body'].indexOf(getNodeName(currentNode)) < 0) {\n    var css = getComputedStyle(currentNode); // This is non-exhaustive but covers the most common CSS properties that\n    // create a containing block.\n    // https://developer.mozilla.org/en-US/docs/Web/CSS/Containing_block#identifying_the_containing_block\n\n    if (css.transform !== 'none' || css.perspective !== 'none' || css.contain === 'paint' || ['transform', 'perspective'].indexOf(css.willChange) !== -1 || isFirefox && css.willChange === 'filter' || isFirefox && css.filter && css.filter !== 'none') {\n      return currentNode;\n    } else {\n      currentNode = currentNode.parentNode;\n    }\n  }\n\n  return null;\n} // Gets the closest ancestor positioned element. Handles some edge cases,\n// such as table ancestors and cross browser bugs.\n\n\nexport default function getOffsetParent(element) {\n  var window = getWindow(element);\n  var offsetParent = getTrueOffsetParent(element);\n\n  while (offsetParent && isTableElement(offsetParent) && getComputedStyle(offsetParent).position === 'static') {\n    offsetParent = getTrueOffsetParent(offsetParent);\n  }\n\n  if (offsetParent && (getNodeName(offsetParent) === 'html' || getNodeName(offsetParent) === 'body' && getComputedStyle(offsetParent).position === 'static')) {\n    return window;\n  }\n\n  return offsetParent || getContainingBlock(element) || window;\n}","export default function getMainAxisFromPlacement(placement) {\n  return ['top', 'bottom'].indexOf(placement) >= 0 ? 'x' : 'y';\n}","import { max as mathMax, min as mathMin } from \"./math.js\";\nexport function within(min, value, max) {\n  return mathMax(min, mathMin(value, max));\n}\nexport function withinMaxClamp(min, value, max) {\n  var v = within(min, value, max);\n  return v > max ? max : v;\n}","import getFreshSideObject from \"./getFreshSideObject.js\";\nexport default function mergePaddingObject(paddingObject) {\n  return Object.assign({}, getFreshSideObject(), paddingObject);\n}","export default function getFreshSideObject() {\n  return {\n    top: 0,\n    right: 0,\n    bottom: 0,\n    left: 0\n  };\n}","export default function expandToHashMap(value, keys) {\n  return keys.reduce(function (hashMap, key) {\n    hashMap[key] = value;\n    return hashMap;\n  }, {});\n}","import getBasePlacement from \"../utils/getBasePlacement.js\";\nimport getLayoutRect from \"../dom-utils/getLayoutRect.js\";\nimport contains from \"../dom-utils/contains.js\";\nimport getOffsetParent from \"../dom-utils/getOffsetParent.js\";\nimport getMainAxisFromPlacement from \"../utils/getMainAxisFromPlacement.js\";\nimport { within } from \"../utils/within.js\";\nimport mergePaddingObject from \"../utils/mergePaddingObject.js\";\nimport expandToHashMap from \"../utils/expandToHashMap.js\";\nimport { left, right, basePlacements, top, bottom } from \"../enums.js\"; // eslint-disable-next-line import/no-unused-modules\n\nvar toPaddingObject = function toPaddingObject(padding, state) {\n  padding = typeof padding === 'function' ? padding(Object.assign({}, state.rects, {\n    placement: state.placement\n  })) : padding;\n  return mergePaddingObject(typeof padding !== 'number' ? padding : expandToHashMap(padding, basePlacements));\n};\n\nfunction arrow(_ref) {\n  var _state$modifiersData$;\n\n  var state = _ref.state,\n      name = _ref.name,\n      options = _ref.options;\n  var arrowElement = state.elements.arrow;\n  var popperOffsets = state.modifiersData.popperOffsets;\n  var basePlacement = getBasePlacement(state.placement);\n  var axis = getMainAxisFromPlacement(basePlacement);\n  var isVertical = [left, right].indexOf(basePlacement) >= 0;\n  var len = isVertical ? 'height' : 'width';\n\n  if (!arrowElement || !popperOffsets) {\n    return;\n  }\n\n  var paddingObject = toPaddingObject(options.padding, state);\n  var arrowRect = getLayoutRect(arrowElement);\n  var minProp = axis === 'y' ? top : left;\n  var maxProp = axis === 'y' ? bottom : right;\n  var endDiff = state.rects.reference[len] + state.rects.reference[axis] - popperOffsets[axis] - state.rects.popper[len];\n  var startDiff = popperOffsets[axis] - state.rects.reference[axis];\n  var arrowOffsetParent = getOffsetParent(arrowElement);\n  var clientSize = arrowOffsetParent ? axis === 'y' ? arrowOffsetParent.clientHeight || 0 : arrowOffsetParent.clientWidth || 0 : 0;\n  var centerToReference = endDiff / 2 - startDiff / 2; // Make sure the arrow doesn't overflow the popper if the center point is\n  // outside of the popper bounds\n\n  var min = paddingObject[minProp];\n  var max = clientSize - arrowRect[len] - paddingObject[maxProp];\n  var center = clientSize / 2 - arrowRect[len] / 2 + centerToReference;\n  var offset = within(min, center, max); // Prevents breaking syntax highlighting...\n\n  var axisProp = axis;\n  state.modifiersData[name] = (_state$modifiersData$ = {}, _state$modifiersData$[axisProp] = offset, _state$modifiersData$.centerOffset = offset - center, _state$modifiersData$);\n}\n\nfunction effect(_ref2) {\n  var state = _ref2.state,\n      options = _ref2.options;\n  var _options$element = options.element,\n      arrowElement = _options$element === void 0 ? '[data-popper-arrow]' : _options$element;\n\n  if (arrowElement == null) {\n    return;\n  } // CSS selector\n\n\n  if (typeof arrowElement === 'string') {\n    arrowElement = state.elements.popper.querySelector(arrowElement);\n\n    if (!arrowElement) {\n      return;\n    }\n  }\n\n  if (!contains(state.elements.popper, arrowElement)) {\n    return;\n  }\n\n  state.elements.arrow = arrowElement;\n} // eslint-disable-next-line import/no-unused-modules\n\n\nexport default {\n  name: 'arrow',\n  enabled: true,\n  phase: 'main',\n  fn: arrow,\n  effect: effect,\n  requires: ['popperOffsets'],\n  requiresIfExists: ['preventOverflow']\n};","export default function getVariation(placement) {\n  return placement.split('-')[1];\n}","import { top, left, right, bottom, end } from \"../enums.js\";\nimport getOffsetParent from \"../dom-utils/getOffsetParent.js\";\nimport getWindow from \"../dom-utils/getWindow.js\";\nimport getDocumentElement from \"../dom-utils/getDocumentElement.js\";\nimport getComputedStyle from \"../dom-utils/getComputedStyle.js\";\nimport getBasePlacement from \"../utils/getBasePlacement.js\";\nimport getVariation from \"../utils/getVariation.js\";\nimport { round } from \"../utils/math.js\"; // eslint-disable-next-line import/no-unused-modules\n\nvar unsetSides = {\n  top: 'auto',\n  right: 'auto',\n  bottom: 'auto',\n  left: 'auto'\n}; // Round the offsets to the nearest suitable subpixel based on the DPR.\n// Zooming can change the DPR, but it seems to report a value that will\n// cleanly divide the values into the appropriate subpixels.\n\nfunction roundOffsetsByDPR(_ref, win) {\n  var x = _ref.x,\n      y = _ref.y;\n  var dpr = win.devicePixelRatio || 1;\n  return {\n    x: round(x * dpr) / dpr || 0,\n    y: round(y * dpr) / dpr || 0\n  };\n}\n\nexport function mapToStyles(_ref2) {\n  var _Object$assign2;\n\n  var popper = _ref2.popper,\n      popperRect = _ref2.popperRect,\n      placement = _ref2.placement,\n      variation = _ref2.variation,\n      offsets = _ref2.offsets,\n      position = _ref2.position,\n      gpuAcceleration = _ref2.gpuAcceleration,\n      adaptive = _ref2.adaptive,\n      roundOffsets = _ref2.roundOffsets,\n      isFixed = _ref2.isFixed;\n  var _offsets$x = offsets.x,\n      x = _offsets$x === void 0 ? 0 : _offsets$x,\n      _offsets$y = offsets.y,\n      y = _offsets$y === void 0 ? 0 : _offsets$y;\n\n  var _ref3 = typeof roundOffsets === 'function' ? roundOffsets({\n    x: x,\n    y: y\n  }) : {\n    x: x,\n    y: y\n  };\n\n  x = _ref3.x;\n  y = _ref3.y;\n  var hasX = offsets.hasOwnProperty('x');\n  var hasY = offsets.hasOwnProperty('y');\n  var sideX = left;\n  var sideY = top;\n  var win = window;\n\n  if (adaptive) {\n    var offsetParent = getOffsetParent(popper);\n    var heightProp = 'clientHeight';\n    var widthProp = 'clientWidth';\n\n    if (offsetParent === getWindow(popper)) {\n      offsetParent = getDocumentElement(popper);\n\n      if (getComputedStyle(offsetParent).position !== 'static' && position === 'absolute') {\n        heightProp = 'scrollHeight';\n        widthProp = 'scrollWidth';\n      }\n    } // $FlowFixMe[incompatible-cast]: force type refinement, we compare offsetParent with window above, but Flow doesn't detect it\n\n\n    offsetParent = offsetParent;\n\n    if (placement === top || (placement === left || placement === right) && variation === end) {\n      sideY = bottom;\n      var offsetY = isFixed && offsetParent === win && win.visualViewport ? win.visualViewport.height : // $FlowFixMe[prop-missing]\n      offsetParent[heightProp];\n      y -= offsetY - popperRect.height;\n      y *= gpuAcceleration ? 1 : -1;\n    }\n\n    if (placement === left || (placement === top || placement === bottom) && variation === end) {\n      sideX = right;\n      var offsetX = isFixed && offsetParent === win && win.visualViewport ? win.visualViewport.width : // $FlowFixMe[prop-missing]\n      offsetParent[widthProp];\n      x -= offsetX - popperRect.width;\n      x *= gpuAcceleration ? 1 : -1;\n    }\n  }\n\n  var commonStyles = Object.assign({\n    position: position\n  }, adaptive && unsetSides);\n\n  var _ref4 = roundOffsets === true ? roundOffsetsByDPR({\n    x: x,\n    y: y\n  }, getWindow(popper)) : {\n    x: x,\n    y: y\n  };\n\n  x = _ref4.x;\n  y = _ref4.y;\n\n  if (gpuAcceleration) {\n    var _Object$assign;\n\n    return Object.assign({}, commonStyles, (_Object$assign = {}, _Object$assign[sideY] = hasY ? '0' : '', _Object$assign[sideX] = hasX ? '0' : '', _Object$assign.transform = (win.devicePixelRatio || 1) <= 1 ? \"translate(\" + x + \"px, \" + y + \"px)\" : \"translate3d(\" + x + \"px, \" + y + \"px, 0)\", _Object$assign));\n  }\n\n  return Object.assign({}, commonStyles, (_Object$assign2 = {}, _Object$assign2[sideY] = hasY ? y + \"px\" : '', _Object$assign2[sideX] = hasX ? x + \"px\" : '', _Object$assign2.transform = '', _Object$assign2));\n}\n\nfunction computeStyles(_ref5) {\n  var state = _ref5.state,\n      options = _ref5.options;\n  var _options$gpuAccelerat = options.gpuAcceleration,\n      gpuAcceleration = _options$gpuAccelerat === void 0 ? true : _options$gpuAccelerat,\n      _options$adaptive = options.adaptive,\n      adaptive = _options$adaptive === void 0 ? true : _options$adaptive,\n      _options$roundOffsets = options.roundOffsets,\n      roundOffsets = _options$roundOffsets === void 0 ? true : _options$roundOffsets;\n  var commonStyles = {\n    placement: getBasePlacement(state.placement),\n    variation: getVariation(state.placement),\n    popper: state.elements.popper,\n    popperRect: state.rects.popper,\n    gpuAcceleration: gpuAcceleration,\n    isFixed: state.options.strategy === 'fixed'\n  };\n\n  if (state.modifiersData.popperOffsets != null) {\n    state.styles.popper = Object.assign({}, state.styles.popper, mapToStyles(Object.assign({}, commonStyles, {\n      offsets: state.modifiersData.popperOffsets,\n      position: state.options.strategy,\n      adaptive: adaptive,\n      roundOffsets: roundOffsets\n    })));\n  }\n\n  if (state.modifiersData.arrow != null) {\n    state.styles.arrow = Object.assign({}, state.styles.arrow, mapToStyles(Object.assign({}, commonStyles, {\n      offsets: state.modifiersData.arrow,\n      position: 'absolute',\n      adaptive: false,\n      roundOffsets: roundOffsets\n    })));\n  }\n\n  state.attributes.popper = Object.assign({}, state.attributes.popper, {\n    'data-popper-placement': state.placement\n  });\n} // eslint-disable-next-line import/no-unused-modules\n\n\nexport default {\n  name: 'computeStyles',\n  enabled: true,\n  phase: 'beforeWrite',\n  fn: computeStyles,\n  data: {}\n};","import getWindow from \"../dom-utils/getWindow.js\"; // eslint-disable-next-line import/no-unused-modules\n\nvar passive = {\n  passive: true\n};\n\nfunction effect(_ref) {\n  var state = _ref.state,\n      instance = _ref.instance,\n      options = _ref.options;\n  var _options$scroll = options.scroll,\n      scroll = _options$scroll === void 0 ? true : _options$scroll,\n      _options$resize = options.resize,\n      resize = _options$resize === void 0 ? true : _options$resize;\n  var window = getWindow(state.elements.popper);\n  var scrollParents = [].concat(state.scrollParents.reference, state.scrollParents.popper);\n\n  if (scroll) {\n    scrollParents.forEach(function (scrollParent) {\n      scrollParent.addEventListener('scroll', instance.update, passive);\n    });\n  }\n\n  if (resize) {\n    window.addEventListener('resize', instance.update, passive);\n  }\n\n  return function () {\n    if (scroll) {\n      scrollParents.forEach(function (scrollParent) {\n        scrollParent.removeEventListener('scroll', instance.update, passive);\n      });\n    }\n\n    if (resize) {\n      window.removeEventListener('resize', instance.update, passive);\n    }\n  };\n} // eslint-disable-next-line import/no-unused-modules\n\n\nexport default {\n  name: 'eventListeners',\n  enabled: true,\n  phase: 'write',\n  fn: function fn() {},\n  effect: effect,\n  data: {}\n};","var hash = {\n  left: 'right',\n  right: 'left',\n  bottom: 'top',\n  top: 'bottom'\n};\nexport default function getOppositePlacement(placement) {\n  return placement.replace(/left|right|bottom|top/g, function (matched) {\n    return hash[matched];\n  });\n}","var hash = {\n  start: 'end',\n  end: 'start'\n};\nexport default function getOppositeVariationPlacement(placement) {\n  return placement.replace(/start|end/g, function (matched) {\n    return hash[matched];\n  });\n}","import getWindow from \"./getWindow.js\";\nexport default function getWindowScroll(node) {\n  var win = getWindow(node);\n  var scrollLeft = win.pageXOffset;\n  var scrollTop = win.pageYOffset;\n  return {\n    scrollLeft: scrollLeft,\n    scrollTop: scrollTop\n  };\n}","import getBoundingClientRect from \"./getBoundingClientRect.js\";\nimport getDocumentElement from \"./getDocumentElement.js\";\nimport getWindowScroll from \"./getWindowScroll.js\";\nexport default function getWindowScrollBarX(element) {\n  // If <html> has a CSS width greater than the viewport, then this will be\n  // incorrect for RTL.\n  // Popper 1 is broken in this case and never had a bug report so let's assume\n  // it's not an issue. I don't think anyone ever specifies width on <html>\n  // anyway.\n  // Browsers where the left scrollbar doesn't cause an issue report `0` for\n  // this (e.g. Edge 2019, IE11, Safari)\n  return getBoundingClientRect(getDocumentElement(element)).left + getWindowScroll(element).scrollLeft;\n}","import getComputedStyle from \"./getComputedStyle.js\";\nexport default function isScrollParent(element) {\n  // Firefox wants us to check `-x` and `-y` variations as well\n  var _getComputedStyle = getComputedStyle(element),\n      overflow = _getComputedStyle.overflow,\n      overflowX = _getComputedStyle.overflowX,\n      overflowY = _getComputedStyle.overflowY;\n\n  return /auto|scroll|overlay|hidden/.test(overflow + overflowY + overflowX);\n}","import getParentNode from \"./getParentNode.js\";\nimport isScrollParent from \"./isScrollParent.js\";\nimport getNodeName from \"./getNodeName.js\";\nimport { isHTMLElement } from \"./instanceOf.js\";\nexport default function getScrollParent(node) {\n  if (['html', 'body', '#document'].indexOf(getNodeName(node)) >= 0) {\n    // $FlowFixMe[incompatible-return]: assume body is always available\n    return node.ownerDocument.body;\n  }\n\n  if (isHTMLElement(node) && isScrollParent(node)) {\n    return node;\n  }\n\n  return getScrollParent(getParentNode(node));\n}","import getScrollParent from \"./getScrollParent.js\";\nimport getParentNode from \"./getParentNode.js\";\nimport getWindow from \"./getWindow.js\";\nimport isScrollParent from \"./isScrollParent.js\";\n/*\ngiven a DOM element, return the list of all scroll parents, up the list of ancesors\nuntil we get to the top window object. This list is what we attach scroll listeners\nto, because if any of these parent elements scroll, we'll need to re-calculate the\nreference element's position.\n*/\n\nexport default function listScrollParents(element, list) {\n  var _element$ownerDocumen;\n\n  if (list === void 0) {\n    list = [];\n  }\n\n  var scrollParent = getScrollParent(element);\n  var isBody = scrollParent === ((_element$ownerDocumen = element.ownerDocument) == null ? void 0 : _element$ownerDocumen.body);\n  var win = getWindow(scrollParent);\n  var target = isBody ? [win].concat(win.visualViewport || [], isScrollParent(scrollParent) ? scrollParent : []) : scrollParent;\n  var updatedList = list.concat(target);\n  return isBody ? updatedList : // $FlowFixMe[incompatible-call]: isBody tells us target will be an HTMLElement here\n  updatedList.concat(listScrollParents(getParentNode(target)));\n}","export default function rectToClientRect(rect) {\n  return Object.assign({}, rect, {\n    left: rect.x,\n    top: rect.y,\n    right: rect.x + rect.width,\n    bottom: rect.y + rect.height\n  });\n}","import { viewport } from \"../enums.js\";\nimport getViewportRect from \"./getViewportRect.js\";\nimport getDocumentRect from \"./getDocumentRect.js\";\nimport listScrollParents from \"./listScrollParents.js\";\nimport getOffsetParent from \"./getOffsetParent.js\";\nimport getDocumentElement from \"./getDocumentElement.js\";\nimport getComputedStyle from \"./getComputedStyle.js\";\nimport { isElement, isHTMLElement } from \"./instanceOf.js\";\nimport getBoundingClientRect from \"./getBoundingClientRect.js\";\nimport getParentNode from \"./getParentNode.js\";\nimport contains from \"./contains.js\";\nimport getNodeName from \"./getNodeName.js\";\nimport rectToClientRect from \"../utils/rectToClientRect.js\";\nimport { max, min } from \"../utils/math.js\";\n\nfunction getInnerBoundingClientRect(element, strategy) {\n  var rect = getBoundingClientRect(element, false, strategy === 'fixed');\n  rect.top = rect.top + element.clientTop;\n  rect.left = rect.left + element.clientLeft;\n  rect.bottom = rect.top + element.clientHeight;\n  rect.right = rect.left + element.clientWidth;\n  rect.width = element.clientWidth;\n  rect.height = element.clientHeight;\n  rect.x = rect.left;\n  rect.y = rect.top;\n  return rect;\n}\n\nfunction getClientRectFromMixedType(element, clippingParent, strategy) {\n  return clippingParent === viewport ? rectToClientRect(getViewportRect(element, strategy)) : isElement(clippingParent) ? getInnerBoundingClientRect(clippingParent, strategy) : rectToClientRect(getDocumentRect(getDocumentElement(element)));\n} // A \"clipping parent\" is an overflowable container with the characteristic of\n// clipping (or hiding) overflowing elements with a position different from\n// `initial`\n\n\nfunction getClippingParents(element) {\n  var clippingParents = listScrollParents(getParentNode(element));\n  var canEscapeClipping = ['absolute', 'fixed'].indexOf(getComputedStyle(element).position) >= 0;\n  var clipperElement = canEscapeClipping && isHTMLElement(element) ? getOffsetParent(element) : element;\n\n  if (!isElement(clipperElement)) {\n    return [];\n  } // $FlowFixMe[incompatible-return]: https://github.com/facebook/flow/issues/1414\n\n\n  return clippingParents.filter(function (clippingParent) {\n    return isElement(clippingParent) && contains(clippingParent, clipperElement) && getNodeName(clippingParent) !== 'body';\n  });\n} // Gets the maximum area that the element is visible in due to any number of\n// clipping parents\n\n\nexport default function getClippingRect(element, boundary, rootBoundary, strategy) {\n  var mainClippingParents = boundary === 'clippingParents' ? getClippingParents(element) : [].concat(boundary);\n  var clippingParents = [].concat(mainClippingParents, [rootBoundary]);\n  var firstClippingParent = clippingParents[0];\n  var clippingRect = clippingParents.reduce(function (accRect, clippingParent) {\n    var rect = getClientRectFromMixedType(element, clippingParent, strategy);\n    accRect.top = max(rect.top, accRect.top);\n    accRect.right = min(rect.right, accRect.right);\n    accRect.bottom = min(rect.bottom, accRect.bottom);\n    accRect.left = max(rect.left, accRect.left);\n    return accRect;\n  }, getClientRectFromMixedType(element, firstClippingParent, strategy));\n  clippingRect.width = clippingRect.right - clippingRect.left;\n  clippingRect.height = clippingRect.bottom - clippingRect.top;\n  clippingRect.x = clippingRect.left;\n  clippingRect.y = clippingRect.top;\n  return clippingRect;\n}","import getWindow from \"./getWindow.js\";\nimport getDocumentElement from \"./getDocumentElement.js\";\nimport getWindowScrollBarX from \"./getWindowScrollBarX.js\";\nimport isLayoutViewport from \"./isLayoutViewport.js\";\nexport default function getViewportRect(element, strategy) {\n  var win = getWindow(element);\n  var html = getDocumentElement(element);\n  var visualViewport = win.visualViewport;\n  var width = html.clientWidth;\n  var height = html.clientHeight;\n  var x = 0;\n  var y = 0;\n\n  if (visualViewport) {\n    width = visualViewport.width;\n    height = visualViewport.height;\n    var layoutViewport = isLayoutViewport();\n\n    if (layoutViewport || !layoutViewport && strategy === 'fixed') {\n      x = visualViewport.offsetLeft;\n      y = visualViewport.offsetTop;\n    }\n  }\n\n  return {\n    width: width,\n    height: height,\n    x: x + getWindowScrollBarX(element),\n    y: y\n  };\n}","import getDocumentElement from \"./getDocumentElement.js\";\nimport getComputedStyle from \"./getComputedStyle.js\";\nimport getWindowScrollBarX from \"./getWindowScrollBarX.js\";\nimport getWindowScroll from \"./getWindowScroll.js\";\nimport { max } from \"../utils/math.js\"; // Gets the entire size of the scrollable document area, even extending outside\n// of the `<html>` and `<body>` rect bounds if horizontally scrollable\n\nexport default function getDocumentRect(element) {\n  var _element$ownerDocumen;\n\n  var html = getDocumentElement(element);\n  var winScroll = getWindowScroll(element);\n  var body = (_element$ownerDocumen = element.ownerDocument) == null ? void 0 : _element$ownerDocumen.body;\n  var width = max(html.scrollWidth, html.clientWidth, body ? body.scrollWidth : 0, body ? body.clientWidth : 0);\n  var height = max(html.scrollHeight, html.clientHeight, body ? body.scrollHeight : 0, body ? body.clientHeight : 0);\n  var x = -winScroll.scrollLeft + getWindowScrollBarX(element);\n  var y = -winScroll.scrollTop;\n\n  if (getComputedStyle(body || html).direction === 'rtl') {\n    x += max(html.clientWidth, body ? body.clientWidth : 0) - width;\n  }\n\n  return {\n    width: width,\n    height: height,\n    x: x,\n    y: y\n  };\n}","import getBasePlacement from \"./getBasePlacement.js\";\nimport getVariation from \"./getVariation.js\";\nimport getMainAxisFromPlacement from \"./getMainAxisFromPlacement.js\";\nimport { top, right, bottom, left, start, end } from \"../enums.js\";\nexport default function computeOffsets(_ref) {\n  var reference = _ref.reference,\n      element = _ref.element,\n      placement = _ref.placement;\n  var basePlacement = placement ? getBasePlacement(placement) : null;\n  var variation = placement ? getVariation(placement) : null;\n  var commonX = reference.x + reference.width / 2 - element.width / 2;\n  var commonY = reference.y + reference.height / 2 - element.height / 2;\n  var offsets;\n\n  switch (basePlacement) {\n    case top:\n      offsets = {\n        x: commonX,\n        y: reference.y - element.height\n      };\n      break;\n\n    case bottom:\n      offsets = {\n        x: commonX,\n        y: reference.y + reference.height\n      };\n      break;\n\n    case right:\n      offsets = {\n        x: reference.x + reference.width,\n        y: commonY\n      };\n      break;\n\n    case left:\n      offsets = {\n        x: reference.x - element.width,\n        y: commonY\n      };\n      break;\n\n    default:\n      offsets = {\n        x: reference.x,\n        y: reference.y\n      };\n  }\n\n  var mainAxis = basePlacement ? getMainAxisFromPlacement(basePlacement) : null;\n\n  if (mainAxis != null) {\n    var len = mainAxis === 'y' ? 'height' : 'width';\n\n    switch (variation) {\n      case start:\n        offsets[mainAxis] = offsets[mainAxis] - (reference[len] / 2 - element[len] / 2);\n        break;\n\n      case end:\n        offsets[mainAxis] = offsets[mainAxis] + (reference[len] / 2 - element[len] / 2);\n        break;\n\n      default:\n    }\n  }\n\n  return offsets;\n}","import getClippingRect from \"../dom-utils/getClippingRect.js\";\nimport getDocumentElement from \"../dom-utils/getDocumentElement.js\";\nimport getBoundingClientRect from \"../dom-utils/getBoundingClientRect.js\";\nimport computeOffsets from \"./computeOffsets.js\";\nimport rectToClientRect from \"./rectToClientRect.js\";\nimport { clippingParents, reference, popper, bottom, top, right, basePlacements, viewport } from \"../enums.js\";\nimport { isElement } from \"../dom-utils/instanceOf.js\";\nimport mergePaddingObject from \"./mergePaddingObject.js\";\nimport expandToHashMap from \"./expandToHashMap.js\"; // eslint-disable-next-line import/no-unused-modules\n\nexport default function detectOverflow(state, options) {\n  if (options === void 0) {\n    options = {};\n  }\n\n  var _options = options,\n      _options$placement = _options.placement,\n      placement = _options$placement === void 0 ? state.placement : _options$placement,\n      _options$strategy = _options.strategy,\n      strategy = _options$strategy === void 0 ? state.strategy : _options$strategy,\n      _options$boundary = _options.boundary,\n      boundary = _options$boundary === void 0 ? clippingParents : _options$boundary,\n      _options$rootBoundary = _options.rootBoundary,\n      rootBoundary = _options$rootBoundary === void 0 ? viewport : _options$rootBoundary,\n      _options$elementConte = _options.elementContext,\n      elementContext = _options$elementConte === void 0 ? popper : _options$elementConte,\n      _options$altBoundary = _options.altBoundary,\n      altBoundary = _options$altBoundary === void 0 ? false : _options$altBoundary,\n      _options$padding = _options.padding,\n      padding = _options$padding === void 0 ? 0 : _options$padding;\n  var paddingObject = mergePaddingObject(typeof padding !== 'number' ? padding : expandToHashMap(padding, basePlacements));\n  var altContext = elementContext === popper ? reference : popper;\n  var popperRect = state.rects.popper;\n  var element = state.elements[altBoundary ? altContext : elementContext];\n  var clippingClientRect = getClippingRect(isElement(element) ? element : element.contextElement || getDocumentElement(state.elements.popper), boundary, rootBoundary, strategy);\n  var referenceClientRect = getBoundingClientRect(state.elements.reference);\n  var popperOffsets = computeOffsets({\n    reference: referenceClientRect,\n    element: popperRect,\n    strategy: 'absolute',\n    placement: placement\n  });\n  var popperClientRect = rectToClientRect(Object.assign({}, popperRect, popperOffsets));\n  var elementClientRect = elementContext === popper ? popperClientRect : referenceClientRect; // positive = overflowing the clipping rect\n  // 0 or negative = within the clipping rect\n\n  var overflowOffsets = {\n    top: clippingClientRect.top - elementClientRect.top + paddingObject.top,\n    bottom: elementClientRect.bottom - clippingClientRect.bottom + paddingObject.bottom,\n    left: clippingClientRect.left - elementClientRect.left + paddingObject.left,\n    right: elementClientRect.right - clippingClientRect.right + paddingObject.right\n  };\n  var offsetData = state.modifiersData.offset; // Offsets can be applied only to the popper element\n\n  if (elementContext === popper && offsetData) {\n    var offset = offsetData[placement];\n    Object.keys(overflowOffsets).forEach(function (key) {\n      var multiply = [right, bottom].indexOf(key) >= 0 ? 1 : -1;\n      var axis = [top, bottom].indexOf(key) >= 0 ? 'y' : 'x';\n      overflowOffsets[key] += offset[axis] * multiply;\n    });\n  }\n\n  return overflowOffsets;\n}","import getVariation from \"./getVariation.js\";\nimport { variationPlacements, basePlacements, placements as allPlacements } from \"../enums.js\";\nimport detectOverflow from \"./detectOverflow.js\";\nimport getBasePlacement from \"./getBasePlacement.js\";\nexport default function computeAutoPlacement(state, options) {\n  if (options === void 0) {\n    options = {};\n  }\n\n  var _options = options,\n      placement = _options.placement,\n      boundary = _options.boundary,\n      rootBoundary = _options.rootBoundary,\n      padding = _options.padding,\n      flipVariations = _options.flipVariations,\n      _options$allowedAutoP = _options.allowedAutoPlacements,\n      allowedAutoPlacements = _options$allowedAutoP === void 0 ? allPlacements : _options$allowedAutoP;\n  var variation = getVariation(placement);\n  var placements = variation ? flipVariations ? variationPlacements : variationPlacements.filter(function (placement) {\n    return getVariation(placement) === variation;\n  }) : basePlacements;\n  var allowedPlacements = placements.filter(function (placement) {\n    return allowedAutoPlacements.indexOf(placement) >= 0;\n  });\n\n  if (allowedPlacements.length === 0) {\n    allowedPlacements = placements;\n  } // $FlowFixMe[incompatible-type]: Flow seems to have problems with two array unions...\n\n\n  var overflows = allowedPlacements.reduce(function (acc, placement) {\n    acc[placement] = detectOverflow(state, {\n      placement: placement,\n      boundary: boundary,\n      rootBoundary: rootBoundary,\n      padding: padding\n    })[getBasePlacement(placement)];\n    return acc;\n  }, {});\n  return Object.keys(overflows).sort(function (a, b) {\n    return overflows[a] - overflows[b];\n  });\n}","import getOppositePlacement from \"../utils/getOppositePlacement.js\";\nimport getBasePlacement from \"../utils/getBasePlacement.js\";\nimport getOppositeVariationPlacement from \"../utils/getOppositeVariationPlacement.js\";\nimport detectOverflow from \"../utils/detectOverflow.js\";\nimport computeAutoPlacement from \"../utils/computeAutoPlacement.js\";\nimport { bottom, top, start, right, left, auto } from \"../enums.js\";\nimport getVariation from \"../utils/getVariation.js\"; // eslint-disable-next-line import/no-unused-modules\n\nfunction getExpandedFallbackPlacements(placement) {\n  if (getBasePlacement(placement) === auto) {\n    return [];\n  }\n\n  var oppositePlacement = getOppositePlacement(placement);\n  return [getOppositeVariationPlacement(placement), oppositePlacement, getOppositeVariationPlacement(oppositePlacement)];\n}\n\nfunction flip(_ref) {\n  var state = _ref.state,\n      options = _ref.options,\n      name = _ref.name;\n\n  if (state.modifiersData[name]._skip) {\n    return;\n  }\n\n  var _options$mainAxis = options.mainAxis,\n      checkMainAxis = _options$mainAxis === void 0 ? true : _options$mainAxis,\n      _options$altAxis = options.altAxis,\n      checkAltAxis = _options$altAxis === void 0 ? true : _options$altAxis,\n      specifiedFallbackPlacements = options.fallbackPlacements,\n      padding = options.padding,\n      boundary = options.boundary,\n      rootBoundary = options.rootBoundary,\n      altBoundary = options.altBoundary,\n      _options$flipVariatio = options.flipVariations,\n      flipVariations = _options$flipVariatio === void 0 ? true : _options$flipVariatio,\n      allowedAutoPlacements = options.allowedAutoPlacements;\n  var preferredPlacement = state.options.placement;\n  var basePlacement = getBasePlacement(preferredPlacement);\n  var isBasePlacement = basePlacement === preferredPlacement;\n  var fallbackPlacements = specifiedFallbackPlacements || (isBasePlacement || !flipVariations ? [getOppositePlacement(preferredPlacement)] : getExpandedFallbackPlacements(preferredPlacement));\n  var placements = [preferredPlacement].concat(fallbackPlacements).reduce(function (acc, placement) {\n    return acc.concat(getBasePlacement(placement) === auto ? computeAutoPlacement(state, {\n      placement: placement,\n      boundary: boundary,\n      rootBoundary: rootBoundary,\n      padding: padding,\n      flipVariations: flipVariations,\n      allowedAutoPlacements: allowedAutoPlacements\n    }) : placement);\n  }, []);\n  var referenceRect = state.rects.reference;\n  var popperRect = state.rects.popper;\n  var checksMap = new Map();\n  var makeFallbackChecks = true;\n  var firstFittingPlacement = placements[0];\n\n  for (var i = 0; i < placements.length; i++) {\n    var placement = placements[i];\n\n    var _basePlacement = getBasePlacement(placement);\n\n    var isStartVariation = getVariation(placement) === start;\n    var isVertical = [top, bottom].indexOf(_basePlacement) >= 0;\n    var len = isVertical ? 'width' : 'height';\n    var overflow = detectOverflow(state, {\n      placement: placement,\n      boundary: boundary,\n      rootBoundary: rootBoundary,\n      altBoundary: altBoundary,\n      padding: padding\n    });\n    var mainVariationSide = isVertical ? isStartVariation ? right : left : isStartVariation ? bottom : top;\n\n    if (referenceRect[len] > popperRect[len]) {\n      mainVariationSide = getOppositePlacement(mainVariationSide);\n    }\n\n    var altVariationSide = getOppositePlacement(mainVariationSide);\n    var checks = [];\n\n    if (checkMainAxis) {\n      checks.push(overflow[_basePlacement] <= 0);\n    }\n\n    if (checkAltAxis) {\n      checks.push(overflow[mainVariationSide] <= 0, overflow[altVariationSide] <= 0);\n    }\n\n    if (checks.every(function (check) {\n      return check;\n    })) {\n      firstFittingPlacement = placement;\n      makeFallbackChecks = false;\n      break;\n    }\n\n    checksMap.set(placement, checks);\n  }\n\n  if (makeFallbackChecks) {\n    // `2` may be desired in some cases – research later\n    var numberOfChecks = flipVariations ? 3 : 1;\n\n    var _loop = function _loop(_i) {\n      var fittingPlacement = placements.find(function (placement) {\n        var checks = checksMap.get(placement);\n\n        if (checks) {\n          return checks.slice(0, _i).every(function (check) {\n            return check;\n          });\n        }\n      });\n\n      if (fittingPlacement) {\n        firstFittingPlacement = fittingPlacement;\n        return \"break\";\n      }\n    };\n\n    for (var _i = numberOfChecks; _i > 0; _i--) {\n      var _ret = _loop(_i);\n\n      if (_ret === \"break\") break;\n    }\n  }\n\n  if (state.placement !== firstFittingPlacement) {\n    state.modifiersData[name]._skip = true;\n    state.placement = firstFittingPlacement;\n    state.reset = true;\n  }\n} // eslint-disable-next-line import/no-unused-modules\n\n\nexport default {\n  name: 'flip',\n  enabled: true,\n  phase: 'main',\n  fn: flip,\n  requiresIfExists: ['offset'],\n  data: {\n    _skip: false\n  }\n};","import { top, bottom, left, right } from \"../enums.js\";\nimport detectOverflow from \"../utils/detectOverflow.js\";\n\nfunction getSideOffsets(overflow, rect, preventedOffsets) {\n  if (preventedOffsets === void 0) {\n    preventedOffsets = {\n      x: 0,\n      y: 0\n    };\n  }\n\n  return {\n    top: overflow.top - rect.height - preventedOffsets.y,\n    right: overflow.right - rect.width + preventedOffsets.x,\n    bottom: overflow.bottom - rect.height + preventedOffsets.y,\n    left: overflow.left - rect.width - preventedOffsets.x\n  };\n}\n\nfunction isAnySideFullyClipped(overflow) {\n  return [top, right, bottom, left].some(function (side) {\n    return overflow[side] >= 0;\n  });\n}\n\nfunction hide(_ref) {\n  var state = _ref.state,\n      name = _ref.name;\n  var referenceRect = state.rects.reference;\n  var popperRect = state.rects.popper;\n  var preventedOffsets = state.modifiersData.preventOverflow;\n  var referenceOverflow = detectOverflow(state, {\n    elementContext: 'reference'\n  });\n  var popperAltOverflow = detectOverflow(state, {\n    altBoundary: true\n  });\n  var referenceClippingOffsets = getSideOffsets(referenceOverflow, referenceRect);\n  var popperEscapeOffsets = getSideOffsets(popperAltOverflow, popperRect, preventedOffsets);\n  var isReferenceHidden = isAnySideFullyClipped(referenceClippingOffsets);\n  var hasPopperEscaped = isAnySideFullyClipped(popperEscapeOffsets);\n  state.modifiersData[name] = {\n    referenceClippingOffsets: referenceClippingOffsets,\n    popperEscapeOffsets: popperEscapeOffsets,\n    isReferenceHidden: isReferenceHidden,\n    hasPopperEscaped: hasPopperEscaped\n  };\n  state.attributes.popper = Object.assign({}, state.attributes.popper, {\n    'data-popper-reference-hidden': isReferenceHidden,\n    'data-popper-escaped': hasPopperEscaped\n  });\n} // eslint-disable-next-line import/no-unused-modules\n\n\nexport default {\n  name: 'hide',\n  enabled: true,\n  phase: 'main',\n  requiresIfExists: ['preventOverflow'],\n  fn: hide\n};","import getBasePlacement from \"../utils/getBasePlacement.js\";\nimport { top, left, right, placements } from \"../enums.js\"; // eslint-disable-next-line import/no-unused-modules\n\nexport function distanceAndSkiddingToXY(placement, rects, offset) {\n  var basePlacement = getBasePlacement(placement);\n  var invertDistance = [left, top].indexOf(basePlacement) >= 0 ? -1 : 1;\n\n  var _ref = typeof offset === 'function' ? offset(Object.assign({}, rects, {\n    placement: placement\n  })) : offset,\n      skidding = _ref[0],\n      distance = _ref[1];\n\n  skidding = skidding || 0;\n  distance = (distance || 0) * invertDistance;\n  return [left, right].indexOf(basePlacement) >= 0 ? {\n    x: distance,\n    y: skidding\n  } : {\n    x: skidding,\n    y: distance\n  };\n}\n\nfunction offset(_ref2) {\n  var state = _ref2.state,\n      options = _ref2.options,\n      name = _ref2.name;\n  var _options$offset = options.offset,\n      offset = _options$offset === void 0 ? [0, 0] : _options$offset;\n  var data = placements.reduce(function (acc, placement) {\n    acc[placement] = distanceAndSkiddingToXY(placement, state.rects, offset);\n    return acc;\n  }, {});\n  var _data$state$placement = data[state.placement],\n      x = _data$state$placement.x,\n      y = _data$state$placement.y;\n\n  if (state.modifiersData.popperOffsets != null) {\n    state.modifiersData.popperOffsets.x += x;\n    state.modifiersData.popperOffsets.y += y;\n  }\n\n  state.modifiersData[name] = data;\n} // eslint-disable-next-line import/no-unused-modules\n\n\nexport default {\n  name: 'offset',\n  enabled: true,\n  phase: 'main',\n  requires: ['popperOffsets'],\n  fn: offset\n};","import computeOffsets from \"../utils/computeOffsets.js\";\n\nfunction popperOffsets(_ref) {\n  var state = _ref.state,\n      name = _ref.name;\n  // Offsets are the actual position the popper needs to have to be\n  // properly positioned near its reference element\n  // This is the most basic placement, and will be adjusted by\n  // the modifiers in the next step\n  state.modifiersData[name] = computeOffsets({\n    reference: state.rects.reference,\n    element: state.rects.popper,\n    strategy: 'absolute',\n    placement: state.placement\n  });\n} // eslint-disable-next-line import/no-unused-modules\n\n\nexport default {\n  name: 'popperOffsets',\n  enabled: true,\n  phase: 'read',\n  fn: popperOffsets,\n  data: {}\n};","import { top, left, right, bottom, start } from \"../enums.js\";\nimport getBasePlacement from \"../utils/getBasePlacement.js\";\nimport getMainAxisFromPlacement from \"../utils/getMainAxisFromPlacement.js\";\nimport getAltAxis from \"../utils/getAltAxis.js\";\nimport { within, withinMaxClamp } from \"../utils/within.js\";\nimport getLayoutRect from \"../dom-utils/getLayoutRect.js\";\nimport getOffsetParent from \"../dom-utils/getOffsetParent.js\";\nimport detectOverflow from \"../utils/detectOverflow.js\";\nimport getVariation from \"../utils/getVariation.js\";\nimport getFreshSideObject from \"../utils/getFreshSideObject.js\";\nimport { min as mathMin, max as mathMax } from \"../utils/math.js\";\n\nfunction preventOverflow(_ref) {\n  var state = _ref.state,\n      options = _ref.options,\n      name = _ref.name;\n  var _options$mainAxis = options.mainAxis,\n      checkMainAxis = _options$mainAxis === void 0 ? true : _options$mainAxis,\n      _options$altAxis = options.altAxis,\n      checkAltAxis = _options$altAxis === void 0 ? false : _options$altAxis,\n      boundary = options.boundary,\n      rootBoundary = options.rootBoundary,\n      altBoundary = options.altBoundary,\n      padding = options.padding,\n      _options$tether = options.tether,\n      tether = _options$tether === void 0 ? true : _options$tether,\n      _options$tetherOffset = options.tetherOffset,\n      tetherOffset = _options$tetherOffset === void 0 ? 0 : _options$tetherOffset;\n  var overflow = detectOverflow(state, {\n    boundary: boundary,\n    rootBoundary: rootBoundary,\n    padding: padding,\n    altBoundary: altBoundary\n  });\n  var basePlacement = getBasePlacement(state.placement);\n  var variation = getVariation(state.placement);\n  var isBasePlacement = !variation;\n  var mainAxis = getMainAxisFromPlacement(basePlacement);\n  var altAxis = getAltAxis(mainAxis);\n  var popperOffsets = state.modifiersData.popperOffsets;\n  var referenceRect = state.rects.reference;\n  var popperRect = state.rects.popper;\n  var tetherOffsetValue = typeof tetherOffset === 'function' ? tetherOffset(Object.assign({}, state.rects, {\n    placement: state.placement\n  })) : tetherOffset;\n  var normalizedTetherOffsetValue = typeof tetherOffsetValue === 'number' ? {\n    mainAxis: tetherOffsetValue,\n    altAxis: tetherOffsetValue\n  } : Object.assign({\n    mainAxis: 0,\n    altAxis: 0\n  }, tetherOffsetValue);\n  var offsetModifierState = state.modifiersData.offset ? state.modifiersData.offset[state.placement] : null;\n  var data = {\n    x: 0,\n    y: 0\n  };\n\n  if (!popperOffsets) {\n    return;\n  }\n\n  if (checkMainAxis) {\n    var _offsetModifierState$;\n\n    var mainSide = mainAxis === 'y' ? top : left;\n    var altSide = mainAxis === 'y' ? bottom : right;\n    var len = mainAxis === 'y' ? 'height' : 'width';\n    var offset = popperOffsets[mainAxis];\n    var min = offset + overflow[mainSide];\n    var max = offset - overflow[altSide];\n    var additive = tether ? -popperRect[len] / 2 : 0;\n    var minLen = variation === start ? referenceRect[len] : popperRect[len];\n    var maxLen = variation === start ? -popperRect[len] : -referenceRect[len]; // We need to include the arrow in the calculation so the arrow doesn't go\n    // outside the reference bounds\n\n    var arrowElement = state.elements.arrow;\n    var arrowRect = tether && arrowElement ? getLayoutRect(arrowElement) : {\n      width: 0,\n      height: 0\n    };\n    var arrowPaddingObject = state.modifiersData['arrow#persistent'] ? state.modifiersData['arrow#persistent'].padding : getFreshSideObject();\n    var arrowPaddingMin = arrowPaddingObject[mainSide];\n    var arrowPaddingMax = arrowPaddingObject[altSide]; // If the reference length is smaller than the arrow length, we don't want\n    // to include its full size in the calculation. If the reference is small\n    // and near the edge of a boundary, the popper can overflow even if the\n    // reference is not overflowing as well (e.g. virtual elements with no\n    // width or height)\n\n    var arrowLen = within(0, referenceRect[len], arrowRect[len]);\n    var minOffset = isBasePlacement ? referenceRect[len] / 2 - additive - arrowLen - arrowPaddingMin - normalizedTetherOffsetValue.mainAxis : minLen - arrowLen - arrowPaddingMin - normalizedTetherOffsetValue.mainAxis;\n    var maxOffset = isBasePlacement ? -referenceRect[len] / 2 + additive + arrowLen + arrowPaddingMax + normalizedTetherOffsetValue.mainAxis : maxLen + arrowLen + arrowPaddingMax + normalizedTetherOffsetValue.mainAxis;\n    var arrowOffsetParent = state.elements.arrow && getOffsetParent(state.elements.arrow);\n    var clientOffset = arrowOffsetParent ? mainAxis === 'y' ? arrowOffsetParent.clientTop || 0 : arrowOffsetParent.clientLeft || 0 : 0;\n    var offsetModifierValue = (_offsetModifierState$ = offsetModifierState == null ? void 0 : offsetModifierState[mainAxis]) != null ? _offsetModifierState$ : 0;\n    var tetherMin = offset + minOffset - offsetModifierValue - clientOffset;\n    var tetherMax = offset + maxOffset - offsetModifierValue;\n    var preventedOffset = within(tether ? mathMin(min, tetherMin) : min, offset, tether ? mathMax(max, tetherMax) : max);\n    popperOffsets[mainAxis] = preventedOffset;\n    data[mainAxis] = preventedOffset - offset;\n  }\n\n  if (checkAltAxis) {\n    var _offsetModifierState$2;\n\n    var _mainSide = mainAxis === 'x' ? top : left;\n\n    var _altSide = mainAxis === 'x' ? bottom : right;\n\n    var _offset = popperOffsets[altAxis];\n\n    var _len = altAxis === 'y' ? 'height' : 'width';\n\n    var _min = _offset + overflow[_mainSide];\n\n    var _max = _offset - overflow[_altSide];\n\n    var isOriginSide = [top, left].indexOf(basePlacement) !== -1;\n\n    var _offsetModifierValue = (_offsetModifierState$2 = offsetModifierState == null ? void 0 : offsetModifierState[altAxis]) != null ? _offsetModifierState$2 : 0;\n\n    var _tetherMin = isOriginSide ? _min : _offset - referenceRect[_len] - popperRect[_len] - _offsetModifierValue + normalizedTetherOffsetValue.altAxis;\n\n    var _tetherMax = isOriginSide ? _offset + referenceRect[_len] + popperRect[_len] - _offsetModifierValue - normalizedTetherOffsetValue.altAxis : _max;\n\n    var _preventedOffset = tether && isOriginSide ? withinMaxClamp(_tetherMin, _offset, _tetherMax) : within(tether ? _tetherMin : _min, _offset, tether ? _tetherMax : _max);\n\n    popperOffsets[altAxis] = _preventedOffset;\n    data[altAxis] = _preventedOffset - _offset;\n  }\n\n  state.modifiersData[name] = data;\n} // eslint-disable-next-line import/no-unused-modules\n\n\nexport default {\n  name: 'preventOverflow',\n  enabled: true,\n  phase: 'main',\n  fn: preventOverflow,\n  requiresIfExists: ['offset']\n};","export default function getAltAxis(axis) {\n  return axis === 'x' ? 'y' : 'x';\n}","import getBoundingClientRect from \"./getBoundingClientRect.js\";\nimport getNodeScroll from \"./getNodeScroll.js\";\nimport getNodeName from \"./getNodeName.js\";\nimport { isHTMLElement } from \"./instanceOf.js\";\nimport getWindowScrollBarX from \"./getWindowScrollBarX.js\";\nimport getDocumentElement from \"./getDocumentElement.js\";\nimport isScrollParent from \"./isScrollParent.js\";\nimport { round } from \"../utils/math.js\";\n\nfunction isElementScaled(element) {\n  var rect = element.getBoundingClientRect();\n  var scaleX = round(rect.width) / element.offsetWidth || 1;\n  var scaleY = round(rect.height) / element.offsetHeight || 1;\n  return scaleX !== 1 || scaleY !== 1;\n} // Returns the composite rect of an element relative to its offsetParent.\n// Composite means it takes into account transforms as well as layout.\n\n\nexport default function getCompositeRect(elementOrVirtualElement, offsetParent, isFixed) {\n  if (isFixed === void 0) {\n    isFixed = false;\n  }\n\n  var isOffsetParentAnElement = isHTMLElement(offsetParent);\n  var offsetParentIsScaled = isHTMLElement(offsetParent) && isElementScaled(offsetParent);\n  var documentElement = getDocumentElement(offsetParent);\n  var rect = getBoundingClientRect(elementOrVirtualElement, offsetParentIsScaled, isFixed);\n  var scroll = {\n    scrollLeft: 0,\n    scrollTop: 0\n  };\n  var offsets = {\n    x: 0,\n    y: 0\n  };\n\n  if (isOffsetParentAnElement || !isOffsetParentAnElement && !isFixed) {\n    if (getNodeName(offsetParent) !== 'body' || // https://github.com/popperjs/popper-core/issues/1078\n    isScrollParent(documentElement)) {\n      scroll = getNodeScroll(offsetParent);\n    }\n\n    if (isHTMLElement(offsetParent)) {\n      offsets = getBoundingClientRect(offsetParent, true);\n      offsets.x += offsetParent.clientLeft;\n      offsets.y += offsetParent.clientTop;\n    } else if (documentElement) {\n      offsets.x = getWindowScrollBarX(documentElement);\n    }\n  }\n\n  return {\n    x: rect.left + scroll.scrollLeft - offsets.x,\n    y: rect.top + scroll.scrollTop - offsets.y,\n    width: rect.width,\n    height: rect.height\n  };\n}","import getWindowScroll from \"./getWindowScroll.js\";\nimport getWindow from \"./getWindow.js\";\nimport { isHTMLElement } from \"./instanceOf.js\";\nimport getHTMLElementScroll from \"./getHTMLElementScroll.js\";\nexport default function getNodeScroll(node) {\n  if (node === getWindow(node) || !isHTMLElement(node)) {\n    return getWindowScroll(node);\n  } else {\n    return getHTMLElementScroll(node);\n  }\n}","export default function getHTMLElementScroll(element) {\n  return {\n    scrollLeft: element.scrollLeft,\n    scrollTop: element.scrollTop\n  };\n}","import { modifierPhases } from \"../enums.js\"; // source: https://stackoverflow.com/questions/49875255\n\nfunction order(modifiers) {\n  var map = new Map();\n  var visited = new Set();\n  var result = [];\n  modifiers.forEach(function (modifier) {\n    map.set(modifier.name, modifier);\n  }); // On visiting object, check for its dependencies and visit them recursively\n\n  function sort(modifier) {\n    visited.add(modifier.name);\n    var requires = [].concat(modifier.requires || [], modifier.requiresIfExists || []);\n    requires.forEach(function (dep) {\n      if (!visited.has(dep)) {\n        var depModifier = map.get(dep);\n\n        if (depModifier) {\n          sort(depModifier);\n        }\n      }\n    });\n    result.push(modifier);\n  }\n\n  modifiers.forEach(function (modifier) {\n    if (!visited.has(modifier.name)) {\n      // check for visited object\n      sort(modifier);\n    }\n  });\n  return result;\n}\n\nexport default function orderModifiers(modifiers) {\n  // order based on dependencies\n  var orderedModifiers = order(modifiers); // order based on phase\n\n  return modifierPhases.reduce(function (acc, phase) {\n    return acc.concat(orderedModifiers.filter(function (modifier) {\n      return modifier.phase === phase;\n    }));\n  }, []);\n}","import getCompositeRect from \"./dom-utils/getCompositeRect.js\";\nimport getLayoutRect from \"./dom-utils/getLayoutRect.js\";\nimport listScrollParents from \"./dom-utils/listScrollParents.js\";\nimport getOffsetParent from \"./dom-utils/getOffsetParent.js\";\nimport orderModifiers from \"./utils/orderModifiers.js\";\nimport debounce from \"./utils/debounce.js\";\nimport mergeByName from \"./utils/mergeByName.js\";\nimport detectOverflow from \"./utils/detectOverflow.js\";\nimport { isElement } from \"./dom-utils/instanceOf.js\";\nvar DEFAULT_OPTIONS = {\n  placement: 'bottom',\n  modifiers: [],\n  strategy: 'absolute'\n};\n\nfunction areValidElements() {\n  for (var _len = arguments.length, args = new Array(_len), _key = 0; _key < _len; _key++) {\n    args[_key] = arguments[_key];\n  }\n\n  return !args.some(function (element) {\n    return !(element && typeof element.getBoundingClientRect === 'function');\n  });\n}\n\nexport function popperGenerator(generatorOptions) {\n  if (generatorOptions === void 0) {\n    generatorOptions = {};\n  }\n\n  var _generatorOptions = generatorOptions,\n      _generatorOptions$def = _generatorOptions.defaultModifiers,\n      defaultModifiers = _generatorOptions$def === void 0 ? [] : _generatorOptions$def,\n      _generatorOptions$def2 = _generatorOptions.defaultOptions,\n      defaultOptions = _generatorOptions$def2 === void 0 ? DEFAULT_OPTIONS : _generatorOptions$def2;\n  return function createPopper(reference, popper, options) {\n    if (options === void 0) {\n      options = defaultOptions;\n    }\n\n    var state = {\n      placement: 'bottom',\n      orderedModifiers: [],\n      options: Object.assign({}, DEFAULT_OPTIONS, defaultOptions),\n      modifiersData: {},\n      elements: {\n        reference: reference,\n        popper: popper\n      },\n      attributes: {},\n      styles: {}\n    };\n    var effectCleanupFns = [];\n    var isDestroyed = false;\n    var instance = {\n      state: state,\n      setOptions: function setOptions(setOptionsAction) {\n        var options = typeof setOptionsAction === 'function' ? setOptionsAction(state.options) : setOptionsAction;\n        cleanupModifierEffects();\n        state.options = Object.assign({}, defaultOptions, state.options, options);\n        state.scrollParents = {\n          reference: isElement(reference) ? listScrollParents(reference) : reference.contextElement ? listScrollParents(reference.contextElement) : [],\n          popper: listScrollParents(popper)\n        }; // Orders the modifiers based on their dependencies and `phase`\n        // properties\n\n        var orderedModifiers = orderModifiers(mergeByName([].concat(defaultModifiers, state.options.modifiers))); // Strip out disabled modifiers\n\n        state.orderedModifiers = orderedModifiers.filter(function (m) {\n          return m.enabled;\n        });\n        runModifierEffects();\n        return instance.update();\n      },\n      // Sync update – it will always be executed, even if not necessary. This\n      // is useful for low frequency updates where sync behavior simplifies the\n      // logic.\n      // For high frequency updates (e.g. `resize` and `scroll` events), always\n      // prefer the async Popper#update method\n      forceUpdate: function forceUpdate() {\n        if (isDestroyed) {\n          return;\n        }\n\n        var _state$elements = state.elements,\n            reference = _state$elements.reference,\n            popper = _state$elements.popper; // Don't proceed if `reference` or `popper` are not valid elements\n        // anymore\n\n        if (!areValidElements(reference, popper)) {\n          return;\n        } // Store the reference and popper rects to be read by modifiers\n\n\n        state.rects = {\n          reference: getCompositeRect(reference, getOffsetParent(popper), state.options.strategy === 'fixed'),\n          popper: getLayoutRect(popper)\n        }; // Modifiers have the ability to reset the current update cycle. The\n        // most common use case for this is the `flip` modifier changing the\n        // placement, which then needs to re-run all the modifiers, because the\n        // logic was previously ran for the previous placement and is therefore\n        // stale/incorrect\n\n        state.reset = false;\n        state.placement = state.options.placement; // On each update cycle, the `modifiersData` property for each modifier\n        // is filled with the initial data specified by the modifier. This means\n        // it doesn't persist and is fresh on each update.\n        // To ensure persistent data, use `${name}#persistent`\n\n        state.orderedModifiers.forEach(function (modifier) {\n          return state.modifiersData[modifier.name] = Object.assign({}, modifier.data);\n        });\n\n        for (var index = 0; index < state.orderedModifiers.length; index++) {\n          if (state.reset === true) {\n            state.reset = false;\n            index = -1;\n            continue;\n          }\n\n          var _state$orderedModifie = state.orderedModifiers[index],\n              fn = _state$orderedModifie.fn,\n              _state$orderedModifie2 = _state$orderedModifie.options,\n              _options = _state$orderedModifie2 === void 0 ? {} : _state$orderedModifie2,\n              name = _state$orderedModifie.name;\n\n          if (typeof fn === 'function') {\n            state = fn({\n              state: state,\n              options: _options,\n              name: name,\n              instance: instance\n            }) || state;\n          }\n        }\n      },\n      // Async and optimistically optimized update – it will not be executed if\n      // not necessary (debounced to run at most once-per-tick)\n      update: debounce(function () {\n        return new Promise(function (resolve) {\n          instance.forceUpdate();\n          resolve(state);\n        });\n      }),\n      destroy: function destroy() {\n        cleanupModifierEffects();\n        isDestroyed = true;\n      }\n    };\n\n    if (!areValidElements(reference, popper)) {\n      return instance;\n    }\n\n    instance.setOptions(options).then(function (state) {\n      if (!isDestroyed && options.onFirstUpdate) {\n        options.onFirstUpdate(state);\n      }\n    }); // Modifiers have the ability to execute arbitrary code before the first\n    // update cycle runs. They will be executed in the same order as the update\n    // cycle. This is useful when a modifier adds some persistent data that\n    // other modifiers need to use, but the modifier is run after the dependent\n    // one.\n\n    function runModifierEffects() {\n      state.orderedModifiers.forEach(function (_ref) {\n        var name = _ref.name,\n            _ref$options = _ref.options,\n            options = _ref$options === void 0 ? {} : _ref$options,\n            effect = _ref.effect;\n\n        if (typeof effect === 'function') {\n          var cleanupFn = effect({\n            state: state,\n            name: name,\n            instance: instance,\n            options: options\n          });\n\n          var noopFn = function noopFn() {};\n\n          effectCleanupFns.push(cleanupFn || noopFn);\n        }\n      });\n    }\n\n    function cleanupModifierEffects() {\n      effectCleanupFns.forEach(function (fn) {\n        return fn();\n      });\n      effectCleanupFns = [];\n    }\n\n    return instance;\n  };\n}\nexport var createPopper = /*#__PURE__*/popperGenerator(); // eslint-disable-next-line import/no-unused-modules\n\nexport { detectOverflow };","export default function debounce(fn) {\n  var pending;\n  return function () {\n    if (!pending) {\n      pending = new Promise(function (resolve) {\n        Promise.resolve().then(function () {\n          pending = undefined;\n          resolve(fn());\n        });\n      });\n    }\n\n    return pending;\n  };\n}","export default function mergeByName(modifiers) {\n  var merged = modifiers.reduce(function (merged, current) {\n    var existing = merged[current.name];\n    merged[current.name] = existing ? Object.assign({}, existing, current, {\n      options: Object.assign({}, existing.options, current.options),\n      data: Object.assign({}, existing.data, current.data)\n    }) : current;\n    return merged;\n  }, {}); // IE11 does not support Object.values\n\n  return Object.keys(merged).map(function (key) {\n    return merged[key];\n  });\n}","import { popperGenerator, detectOverflow } from \"./createPopper.js\";\nimport eventListeners from \"./modifiers/eventListeners.js\";\nimport popperOffsets from \"./modifiers/popperOffsets.js\";\nimport computeStyles from \"./modifiers/computeStyles.js\";\nimport applyStyles from \"./modifiers/applyStyles.js\";\nvar defaultModifiers = [eventListeners, popperOffsets, computeStyles, applyStyles];\nvar createPopper = /*#__PURE__*/popperGenerator({\n  defaultModifiers: defaultModifiers\n}); // eslint-disable-next-line import/no-unused-modules\n\nexport { createPopper, popperGenerator, defaultModifiers, detectOverflow };","import { popperGenerator, detectOverflow } from \"./createPopper.js\";\nimport eventListeners from \"./modifiers/eventListeners.js\";\nimport popperOffsets from \"./modifiers/popperOffsets.js\";\nimport computeStyles from \"./modifiers/computeStyles.js\";\nimport applyStyles from \"./modifiers/applyStyles.js\";\nimport offset from \"./modifiers/offset.js\";\nimport flip from \"./modifiers/flip.js\";\nimport preventOverflow from \"./modifiers/preventOverflow.js\";\nimport arrow from \"./modifiers/arrow.js\";\nimport hide from \"./modifiers/hide.js\";\nvar defaultModifiers = [eventListeners, popperOffsets, computeStyles, applyStyles, offset, flip, preventOverflow, arrow, hide];\nvar createPopper = /*#__PURE__*/popperGenerator({\n  defaultModifiers: defaultModifiers\n}); // eslint-disable-next-line import/no-unused-modules\n\nexport { createPopper, popperGenerator, defaultModifiers, detectOverflow }; // eslint-disable-next-line import/no-unused-modules\n\nexport { createPopper as createPopperLite } from \"./popper-lite.js\"; // eslint-disable-next-line import/no-unused-modules\n\nexport * from \"./modifiers/index.js\";","/**\n * --------------------------------------------------------------------------\n * Bootstrap dropdown.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport * as Popper from '@popperjs/core'\nimport BaseComponent from './base-component.js'\nimport EventHandler from './dom/event-handler.js'\nimport Manipulator from './dom/manipulator.js'\nimport SelectorEngine from './dom/selector-engine.js'\nimport {\n  defineJQueryPlugin,\n  execute,\n  getElement,\n  getNextActiveElement,\n  isDisabled,\n  isElement,\n  isRTL,\n  isVisible,\n  noop\n} from './util/index.js'\n\n/**\n * Constants\n */\n\nconst NAME = 'dropdown'\nconst DATA_KEY = 'bs.dropdown'\nconst EVENT_KEY = `.${DATA_KEY}`\nconst DATA_API_KEY = '.data-api'\n\nconst ESCAPE_KEY = 'Escape'\nconst TAB_KEY = 'Tab'\nconst ARROW_UP_KEY = 'ArrowUp'\nconst ARROW_DOWN_KEY = 'ArrowDown'\nconst RIGHT_MOUSE_BUTTON = 2 // MouseEvent.button value for the secondary button, usually the right button\n\nconst EVENT_HIDE = `hide${EVENT_KEY}`\nconst EVENT_HIDDEN = `hidden${EVENT_KEY}`\nconst EVENT_SHOW = `show${EVENT_KEY}`\nconst EVENT_SHOWN = `shown${EVENT_KEY}`\nconst EVENT_CLICK_DATA_API = `click${EVENT_KEY}${DATA_API_KEY}`\nconst EVENT_KEYDOWN_DATA_API = `keydown${EVENT_KEY}${DATA_API_KEY}`\nconst EVENT_KEYUP_DATA_API = `keyup${EVENT_KEY}${DATA_API_KEY}`\n\nconst CLASS_NAME_SHOW = 'show'\nconst CLASS_NAME_DROPUP = 'dropup'\nconst CLASS_NAME_DROPEND = 'dropend'\nconst CLASS_NAME_DROPSTART = 'dropstart'\nconst CLASS_NAME_DROPUP_CENTER = 'dropup-center'\nconst CLASS_NAME_DROPDOWN_CENTER = 'dropdown-center'\n\nconst SELECTOR_DATA_TOGGLE = '[data-bs-toggle=\"dropdown\"]:not(.disabled):not(:disabled)'\nconst SELECTOR_DATA_TOGGLE_SHOWN = `${SELECTOR_DATA_TOGGLE}.${CLASS_NAME_SHOW}`\nconst SELECTOR_MENU = '.dropdown-menu'\nconst SELECTOR_NAVBAR = '.navbar'\nconst SELECTOR_NAVBAR_NAV = '.navbar-nav'\nconst SELECTOR_VISIBLE_ITEMS = '.dropdown-menu .dropdown-item:not(.disabled):not(:disabled)'\n\nconst PLACEMENT_TOP = isRTL() ? 'top-end' : 'top-start'\nconst PLACEMENT_TOPEND = isRTL() ? 'top-start' : 'top-end'\nconst PLACEMENT_BOTTOM = isRTL() ? 'bottom-end' : 'bottom-start'\nconst PLACEMENT_BOTTOMEND = isRTL() ? 'bottom-start' : 'bottom-end'\nconst PLACEMENT_RIGHT = isRTL() ? 'left-start' : 'right-start'\nconst PLACEMENT_LEFT = isRTL() ? 'right-start' : 'left-start'\nconst PLACEMENT_TOPCENTER = 'top'\nconst PLACEMENT_BOTTOMCENTER = 'bottom'\n\nconst Default = {\n  autoClose: true,\n  boundary: 'clippingParents',\n  display: 'dynamic',\n  offset: [0, 2],\n  popperConfig: null,\n  reference: 'toggle'\n}\n\nconst DefaultType = {\n  autoClose: '(boolean|string)',\n  boundary: '(string|element)',\n  display: 'string',\n  offset: '(array|string|function)',\n  popperConfig: '(null|object|function)',\n  reference: '(string|element|object)'\n}\n\n/**\n * Class definition\n */\n\nclass Dropdown extends BaseComponent {\n  constructor(element, config) {\n    super(element, config)\n\n    this._popper = null\n    this._parent = this._element.parentNode // dropdown wrapper\n    // TODO: v6 revert #37011 & change markup https://getbootstrap.com/docs/5.3/forms/input-group/\n    this._menu = SelectorEngine.next(this._element, SELECTOR_MENU)[0] ||\n      SelectorEngine.prev(this._element, SELECTOR_MENU)[0] ||\n      SelectorEngine.findOne(SELECTOR_MENU, this._parent)\n    this._inNavbar = this._detectNavbar()\n  }\n\n  // Getters\n  static get Default() {\n    return Default\n  }\n\n  static get DefaultType() {\n    return DefaultType\n  }\n\n  static get NAME() {\n    return NAME\n  }\n\n  // Public\n  toggle() {\n    return this._isShown() ? this.hide() : this.show()\n  }\n\n  show() {\n    if (isDisabled(this._element) || this._isShown()) {\n      return\n    }\n\n    const relatedTarget = {\n      relatedTarget: this._element\n    }\n\n    const showEvent = EventHandler.trigger(this._element, EVENT_SHOW, relatedTarget)\n\n    if (showEvent.defaultPrevented) {\n      return\n    }\n\n    this._createPopper()\n\n    // If this is a touch-enabled device we add extra\n    // empty mouseover listeners to the body's immediate children;\n    // only needed because of broken event delegation on iOS\n    // https://www.quirksmode.org/blog/archives/2014/02/mouse_event_bub.html\n    if ('ontouchstart' in document.documentElement && !this._parent.closest(SELECTOR_NAVBAR_NAV)) {\n      for (const element of [].concat(...document.body.children)) {\n        EventHandler.on(element, 'mouseover', noop)\n      }\n    }\n\n    this._element.focus()\n    this._element.setAttribute('aria-expanded', true)\n\n    this._menu.classList.add(CLASS_NAME_SHOW)\n    this._element.classList.add(CLASS_NAME_SHOW)\n    EventHandler.trigger(this._element, EVENT_SHOWN, relatedTarget)\n  }\n\n  hide() {\n    if (isDisabled(this._element) || !this._isShown()) {\n      return\n    }\n\n    const relatedTarget = {\n      relatedTarget: this._element\n    }\n\n    this._completeHide(relatedTarget)\n  }\n\n  dispose() {\n    if (this._popper) {\n      this._popper.destroy()\n    }\n\n    super.dispose()\n  }\n\n  update() {\n    this._inNavbar = this._detectNavbar()\n    if (this._popper) {\n      this._popper.update()\n    }\n  }\n\n  // Private\n  _completeHide(relatedTarget) {\n    const hideEvent = EventHandler.trigger(this._element, EVENT_HIDE, relatedTarget)\n    if (hideEvent.defaultPrevented) {\n      return\n    }\n\n    // If this is a touch-enabled device we remove the extra\n    // empty mouseover listeners we added for iOS support\n    if ('ontouchstart' in document.documentElement) {\n      for (const element of [].concat(...document.body.children)) {\n        EventHandler.off(element, 'mouseover', noop)\n      }\n    }\n\n    if (this._popper) {\n      this._popper.destroy()\n    }\n\n    this._menu.classList.remove(CLASS_NAME_SHOW)\n    this._element.classList.remove(CLASS_NAME_SHOW)\n    this._element.setAttribute('aria-expanded', 'false')\n    Manipulator.removeDataAttribute(this._menu, 'popper')\n    EventHandler.trigger(this._element, EVENT_HIDDEN, relatedTarget)\n  }\n\n  _getConfig(config) {\n    config = super._getConfig(config)\n\n    if (typeof config.reference === 'object' && !isElement(config.reference) &&\n      typeof config.reference.getBoundingClientRect !== 'function'\n    ) {\n      // Popper virtual elements require a getBoundingClientRect method\n      throw new TypeError(`${NAME.toUpperCase()}: Option \"reference\" provided type \"object\" without a required \"getBoundingClientRect\" method.`)\n    }\n\n    return config\n  }\n\n  _createPopper() {\n    if (typeof Popper === 'undefined') {\n      throw new TypeError('Bootstrap\\'s dropdowns require Popper (https://popper.js.org)')\n    }\n\n    let referenceElement = this._element\n\n    if (this._config.reference === 'parent') {\n      referenceElement = this._parent\n    } else if (isElement(this._config.reference)) {\n      referenceElement = getElement(this._config.reference)\n    } else if (typeof this._config.reference === 'object') {\n      referenceElement = this._config.reference\n    }\n\n    const popperConfig = this._getPopperConfig()\n    this._popper = Popper.createPopper(referenceElement, this._menu, popperConfig)\n  }\n\n  _isShown() {\n    return this._menu.classList.contains(CLASS_NAME_SHOW)\n  }\n\n  _getPlacement() {\n    const parentDropdown = this._parent\n\n    if (parentDropdown.classList.contains(CLASS_NAME_DROPEND)) {\n      return PLACEMENT_RIGHT\n    }\n\n    if (parentDropdown.classList.contains(CLASS_NAME_DROPSTART)) {\n      return PLACEMENT_LEFT\n    }\n\n    if (parentDropdown.classList.contains(CLASS_NAME_DROPUP_CENTER)) {\n      return PLACEMENT_TOPCENTER\n    }\n\n    if (parentDropdown.classList.contains(CLASS_NAME_DROPDOWN_CENTER)) {\n      return PLACEMENT_BOTTOMCENTER\n    }\n\n    // We need to trim the value because custom properties can also include spaces\n    const isEnd = getComputedStyle(this._menu).getPropertyValue('--bs-position').trim() === 'end'\n\n    if (parentDropdown.classList.contains(CLASS_NAME_DROPUP)) {\n      return isEnd ? PLACEMENT_TOPEND : PLACEMENT_TOP\n    }\n\n    return isEnd ? PLACEMENT_BOTTOMEND : PLACEMENT_BOTTOM\n  }\n\n  _detectNavbar() {\n    return this._element.closest(SELECTOR_NAVBAR) !== null\n  }\n\n  _getOffset() {\n    const { offset } = this._config\n\n    if (typeof offset === 'string') {\n      return offset.split(',').map(value => Number.parseInt(value, 10))\n    }\n\n    if (typeof offset === 'function') {\n      return popperData => offset(popperData, this._element)\n    }\n\n    return offset\n  }\n\n  _getPopperConfig() {\n    const defaultBsPopperConfig = {\n      placement: this._getPlacement(),\n      modifiers: [{\n        name: 'preventOverflow',\n        options: {\n          boundary: this._config.boundary\n        }\n      },\n      {\n        name: 'offset',\n        options: {\n          offset: this._getOffset()\n        }\n      }]\n    }\n\n    // Disable Popper if we have a static display or Dropdown is in Navbar\n    if (this._inNavbar || this._config.display === 'static') {\n      Manipulator.setDataAttribute(this._menu, 'popper', 'static') // TODO: v6 remove\n      defaultBsPopperConfig.modifiers = [{\n        name: 'applyStyles',\n        enabled: false\n      }]\n    }\n\n    return {\n      ...defaultBsPopperConfig,\n      ...execute(this._config.popperConfig, [defaultBsPopperConfig])\n    }\n  }\n\n  _selectMenuItem({ key, target }) {\n    const items = SelectorEngine.find(SELECTOR_VISIBLE_ITEMS, this._menu).filter(element => isVisible(element))\n\n    if (!items.length) {\n      return\n    }\n\n    // if target isn't included in items (e.g. when expanding the dropdown)\n    // allow cycling to get the last item in case key equals ARROW_UP_KEY\n    getNextActiveElement(items, target, key === ARROW_DOWN_KEY, !items.includes(target)).focus()\n  }\n\n  // Static\n  static jQueryInterface(config) {\n    return this.each(function () {\n      const data = Dropdown.getOrCreateInstance(this, config)\n\n      if (typeof config !== 'string') {\n        return\n      }\n\n      if (typeof data[config] === 'undefined') {\n        throw new TypeError(`No method named \"${config}\"`)\n      }\n\n      data[config]()\n    })\n  }\n\n  static clearMenus(event) {\n    if (event.button === RIGHT_MOUSE_BUTTON || (event.type === 'keyup' && event.key !== TAB_KEY)) {\n      return\n    }\n\n    const openToggles = SelectorEngine.find(SELECTOR_DATA_TOGGLE_SHOWN)\n\n    for (const toggle of openToggles) {\n      const context = Dropdown.getInstance(toggle)\n      if (!context || context._config.autoClose === false) {\n        continue\n      }\n\n      const composedPath = event.composedPath()\n      const isMenuTarget = composedPath.includes(context._menu)\n      if (\n        composedPath.includes(context._element) ||\n        (context._config.autoClose === 'inside' && !isMenuTarget) ||\n        (context._config.autoClose === 'outside' && isMenuTarget)\n      ) {\n        continue\n      }\n\n      // Tab navigation through the dropdown menu or events from contained inputs shouldn't close the menu\n      if (context._menu.contains(event.target) && ((event.type === 'keyup' && event.key === TAB_KEY) || /input|select|option|textarea|form/i.test(event.target.tagName))) {\n        continue\n      }\n\n      const relatedTarget = { relatedTarget: context._element }\n\n      if (event.type === 'click') {\n        relatedTarget.clickEvent = event\n      }\n\n      context._completeHide(relatedTarget)\n    }\n  }\n\n  static dataApiKeydownHandler(event) {\n    // If not an UP | DOWN | ESCAPE key => not a dropdown command\n    // If input/textarea && if key is other than ESCAPE => not a dropdown command\n\n    const isInput = /input|textarea/i.test(event.target.tagName)\n    const isEscapeEvent = event.key === ESCAPE_KEY\n    const isUpOrDownEvent = [ARROW_UP_KEY, ARROW_DOWN_KEY].includes(event.key)\n\n    if (!isUpOrDownEvent && !isEscapeEvent) {\n      return\n    }\n\n    if (isInput && !isEscapeEvent) {\n      return\n    }\n\n    event.preventDefault()\n\n    // TODO: v6 revert #37011 & change markup https://getbootstrap.com/docs/5.3/forms/input-group/\n    const getToggleButton = this.matches(SELECTOR_DATA_TOGGLE) ?\n      this :\n      (SelectorEngine.prev(this, SELECTOR_DATA_TOGGLE)[0] ||\n        SelectorEngine.next(this, SELECTOR_DATA_TOGGLE)[0] ||\n        SelectorEngine.findOne(SELECTOR_DATA_TOGGLE, event.delegateTarget.parentNode))\n\n    const instance = Dropdown.getOrCreateInstance(getToggleButton)\n\n    if (isUpOrDownEvent) {\n      event.stopPropagation()\n      instance.show()\n      instance._selectMenuItem(event)\n      return\n    }\n\n    if (instance._isShown()) { // else is escape and we check if it is shown\n      event.stopPropagation()\n      instance.hide()\n      getToggleButton.focus()\n    }\n  }\n}\n\n/**\n * Data API implementation\n */\n\nEventHandler.on(document, EVENT_KEYDOWN_DATA_API, SELECTOR_DATA_TOGGLE, Dropdown.dataApiKeydownHandler)\nEventHandler.on(document, EVENT_KEYDOWN_DATA_API, SELECTOR_MENU, Dropdown.dataApiKeydownHandler)\nEventHandler.on(document, EVENT_CLICK_DATA_API, Dropdown.clearMenus)\nEventHandler.on(document, EVENT_KEYUP_DATA_API, Dropdown.clearMenus)\nEventHandler.on(document, EVENT_CLICK_DATA_API, SELECTOR_DATA_TOGGLE, function (event) {\n  event.preventDefault()\n  Dropdown.getOrCreateInstance(this).toggle()\n})\n\n/**\n * jQuery\n */\n\ndefineJQueryPlugin(Dropdown)\n\nexport default Dropdown\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap util/backdrop.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport EventHandler from '../dom/event-handler.js'\nimport Config from './config.js'\nimport { execute, executeAfterTransition, getElement, reflow } from './index.js'\n\n/**\n * Constants\n */\n\nconst NAME = 'backdrop'\nconst CLASS_NAME_FADE = 'fade'\nconst CLASS_NAME_SHOW = 'show'\nconst EVENT_MOUSEDOWN = `mousedown.bs.${NAME}`\n\nconst Default = {\n  className: 'modal-backdrop',\n  clickCallback: null,\n  isAnimated: false,\n  isVisible: true, // if false, we use the backdrop helper without adding any element to the dom\n  rootElement: 'body' // give the choice to place backdrop under different elements\n}\n\nconst DefaultType = {\n  className: 'string',\n  clickCallback: '(function|null)',\n  isAnimated: 'boolean',\n  isVisible: 'boolean',\n  rootElement: '(element|string)'\n}\n\n/**\n * Class definition\n */\n\nclass Backdrop extends Config {\n  constructor(config) {\n    super()\n    this._config = this._getConfig(config)\n    this._isAppended = false\n    this._element = null\n  }\n\n  // Getters\n  static get Default() {\n    return Default\n  }\n\n  static get DefaultType() {\n    return DefaultType\n  }\n\n  static get NAME() {\n    return NAME\n  }\n\n  // Public\n  show(callback) {\n    if (!this._config.isVisible) {\n      execute(callback)\n      return\n    }\n\n    this._append()\n\n    const element = this._getElement()\n    if (this._config.isAnimated) {\n      reflow(element)\n    }\n\n    element.classList.add(CLASS_NAME_SHOW)\n\n    this._emulateAnimation(() => {\n      execute(callback)\n    })\n  }\n\n  hide(callback) {\n    if (!this._config.isVisible) {\n      execute(callback)\n      return\n    }\n\n    this._getElement().classList.remove(CLASS_NAME_SHOW)\n\n    this._emulateAnimation(() => {\n      this.dispose()\n      execute(callback)\n    })\n  }\n\n  dispose() {\n    if (!this._isAppended) {\n      return\n    }\n\n    EventHandler.off(this._element, EVENT_MOUSEDOWN)\n\n    this._element.remove()\n    this._isAppended = false\n  }\n\n  // Private\n  _getElement() {\n    if (!this._element) {\n      const backdrop = document.createElement('div')\n      backdrop.className = this._config.className\n      if (this._config.isAnimated) {\n        backdrop.classList.add(CLASS_NAME_FADE)\n      }\n\n      this._element = backdrop\n    }\n\n    return this._element\n  }\n\n  _configAfterMerge(config) {\n    // use getElement() with the default \"body\" to get a fresh Element on each instantiation\n    config.rootElement = getElement(config.rootElement)\n    return config\n  }\n\n  _append() {\n    if (this._isAppended) {\n      return\n    }\n\n    const element = this._getElement()\n    this._config.rootElement.append(element)\n\n    EventHandler.on(element, EVENT_MOUSEDOWN, () => {\n      execute(this._config.clickCallback)\n    })\n\n    this._isAppended = true\n  }\n\n  _emulateAnimation(callback) {\n    executeAfterTransition(callback, this._getElement(), this._config.isAnimated)\n  }\n}\n\nexport default Backdrop\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap util/focustrap.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport EventHandler from '../dom/event-handler.js'\nimport SelectorEngine from '../dom/selector-engine.js'\nimport Config from './config.js'\n\n/**\n * Constants\n */\n\nconst NAME = 'focustrap'\nconst DATA_KEY = 'bs.focustrap'\nconst EVENT_KEY = `.${DATA_KEY}`\nconst EVENT_FOCUSIN = `focusin${EVENT_KEY}`\nconst EVENT_KEYDOWN_TAB = `keydown.tab${EVENT_KEY}`\n\nconst TAB_KEY = 'Tab'\nconst TAB_NAV_FORWARD = 'forward'\nconst TAB_NAV_BACKWARD = 'backward'\n\nconst Default = {\n  autofocus: true,\n  trapElement: null // The element to trap focus inside of\n}\n\nconst DefaultType = {\n  autofocus: 'boolean',\n  trapElement: 'element'\n}\n\n/**\n * Class definition\n */\n\nclass FocusTrap extends Config {\n  constructor(config) {\n    super()\n    this._config = this._getConfig(config)\n    this._isActive = false\n    this._lastTabNavDirection = null\n  }\n\n  // Getters\n  static get Default() {\n    return Default\n  }\n\n  static get DefaultType() {\n    return DefaultType\n  }\n\n  static get NAME() {\n    return NAME\n  }\n\n  // Public\n  activate() {\n    if (this._isActive) {\n      return\n    }\n\n    if (this._config.autofocus) {\n      this._config.trapElement.focus()\n    }\n\n    EventHandler.off(document, EVENT_KEY) // guard against infinite focus loop\n    EventHandler.on(document, EVENT_FOCUSIN, event => this._handleFocusin(event))\n    EventHandler.on(document, EVENT_KEYDOWN_TAB, event => this._handleKeydown(event))\n\n    this._isActive = true\n  }\n\n  deactivate() {\n    if (!this._isActive) {\n      return\n    }\n\n    this._isActive = false\n    EventHandler.off(document, EVENT_KEY)\n  }\n\n  // Private\n  _handleFocusin(event) {\n    const { trapElement } = this._config\n\n    if (event.target === document || event.target === trapElement || trapElement.contains(event.target)) {\n      return\n    }\n\n    const elements = SelectorEngine.focusableChildren(trapElement)\n\n    if (elements.length === 0) {\n      trapElement.focus()\n    } else if (this._lastTabNavDirection === TAB_NAV_BACKWARD) {\n      elements[elements.length - 1].focus()\n    } else {\n      elements[0].focus()\n    }\n  }\n\n  _handleKeydown(event) {\n    if (event.key !== TAB_KEY) {\n      return\n    }\n\n    this._lastTabNavDirection = event.shiftKey ? TAB_NAV_BACKWARD : TAB_NAV_FORWARD\n  }\n}\n\nexport default FocusTrap\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap util/scrollBar.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport Manipulator from '../dom/manipulator.js'\nimport SelectorEngine from '../dom/selector-engine.js'\nimport { isElement } from './index.js'\n\n/**\n * Constants\n */\n\nconst SELECTOR_FIXED_CONTENT = '.fixed-top, .fixed-bottom, .is-fixed, .sticky-top'\nconst SELECTOR_STICKY_CONTENT = '.sticky-top'\nconst PROPERTY_PADDING = 'padding-right'\nconst PROPERTY_MARGIN = 'margin-right'\n\n/**\n * Class definition\n */\n\nclass ScrollBarHelper {\n  constructor() {\n    this._element = document.body\n  }\n\n  // Public\n  getWidth() {\n    // https://developer.mozilla.org/en-US/docs/Web/API/Window/innerWidth#usage_notes\n    const documentWidth = document.documentElement.clientWidth\n    return Math.abs(window.innerWidth - documentWidth)\n  }\n\n  hide() {\n    const width = this.getWidth()\n    this._disableOverFlow()\n    // give padding to element to balance the hidden scrollbar width\n    this._setElementAttributes(this._element, PROPERTY_PADDING, calculatedValue => calculatedValue + width)\n    // trick: We adjust positive paddingRight and negative marginRight to sticky-top elements to keep showing fullwidth\n    this._setElementAttributes(SELECTOR_FIXED_CONTENT, PROPERTY_PADDING, calculatedValue => calculatedValue + width)\n    this._setElementAttributes(SELECTOR_STICKY_CONTENT, PROPERTY_MARGIN, calculatedValue => calculatedValue - width)\n  }\n\n  reset() {\n    this._resetElementAttributes(this._element, 'overflow')\n    this._resetElementAttributes(this._element, PROPERTY_PADDING)\n    this._resetElementAttributes(SELECTOR_FIXED_CONTENT, PROPERTY_PADDING)\n    this._resetElementAttributes(SELECTOR_STICKY_CONTENT, PROPERTY_MARGIN)\n  }\n\n  isOverflowing() {\n    return this.getWidth() > 0\n  }\n\n  // Private\n  _disableOverFlow() {\n    this._saveInitialAttribute(this._element, 'overflow')\n    this._element.style.overflow = 'hidden'\n  }\n\n  _setElementAttributes(selector, styleProperty, callback) {\n    const scrollbarWidth = this.getWidth()\n    const manipulationCallBack = element => {\n      if (element !== this._element && window.innerWidth > element.clientWidth + scrollbarWidth) {\n        return\n      }\n\n      this._saveInitialAttribute(element, styleProperty)\n      const calculatedValue = window.getComputedStyle(element).getPropertyValue(styleProperty)\n      element.style.setProperty(styleProperty, `${callback(Number.parseFloat(calculatedValue))}px`)\n    }\n\n    this._applyManipulationCallback(selector, manipulationCallBack)\n  }\n\n  _saveInitialAttribute(element, styleProperty) {\n    const actualValue = element.style.getPropertyValue(styleProperty)\n    if (actualValue) {\n      Manipulator.setDataAttribute(element, styleProperty, actualValue)\n    }\n  }\n\n  _resetElementAttributes(selector, styleProperty) {\n    const manipulationCallBack = element => {\n      const value = Manipulator.getDataAttribute(element, styleProperty)\n      // We only want to remove the property if the value is `null`; the value can also be zero\n      if (value === null) {\n        element.style.removeProperty(styleProperty)\n        return\n      }\n\n      Manipulator.removeDataAttribute(element, styleProperty)\n      element.style.setProperty(styleProperty, value)\n    }\n\n    this._applyManipulationCallback(selector, manipulationCallBack)\n  }\n\n  _applyManipulationCallback(selector, callBack) {\n    if (isElement(selector)) {\n      callBack(selector)\n      return\n    }\n\n    for (const sel of SelectorEngine.find(selector, this._element)) {\n      callBack(sel)\n    }\n  }\n}\n\nexport default ScrollBarHelper\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap modal.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport BaseComponent from './base-component.js'\nimport EventHandler from './dom/event-handler.js'\nimport SelectorEngine from './dom/selector-engine.js'\nimport Backdrop from './util/backdrop.js'\nimport { enableDismissTrigger } from './util/component-functions.js'\nimport FocusTrap from './util/focustrap.js'\nimport { defineJQueryPlugin, isRTL, isVisible, reflow } from './util/index.js'\nimport ScrollBarHelper from './util/scrollbar.js'\n\n/**\n * Constants\n */\n\nconst NAME = 'modal'\nconst DATA_KEY = 'bs.modal'\nconst EVENT_KEY = `.${DATA_KEY}`\nconst DATA_API_KEY = '.data-api'\nconst ESCAPE_KEY = 'Escape'\n\nconst EVENT_HIDE = `hide${EVENT_KEY}`\nconst EVENT_HIDE_PREVENTED = `hidePrevented${EVENT_KEY}`\nconst EVENT_HIDDEN = `hidden${EVENT_KEY}`\nconst EVENT_SHOW = `show${EVENT_KEY}`\nconst EVENT_SHOWN = `shown${EVENT_KEY}`\nconst EVENT_RESIZE = `resize${EVENT_KEY}`\nconst EVENT_CLICK_DISMISS = `click.dismiss${EVENT_KEY}`\nconst EVENT_MOUSEDOWN_DISMISS = `mousedown.dismiss${EVENT_KEY}`\nconst EVENT_KEYDOWN_DISMISS = `keydown.dismiss${EVENT_KEY}`\nconst EVENT_CLICK_DATA_API = `click${EVENT_KEY}${DATA_API_KEY}`\n\nconst CLASS_NAME_OPEN = 'modal-open'\nconst CLASS_NAME_FADE = 'fade'\nconst CLASS_NAME_SHOW = 'show'\nconst CLASS_NAME_STATIC = 'modal-static'\n\nconst OPEN_SELECTOR = '.modal.show'\nconst SELECTOR_DIALOG = '.modal-dialog'\nconst SELECTOR_MODAL_BODY = '.modal-body'\nconst SELECTOR_DATA_TOGGLE = '[data-bs-toggle=\"modal\"]'\n\nconst Default = {\n  backdrop: true,\n  focus: true,\n  keyboard: true\n}\n\nconst DefaultType = {\n  backdrop: '(boolean|string)',\n  focus: 'boolean',\n  keyboard: 'boolean'\n}\n\n/**\n * Class definition\n */\n\nclass Modal extends BaseComponent {\n  constructor(element, config) {\n    super(element, config)\n\n    this._dialog = SelectorEngine.findOne(SELECTOR_DIALOG, this._element)\n    this._backdrop = this._initializeBackDrop()\n    this._focustrap = this._initializeFocusTrap()\n    this._isShown = false\n    this._isTransitioning = false\n    this._scrollBar = new ScrollBarHelper()\n\n    this._addEventListeners()\n  }\n\n  // Getters\n  static get Default() {\n    return Default\n  }\n\n  static get DefaultType() {\n    return DefaultType\n  }\n\n  static get NAME() {\n    return NAME\n  }\n\n  // Public\n  toggle(relatedTarget) {\n    return this._isShown ? this.hide() : this.show(relatedTarget)\n  }\n\n  show(relatedTarget) {\n    if (this._isShown || this._isTransitioning) {\n      return\n    }\n\n    const showEvent = EventHandler.trigger(this._element, EVENT_SHOW, {\n      relatedTarget\n    })\n\n    if (showEvent.defaultPrevented) {\n      return\n    }\n\n    this._isShown = true\n    this._isTransitioning = true\n\n    this._scrollBar.hide()\n\n    document.body.classList.add(CLASS_NAME_OPEN)\n\n    this._adjustDialog()\n\n    this._backdrop.show(() => this._showElement(relatedTarget))\n  }\n\n  hide() {\n    if (!this._isShown || this._isTransitioning) {\n      return\n    }\n\n    const hideEvent = EventHandler.trigger(this._element, EVENT_HIDE)\n\n    if (hideEvent.defaultPrevented) {\n      return\n    }\n\n    this._isShown = false\n    this._isTransitioning = true\n    this._focustrap.deactivate()\n\n    this._element.classList.remove(CLASS_NAME_SHOW)\n\n    this._queueCallback(() => this._hideModal(), this._element, this._isAnimated())\n  }\n\n  dispose() {\n    EventHandler.off(window, EVENT_KEY)\n    EventHandler.off(this._dialog, EVENT_KEY)\n\n    this._backdrop.dispose()\n    this._focustrap.deactivate()\n\n    super.dispose()\n  }\n\n  handleUpdate() {\n    this._adjustDialog()\n  }\n\n  // Private\n  _initializeBackDrop() {\n    return new Backdrop({\n      isVisible: Boolean(this._config.backdrop), // 'static' option will be translated to true, and booleans will keep their value,\n      isAnimated: this._isAnimated()\n    })\n  }\n\n  _initializeFocusTrap() {\n    return new FocusTrap({\n      trapElement: this._element\n    })\n  }\n\n  _showElement(relatedTarget) {\n    // try to append dynamic modal\n    if (!document.body.contains(this._element)) {\n      document.body.append(this._element)\n    }\n\n    this._element.style.display = 'block'\n    this._element.removeAttribute('aria-hidden')\n    this._element.setAttribute('aria-modal', true)\n    this._element.setAttribute('role', 'dialog')\n    this._element.scrollTop = 0\n\n    const modalBody = SelectorEngine.findOne(SELECTOR_MODAL_BODY, this._dialog)\n    if (modalBody) {\n      modalBody.scrollTop = 0\n    }\n\n    reflow(this._element)\n\n    this._element.classList.add(CLASS_NAME_SHOW)\n\n    const transitionComplete = () => {\n      if (this._config.focus) {\n        this._focustrap.activate()\n      }\n\n      this._isTransitioning = false\n      EventHandler.trigger(this._element, EVENT_SHOWN, {\n        relatedTarget\n      })\n    }\n\n    this._queueCallback(transitionComplete, this._dialog, this._isAnimated())\n  }\n\n  _addEventListeners() {\n    EventHandler.on(this._element, EVENT_KEYDOWN_DISMISS, event => {\n      if (event.key !== ESCAPE_KEY) {\n        return\n      }\n\n      if (this._config.keyboard) {\n        this.hide()\n        return\n      }\n\n      this._triggerBackdropTransition()\n    })\n\n    EventHandler.on(window, EVENT_RESIZE, () => {\n      if (this._isShown && !this._isTransitioning) {\n        this._adjustDialog()\n      }\n    })\n\n    EventHandler.on(this._element, EVENT_MOUSEDOWN_DISMISS, event => {\n      // a bad trick to segregate clicks that may start inside dialog but end outside, and avoid listen to scrollbar clicks\n      EventHandler.one(this._element, EVENT_CLICK_DISMISS, event2 => {\n        if (this._element !== event.target || this._element !== event2.target) {\n          return\n        }\n\n        if (this._config.backdrop === 'static') {\n          this._triggerBackdropTransition()\n          return\n        }\n\n        if (this._config.backdrop) {\n          this.hide()\n        }\n      })\n    })\n  }\n\n  _hideModal() {\n    this._element.style.display = 'none'\n    this._element.setAttribute('aria-hidden', true)\n    this._element.removeAttribute('aria-modal')\n    this._element.removeAttribute('role')\n    this._isTransitioning = false\n\n    this._backdrop.hide(() => {\n      document.body.classList.remove(CLASS_NAME_OPEN)\n      this._resetAdjustments()\n      this._scrollBar.reset()\n      EventHandler.trigger(this._element, EVENT_HIDDEN)\n    })\n  }\n\n  _isAnimated() {\n    return this._element.classList.contains(CLASS_NAME_FADE)\n  }\n\n  _triggerBackdropTransition() {\n    const hideEvent = EventHandler.trigger(this._element, EVENT_HIDE_PREVENTED)\n    if (hideEvent.defaultPrevented) {\n      return\n    }\n\n    const isModalOverflowing = this._element.scrollHeight > document.documentElement.clientHeight\n    const initialOverflowY = this._element.style.overflowY\n    // return if the following background transition hasn't yet completed\n    if (initialOverflowY === 'hidden' || this._element.classList.contains(CLASS_NAME_STATIC)) {\n      return\n    }\n\n    if (!isModalOverflowing) {\n      this._element.style.overflowY = 'hidden'\n    }\n\n    this._element.classList.add(CLASS_NAME_STATIC)\n    this._queueCallback(() => {\n      this._element.classList.remove(CLASS_NAME_STATIC)\n      this._queueCallback(() => {\n        this._element.style.overflowY = initialOverflowY\n      }, this._dialog)\n    }, this._dialog)\n\n    this._element.focus()\n  }\n\n  /**\n   * The following methods are used to handle overflowing modals\n   */\n\n  _adjustDialog() {\n    const isModalOverflowing = this._element.scrollHeight > document.documentElement.clientHeight\n    const scrollbarWidth = this._scrollBar.getWidth()\n    const isBodyOverflowing = scrollbarWidth > 0\n\n    if (isBodyOverflowing && !isModalOverflowing) {\n      const property = isRTL() ? 'paddingLeft' : 'paddingRight'\n      this._element.style[property] = `${scrollbarWidth}px`\n    }\n\n    if (!isBodyOverflowing && isModalOverflowing) {\n      const property = isRTL() ? 'paddingRight' : 'paddingLeft'\n      this._element.style[property] = `${scrollbarWidth}px`\n    }\n  }\n\n  _resetAdjustments() {\n    this._element.style.paddingLeft = ''\n    this._element.style.paddingRight = ''\n  }\n\n  // Static\n  static jQueryInterface(config, relatedTarget) {\n    return this.each(function () {\n      const data = Modal.getOrCreateInstance(this, config)\n\n      if (typeof config !== 'string') {\n        return\n      }\n\n      if (typeof data[config] === 'undefined') {\n        throw new TypeError(`No method named \"${config}\"`)\n      }\n\n      data[config](relatedTarget)\n    })\n  }\n}\n\n/**\n * Data API implementation\n */\n\nEventHandler.on(document, EVENT_CLICK_DATA_API, SELECTOR_DATA_TOGGLE, function (event) {\n  const target = SelectorEngine.getElementFromSelector(this)\n\n  if (['A', 'AREA'].includes(this.tagName)) {\n    event.preventDefault()\n  }\n\n  EventHandler.one(target, EVENT_SHOW, showEvent => {\n    if (showEvent.defaultPrevented) {\n      // only register focus restorer if modal will actually get shown\n      return\n    }\n\n    EventHandler.one(target, EVENT_HIDDEN, () => {\n      if (isVisible(this)) {\n        this.focus()\n      }\n    })\n  })\n\n  // avoid conflict when clicking modal toggler while another one is open\n  const alreadyOpen = SelectorEngine.findOne(OPEN_SELECTOR)\n  if (alreadyOpen) {\n    Modal.getInstance(alreadyOpen).hide()\n  }\n\n  const data = Modal.getOrCreateInstance(target)\n\n  data.toggle(this)\n})\n\nenableDismissTrigger(Modal)\n\n/**\n * jQuery\n */\n\ndefineJQueryPlugin(Modal)\n\nexport default Modal\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap offcanvas.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport BaseComponent from './base-component.js'\nimport EventHandler from './dom/event-handler.js'\nimport SelectorEngine from './dom/selector-engine.js'\nimport Backdrop from './util/backdrop.js'\nimport { enableDismissTrigger } from './util/component-functions.js'\nimport FocusTrap from './util/focustrap.js'\nimport {\n  defineJQueryPlugin,\n  isDisabled,\n  isVisible\n} from './util/index.js'\nimport ScrollBarHelper from './util/scrollbar.js'\n\n/**\n * Constants\n */\n\nconst NAME = 'offcanvas'\nconst DATA_KEY = 'bs.offcanvas'\nconst EVENT_KEY = `.${DATA_KEY}`\nconst DATA_API_KEY = '.data-api'\nconst EVENT_LOAD_DATA_API = `load${EVENT_KEY}${DATA_API_KEY}`\nconst ESCAPE_KEY = 'Escape'\n\nconst CLASS_NAME_SHOW = 'show'\nconst CLASS_NAME_SHOWING = 'showing'\nconst CLASS_NAME_HIDING = 'hiding'\nconst CLASS_NAME_BACKDROP = 'offcanvas-backdrop'\nconst OPEN_SELECTOR = '.offcanvas.show'\n\nconst EVENT_SHOW = `show${EVENT_KEY}`\nconst EVENT_SHOWN = `shown${EVENT_KEY}`\nconst EVENT_HIDE = `hide${EVENT_KEY}`\nconst EVENT_HIDE_PREVENTED = `hidePrevented${EVENT_KEY}`\nconst EVENT_HIDDEN = `hidden${EVENT_KEY}`\nconst EVENT_RESIZE = `resize${EVENT_KEY}`\nconst EVENT_CLICK_DATA_API = `click${EVENT_KEY}${DATA_API_KEY}`\nconst EVENT_KEYDOWN_DISMISS = `keydown.dismiss${EVENT_KEY}`\n\nconst SELECTOR_DATA_TOGGLE = '[data-bs-toggle=\"offcanvas\"]'\n\nconst Default = {\n  backdrop: true,\n  keyboard: true,\n  scroll: false\n}\n\nconst DefaultType = {\n  backdrop: '(boolean|string)',\n  keyboard: 'boolean',\n  scroll: 'boolean'\n}\n\n/**\n * Class definition\n */\n\nclass Offcanvas extends BaseComponent {\n  constructor(element, config) {\n    super(element, config)\n\n    this._isShown = false\n    this._backdrop = this._initializeBackDrop()\n    this._focustrap = this._initializeFocusTrap()\n    this._addEventListeners()\n  }\n\n  // Getters\n  static get Default() {\n    return Default\n  }\n\n  static get DefaultType() {\n    return DefaultType\n  }\n\n  static get NAME() {\n    return NAME\n  }\n\n  // Public\n  toggle(relatedTarget) {\n    return this._isShown ? this.hide() : this.show(relatedTarget)\n  }\n\n  show(relatedTarget) {\n    if (this._isShown) {\n      return\n    }\n\n    const showEvent = EventHandler.trigger(this._element, EVENT_SHOW, { relatedTarget })\n\n    if (showEvent.defaultPrevented) {\n      return\n    }\n\n    this._isShown = true\n    this._backdrop.show()\n\n    if (!this._config.scroll) {\n      new ScrollBarHelper().hide()\n    }\n\n    this._element.setAttribute('aria-modal', true)\n    this._element.setAttribute('role', 'dialog')\n    this._element.classList.add(CLASS_NAME_SHOWING)\n\n    const completeCallBack = () => {\n      if (!this._config.scroll || this._config.backdrop) {\n        this._focustrap.activate()\n      }\n\n      this._element.classList.add(CLASS_NAME_SHOW)\n      this._element.classList.remove(CLASS_NAME_SHOWING)\n      EventHandler.trigger(this._element, EVENT_SHOWN, { relatedTarget })\n    }\n\n    this._queueCallback(completeCallBack, this._element, true)\n  }\n\n  hide() {\n    if (!this._isShown) {\n      return\n    }\n\n    const hideEvent = EventHandler.trigger(this._element, EVENT_HIDE)\n\n    if (hideEvent.defaultPrevented) {\n      return\n    }\n\n    this._focustrap.deactivate()\n    this._element.blur()\n    this._isShown = false\n    this._element.classList.add(CLASS_NAME_HIDING)\n    this._backdrop.hide()\n\n    const completeCallback = () => {\n      this._element.classList.remove(CLASS_NAME_SHOW, CLASS_NAME_HIDING)\n      this._element.removeAttribute('aria-modal')\n      this._element.removeAttribute('role')\n\n      if (!this._config.scroll) {\n        new ScrollBarHelper().reset()\n      }\n\n      EventHandler.trigger(this._element, EVENT_HIDDEN)\n    }\n\n    this._queueCallback(completeCallback, this._element, true)\n  }\n\n  dispose() {\n    this._backdrop.dispose()\n    this._focustrap.deactivate()\n    super.dispose()\n  }\n\n  // Private\n  _initializeBackDrop() {\n    const clickCallback = () => {\n      if (this._config.backdrop === 'static') {\n        EventHandler.trigger(this._element, EVENT_HIDE_PREVENTED)\n        return\n      }\n\n      this.hide()\n    }\n\n    // 'static' option will be translated to true, and booleans will keep their value\n    const isVisible = Boolean(this._config.backdrop)\n\n    return new Backdrop({\n      className: CLASS_NAME_BACKDROP,\n      isVisible,\n      isAnimated: true,\n      rootElement: this._element.parentNode,\n      clickCallback: isVisible ? clickCallback : null\n    })\n  }\n\n  _initializeFocusTrap() {\n    return new FocusTrap({\n      trapElement: this._element\n    })\n  }\n\n  _addEventListeners() {\n    EventHandler.on(this._element, EVENT_KEYDOWN_DISMISS, event => {\n      if (event.key !== ESCAPE_KEY) {\n        return\n      }\n\n      if (this._config.keyboard) {\n        this.hide()\n        return\n      }\n\n      EventHandler.trigger(this._element, EVENT_HIDE_PREVENTED)\n    })\n  }\n\n  // Static\n  static jQueryInterface(config) {\n    return this.each(function () {\n      const data = Offcanvas.getOrCreateInstance(this, config)\n\n      if (typeof config !== 'string') {\n        return\n      }\n\n      if (data[config] === undefined || config.startsWith('_') || config === 'constructor') {\n        throw new TypeError(`No method named \"${config}\"`)\n      }\n\n      data[config](this)\n    })\n  }\n}\n\n/**\n * Data API implementation\n */\n\nEventHandler.on(document, EVENT_CLICK_DATA_API, SELECTOR_DATA_TOGGLE, function (event) {\n  const target = SelectorEngine.getElementFromSelector(this)\n\n  if (['A', 'AREA'].includes(this.tagName)) {\n    event.preventDefault()\n  }\n\n  if (isDisabled(this)) {\n    return\n  }\n\n  EventHandler.one(target, EVENT_HIDDEN, () => {\n    // focus on trigger when it is closed\n    if (isVisible(this)) {\n      this.focus()\n    }\n  })\n\n  // avoid conflict when clicking a toggler of an offcanvas, while another is open\n  const alreadyOpen = SelectorEngine.findOne(OPEN_SELECTOR)\n  if (alreadyOpen && alreadyOpen !== target) {\n    Offcanvas.getInstance(alreadyOpen).hide()\n  }\n\n  const data = Offcanvas.getOrCreateInstance(target)\n  data.toggle(this)\n})\n\nEventHandler.on(window, EVENT_LOAD_DATA_API, () => {\n  for (const selector of SelectorEngine.find(OPEN_SELECTOR)) {\n    Offcanvas.getOrCreateInstance(selector).show()\n  }\n})\n\nEventHandler.on(window, EVENT_RESIZE, () => {\n  for (const element of SelectorEngine.find('[aria-modal][class*=show][class*=offcanvas-]')) {\n    if (getComputedStyle(element).position !== 'fixed') {\n      Offcanvas.getOrCreateInstance(element).hide()\n    }\n  }\n})\n\nenableDismissTrigger(Offcanvas)\n\n/**\n * jQuery\n */\n\ndefineJQueryPlugin(Offcanvas)\n\nexport default Offcanvas\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap util/sanitizer.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\n// js-docs-start allow-list\nconst ARIA_ATTRIBUTE_PATTERN = /^aria-[\\w-]*$/i\n\nexport const DefaultAllowlist = {\n  // Global attributes allowed on any supplied element below.\n  '*': ['class', 'dir', 'id', 'lang', 'role', ARIA_ATTRIBUTE_PATTERN],\n  a: ['target', 'href', 'title', 'rel'],\n  area: [],\n  b: [],\n  br: [],\n  col: [],\n  code: [],\n  div: [],\n  em: [],\n  hr: [],\n  h1: [],\n  h2: [],\n  h3: [],\n  h4: [],\n  h5: [],\n  h6: [],\n  i: [],\n  img: ['src', 'srcset', 'alt', 'title', 'width', 'height'],\n  li: [],\n  ol: [],\n  p: [],\n  pre: [],\n  s: [],\n  small: [],\n  span: [],\n  sub: [],\n  sup: [],\n  strong: [],\n  u: [],\n  ul: []\n}\n// js-docs-end allow-list\n\nconst uriAttributes = new Set([\n  'background',\n  'cite',\n  'href',\n  'itemtype',\n  'longdesc',\n  'poster',\n  'src',\n  'xlink:href'\n])\n\n/**\n * A pattern that recognizes URLs that are safe wrt. XSS in URL navigation\n * contexts.\n *\n * Shout-out to Angular https://github.com/angular/angular/blob/15.2.8/packages/core/src/sanitization/url_sanitizer.ts#L38\n */\n// eslint-disable-next-line unicorn/better-regex\nconst SAFE_URL_PATTERN = /^(?!javascript:)(?:[a-z0-9+.-]+:|[^&:/?#]*(?:[/?#]|$))/i\n\nconst allowedAttribute = (attribute, allowedAttributeList) => {\n  const attributeName = attribute.nodeName.toLowerCase()\n\n  if (allowedAttributeList.includes(attributeName)) {\n    if (uriAttributes.has(attributeName)) {\n      return Boolean(SAFE_URL_PATTERN.test(attribute.nodeValue))\n    }\n\n    return true\n  }\n\n  // Check if a regular expression validates the attribute.\n  return allowedAttributeList.filter(attributeRegex => attributeRegex instanceof RegExp)\n    .some(regex => regex.test(attributeName))\n}\n\nexport function sanitizeHtml(unsafeHtml, allowList, sanitizeFunction) {\n  if (!unsafeHtml.length) {\n    return unsafeHtml\n  }\n\n  if (sanitizeFunction && typeof sanitizeFunction === 'function') {\n    return sanitizeFunction(unsafeHtml)\n  }\n\n  const domParser = new window.DOMParser()\n  const createdDocument = domParser.parseFromString(unsafeHtml, 'text/html')\n  const elements = [].concat(...createdDocument.body.querySelectorAll('*'))\n\n  for (const element of elements) {\n    const elementName = element.nodeName.toLowerCase()\n\n    if (!Object.keys(allowList).includes(elementName)) {\n      element.remove()\n      continue\n    }\n\n    const attributeList = [].concat(...element.attributes)\n    const allowedAttributes = [].concat(allowList['*'] || [], allowList[elementName] || [])\n\n    for (const attribute of attributeList) {\n      if (!allowedAttribute(attribute, allowedAttributes)) {\n        element.removeAttribute(attribute.nodeName)\n      }\n    }\n  }\n\n  return createdDocument.body.innerHTML\n}\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap util/template-factory.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport SelectorEngine from '../dom/selector-engine.js'\nimport Config from './config.js'\nimport { DefaultAllowlist, sanitizeHtml } from './sanitizer.js'\nimport { execute, getElement, isElement } from './index.js'\n\n/**\n * Constants\n */\n\nconst NAME = 'TemplateFactory'\n\nconst Default = {\n  allowList: DefaultAllowlist,\n  content: {}, // { selector : text ,  selector2 : text2 , }\n  extraClass: '',\n  html: false,\n  sanitize: true,\n  sanitizeFn: null,\n  template: '<div></div>'\n}\n\nconst DefaultType = {\n  allowList: 'object',\n  content: 'object',\n  extraClass: '(string|function)',\n  html: 'boolean',\n  sanitize: 'boolean',\n  sanitizeFn: '(null|function)',\n  template: 'string'\n}\n\nconst DefaultContentType = {\n  entry: '(string|element|function|null)',\n  selector: '(string|element)'\n}\n\n/**\n * Class definition\n */\n\nclass TemplateFactory extends Config {\n  constructor(config) {\n    super()\n    this._config = this._getConfig(config)\n  }\n\n  // Getters\n  static get Default() {\n    return Default\n  }\n\n  static get DefaultType() {\n    return DefaultType\n  }\n\n  static get NAME() {\n    return NAME\n  }\n\n  // Public\n  getContent() {\n    return Object.values(this._config.content)\n      .map(config => this._resolvePossibleFunction(config))\n      .filter(Boolean)\n  }\n\n  hasContent() {\n    return this.getContent().length > 0\n  }\n\n  changeContent(content) {\n    this._checkContent(content)\n    this._config.content = { ...this._config.content, ...content }\n    return this\n  }\n\n  toHtml() {\n    const templateWrapper = document.createElement('div')\n    templateWrapper.innerHTML = this._maybeSanitize(this._config.template)\n\n    for (const [selector, text] of Object.entries(this._config.content)) {\n      this._setContent(templateWrapper, text, selector)\n    }\n\n    const template = templateWrapper.children[0]\n    const extraClass = this._resolvePossibleFunction(this._config.extraClass)\n\n    if (extraClass) {\n      template.classList.add(...extraClass.split(' '))\n    }\n\n    return template\n  }\n\n  // Private\n  _typeCheckConfig(config) {\n    super._typeCheckConfig(config)\n    this._checkContent(config.content)\n  }\n\n  _checkContent(arg) {\n    for (const [selector, content] of Object.entries(arg)) {\n      super._typeCheckConfig({ selector, entry: content }, DefaultContentType)\n    }\n  }\n\n  _setContent(template, content, selector) {\n    const templateElement = SelectorEngine.findOne(selector, template)\n\n    if (!templateElement) {\n      return\n    }\n\n    content = this._resolvePossibleFunction(content)\n\n    if (!content) {\n      templateElement.remove()\n      return\n    }\n\n    if (isElement(content)) {\n      this._putElementInTemplate(getElement(content), templateElement)\n      return\n    }\n\n    if (this._config.html) {\n      templateElement.innerHTML = this._maybeSanitize(content)\n      return\n    }\n\n    templateElement.textContent = content\n  }\n\n  _maybeSanitize(arg) {\n    return this._config.sanitize ? sanitizeHtml(arg, this._config.allowList, this._config.sanitizeFn) : arg\n  }\n\n  _resolvePossibleFunction(arg) {\n    return execute(arg, [this])\n  }\n\n  _putElementInTemplate(element, templateElement) {\n    if (this._config.html) {\n      templateElement.innerHTML = ''\n      templateElement.append(element)\n      return\n    }\n\n    templateElement.textContent = element.textContent\n  }\n}\n\nexport default TemplateFactory\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap tooltip.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport * as Popper from '@popperjs/core'\nimport BaseComponent from './base-component.js'\nimport EventHandler from './dom/event-handler.js'\nimport Manipulator from './dom/manipulator.js'\nimport { defineJQueryPlugin, execute, findShadowRoot, getElement, getUID, isRTL, noop } from './util/index.js'\nimport { DefaultAllowlist } from './util/sanitizer.js'\nimport TemplateFactory from './util/template-factory.js'\n\n/**\n * Constants\n */\n\nconst NAME = 'tooltip'\nconst DISALLOWED_ATTRIBUTES = new Set(['sanitize', 'allowList', 'sanitizeFn'])\n\nconst CLASS_NAME_FADE = 'fade'\nconst CLASS_NAME_MODAL = 'modal'\nconst CLASS_NAME_SHOW = 'show'\n\nconst SELECTOR_TOOLTIP_INNER = '.tooltip-inner'\nconst SELECTOR_MODAL = `.${CLASS_NAME_MODAL}`\n\nconst EVENT_MODAL_HIDE = 'hide.bs.modal'\n\nconst TRIGGER_HOVER = 'hover'\nconst TRIGGER_FOCUS = 'focus'\nconst TRIGGER_CLICK = 'click'\nconst TRIGGER_MANUAL = 'manual'\n\nconst EVENT_HIDE = 'hide'\nconst EVENT_HIDDEN = 'hidden'\nconst EVENT_SHOW = 'show'\nconst EVENT_SHOWN = 'shown'\nconst EVENT_INSERTED = 'inserted'\nconst EVENT_CLICK = 'click'\nconst EVENT_FOCUSIN = 'focusin'\nconst EVENT_FOCUSOUT = 'focusout'\nconst EVENT_MOUSEENTER = 'mouseenter'\nconst EVENT_MOUSELEAVE = 'mouseleave'\n\nconst AttachmentMap = {\n  AUTO: 'auto',\n  TOP: 'top',\n  RIGHT: isRTL() ? 'left' : 'right',\n  BOTTOM: 'bottom',\n  LEFT: isRTL() ? 'right' : 'left'\n}\n\nconst Default = {\n  allowList: DefaultAllowlist,\n  animation: true,\n  boundary: 'clippingParents',\n  container: false,\n  customClass: '',\n  delay: 0,\n  fallbackPlacements: ['top', 'right', 'bottom', 'left'],\n  html: false,\n  offset: [0, 6],\n  placement: 'top',\n  popperConfig: null,\n  sanitize: true,\n  sanitizeFn: null,\n  selector: false,\n  template: '<div class=\"tooltip\" role=\"tooltip\">' +\n            '<div class=\"tooltip-arrow\"></div>' +\n            '<div class=\"tooltip-inner\"></div>' +\n            '</div>',\n  title: '',\n  trigger: 'hover focus'\n}\n\nconst DefaultType = {\n  allowList: 'object',\n  animation: 'boolean',\n  boundary: '(string|element)',\n  container: '(string|element|boolean)',\n  customClass: '(string|function)',\n  delay: '(number|object)',\n  fallbackPlacements: 'array',\n  html: 'boolean',\n  offset: '(array|string|function)',\n  placement: '(string|function)',\n  popperConfig: '(null|object|function)',\n  sanitize: 'boolean',\n  sanitizeFn: '(null|function)',\n  selector: '(string|boolean)',\n  template: 'string',\n  title: '(string|element|function)',\n  trigger: 'string'\n}\n\n/**\n * Class definition\n */\n\nclass Tooltip extends BaseComponent {\n  constructor(element, config) {\n    if (typeof Popper === 'undefined') {\n      throw new TypeError('Bootstrap\\'s tooltips require Popper (https://popper.js.org)')\n    }\n\n    super(element, config)\n\n    // Private\n    this._isEnabled = true\n    this._timeout = 0\n    this._isHovered = null\n    this._activeTrigger = {}\n    this._popper = null\n    this._templateFactory = null\n    this._newContent = null\n\n    // Protected\n    this.tip = null\n\n    this._setListeners()\n\n    if (!this._config.selector) {\n      this._fixTitle()\n    }\n  }\n\n  // Getters\n  static get Default() {\n    return Default\n  }\n\n  static get DefaultType() {\n    return DefaultType\n  }\n\n  static get NAME() {\n    return NAME\n  }\n\n  // Public\n  enable() {\n    this._isEnabled = true\n  }\n\n  disable() {\n    this._isEnabled = false\n  }\n\n  toggleEnabled() {\n    this._isEnabled = !this._isEnabled\n  }\n\n  toggle() {\n    if (!this._isEnabled) {\n      return\n    }\n\n    this._activeTrigger.click = !this._activeTrigger.click\n    if (this._isShown()) {\n      this._leave()\n      return\n    }\n\n    this._enter()\n  }\n\n  dispose() {\n    clearTimeout(this._timeout)\n\n    EventHandler.off(this._element.closest(SELECTOR_MODAL), EVENT_MODAL_HIDE, this._hideModalHandler)\n\n    if (this._element.getAttribute('data-bs-original-title')) {\n      this._element.setAttribute('title', this._element.getAttribute('data-bs-original-title'))\n    }\n\n    this._disposePopper()\n    super.dispose()\n  }\n\n  show() {\n    if (this._element.style.display === 'none') {\n      throw new Error('Please use show on visible elements')\n    }\n\n    if (!(this._isWithContent() && this._isEnabled)) {\n      return\n    }\n\n    const showEvent = EventHandler.trigger(this._element, this.constructor.eventName(EVENT_SHOW))\n    const shadowRoot = findShadowRoot(this._element)\n    const isInTheDom = (shadowRoot || this._element.ownerDocument.documentElement).contains(this._element)\n\n    if (showEvent.defaultPrevented || !isInTheDom) {\n      return\n    }\n\n    // TODO: v6 remove this or make it optional\n    this._disposePopper()\n\n    const tip = this._getTipElement()\n\n    this._element.setAttribute('aria-describedby', tip.getAttribute('id'))\n\n    const { container } = this._config\n\n    if (!this._element.ownerDocument.documentElement.contains(this.tip)) {\n      container.append(tip)\n      EventHandler.trigger(this._element, this.constructor.eventName(EVENT_INSERTED))\n    }\n\n    this._popper = this._createPopper(tip)\n\n    tip.classList.add(CLASS_NAME_SHOW)\n\n    // If this is a touch-enabled device we add extra\n    // empty mouseover listeners to the body's immediate children;\n    // only needed because of broken event delegation on iOS\n    // https://www.quirksmode.org/blog/archives/2014/02/mouse_event_bub.html\n    if ('ontouchstart' in document.documentElement) {\n      for (const element of [].concat(...document.body.children)) {\n        EventHandler.on(element, 'mouseover', noop)\n      }\n    }\n\n    const complete = () => {\n      EventHandler.trigger(this._element, this.constructor.eventName(EVENT_SHOWN))\n\n      if (this._isHovered === false) {\n        this._leave()\n      }\n\n      this._isHovered = false\n    }\n\n    this._queueCallback(complete, this.tip, this._isAnimated())\n  }\n\n  hide() {\n    if (!this._isShown()) {\n      return\n    }\n\n    const hideEvent = EventHandler.trigger(this._element, this.constructor.eventName(EVENT_HIDE))\n    if (hideEvent.defaultPrevented) {\n      return\n    }\n\n    const tip = this._getTipElement()\n    tip.classList.remove(CLASS_NAME_SHOW)\n\n    // If this is a touch-enabled device we remove the extra\n    // empty mouseover listeners we added for iOS support\n    if ('ontouchstart' in document.documentElement) {\n      for (const element of [].concat(...document.body.children)) {\n        EventHandler.off(element, 'mouseover', noop)\n      }\n    }\n\n    this._activeTrigger[TRIGGER_CLICK] = false\n    this._activeTrigger[TRIGGER_FOCUS] = false\n    this._activeTrigger[TRIGGER_HOVER] = false\n    this._isHovered = null // it is a trick to support manual triggering\n\n    const complete = () => {\n      if (this._isWithActiveTrigger()) {\n        return\n      }\n\n      if (!this._isHovered) {\n        this._disposePopper()\n      }\n\n      this._element.removeAttribute('aria-describedby')\n      EventHandler.trigger(this._element, this.constructor.eventName(EVENT_HIDDEN))\n    }\n\n    this._queueCallback(complete, this.tip, this._isAnimated())\n  }\n\n  update() {\n    if (this._popper) {\n      this._popper.update()\n    }\n  }\n\n  // Protected\n  _isWithContent() {\n    return Boolean(this._getTitle())\n  }\n\n  _getTipElement() {\n    if (!this.tip) {\n      this.tip = this._createTipElement(this._newContent || this._getContentForTemplate())\n    }\n\n    return this.tip\n  }\n\n  _createTipElement(content) {\n    const tip = this._getTemplateFactory(content).toHtml()\n\n    // TODO: remove this check in v6\n    if (!tip) {\n      return null\n    }\n\n    tip.classList.remove(CLASS_NAME_FADE, CLASS_NAME_SHOW)\n    // TODO: v6 the following can be achieved with CSS only\n    tip.classList.add(`bs-${this.constructor.NAME}-auto`)\n\n    const tipId = getUID(this.constructor.NAME).toString()\n\n    tip.setAttribute('id', tipId)\n\n    if (this._isAnimated()) {\n      tip.classList.add(CLASS_NAME_FADE)\n    }\n\n    return tip\n  }\n\n  setContent(content) {\n    this._newContent = content\n    if (this._isShown()) {\n      this._disposePopper()\n      this.show()\n    }\n  }\n\n  _getTemplateFactory(content) {\n    if (this._templateFactory) {\n      this._templateFactory.changeContent(content)\n    } else {\n      this._templateFactory = new TemplateFactory({\n        ...this._config,\n        // the `content` var has to be after `this._config`\n        // to override config.content in case of popover\n        content,\n        extraClass: this._resolvePossibleFunction(this._config.customClass)\n      })\n    }\n\n    return this._templateFactory\n  }\n\n  _getContentForTemplate() {\n    return {\n      [SELECTOR_TOOLTIP_INNER]: this._getTitle()\n    }\n  }\n\n  _getTitle() {\n    return this._resolvePossibleFunction(this._config.title) || this._element.getAttribute('data-bs-original-title')\n  }\n\n  // Private\n  _initializeOnDelegatedTarget(event) {\n    return this.constructor.getOrCreateInstance(event.delegateTarget, this._getDelegateConfig())\n  }\n\n  _isAnimated() {\n    return this._config.animation || (this.tip && this.tip.classList.contains(CLASS_NAME_FADE))\n  }\n\n  _isShown() {\n    return this.tip && this.tip.classList.contains(CLASS_NAME_SHOW)\n  }\n\n  _createPopper(tip) {\n    const placement = execute(this._config.placement, [this, tip, this._element])\n    const attachment = AttachmentMap[placement.toUpperCase()]\n    return Popper.createPopper(this._element, tip, this._getPopperConfig(attachment))\n  }\n\n  _getOffset() {\n    const { offset } = this._config\n\n    if (typeof offset === 'string') {\n      return offset.split(',').map(value => Number.parseInt(value, 10))\n    }\n\n    if (typeof offset === 'function') {\n      return popperData => offset(popperData, this._element)\n    }\n\n    return offset\n  }\n\n  _resolvePossibleFunction(arg) {\n    return execute(arg, [this._element])\n  }\n\n  _getPopperConfig(attachment) {\n    const defaultBsPopperConfig = {\n      placement: attachment,\n      modifiers: [\n        {\n          name: 'flip',\n          options: {\n            fallbackPlacements: this._config.fallbackPlacements\n          }\n        },\n        {\n          name: 'offset',\n          options: {\n            offset: this._getOffset()\n          }\n        },\n        {\n          name: 'preventOverflow',\n          options: {\n            boundary: this._config.boundary\n          }\n        },\n        {\n          name: 'arrow',\n          options: {\n            element: `.${this.constructor.NAME}-arrow`\n          }\n        },\n        {\n          name: 'preSetPlacement',\n          enabled: true,\n          phase: 'beforeMain',\n          fn: data => {\n            // Pre-set Popper's placement attribute in order to read the arrow sizes properly.\n            // Otherwise, Popper mixes up the width and height dimensions since the initial arrow style is for top placement\n            this._getTipElement().setAttribute('data-popper-placement', data.state.placement)\n          }\n        }\n      ]\n    }\n\n    return {\n      ...defaultBsPopperConfig,\n      ...execute(this._config.popperConfig, [defaultBsPopperConfig])\n    }\n  }\n\n  _setListeners() {\n    const triggers = this._config.trigger.split(' ')\n\n    for (const trigger of triggers) {\n      if (trigger === 'click') {\n        EventHandler.on(this._element, this.constructor.eventName(EVENT_CLICK), this._config.selector, event => {\n          const context = this._initializeOnDelegatedTarget(event)\n          context.toggle()\n        })\n      } else if (trigger !== TRIGGER_MANUAL) {\n        const eventIn = trigger === TRIGGER_HOVER ?\n          this.constructor.eventName(EVENT_MOUSEENTER) :\n          this.constructor.eventName(EVENT_FOCUSIN)\n        const eventOut = trigger === TRIGGER_HOVER ?\n          this.constructor.eventName(EVENT_MOUSELEAVE) :\n          this.constructor.eventName(EVENT_FOCUSOUT)\n\n        EventHandler.on(this._element, eventIn, this._config.selector, event => {\n          const context = this._initializeOnDelegatedTarget(event)\n          context._activeTrigger[event.type === 'focusin' ? TRIGGER_FOCUS : TRIGGER_HOVER] = true\n          context._enter()\n        })\n        EventHandler.on(this._element, eventOut, this._config.selector, event => {\n          const context = this._initializeOnDelegatedTarget(event)\n          context._activeTrigger[event.type === 'focusout' ? TRIGGER_FOCUS : TRIGGER_HOVER] =\n            context._element.contains(event.relatedTarget)\n\n          context._leave()\n        })\n      }\n    }\n\n    this._hideModalHandler = () => {\n      if (this._element) {\n        this.hide()\n      }\n    }\n\n    EventHandler.on(this._element.closest(SELECTOR_MODAL), EVENT_MODAL_HIDE, this._hideModalHandler)\n  }\n\n  _fixTitle() {\n    const title = this._element.getAttribute('title')\n\n    if (!title) {\n      return\n    }\n\n    if (!this._element.getAttribute('aria-label') && !this._element.textContent.trim()) {\n      this._element.setAttribute('aria-label', title)\n    }\n\n    this._element.setAttribute('data-bs-original-title', title) // DO NOT USE IT. Is only for backwards compatibility\n    this._element.removeAttribute('title')\n  }\n\n  _enter() {\n    if (this._isShown() || this._isHovered) {\n      this._isHovered = true\n      return\n    }\n\n    this._isHovered = true\n\n    this._setTimeout(() => {\n      if (this._isHovered) {\n        this.show()\n      }\n    }, this._config.delay.show)\n  }\n\n  _leave() {\n    if (this._isWithActiveTrigger()) {\n      return\n    }\n\n    this._isHovered = false\n\n    this._setTimeout(() => {\n      if (!this._isHovered) {\n        this.hide()\n      }\n    }, this._config.delay.hide)\n  }\n\n  _setTimeout(handler, timeout) {\n    clearTimeout(this._timeout)\n    this._timeout = setTimeout(handler, timeout)\n  }\n\n  _isWithActiveTrigger() {\n    return Object.values(this._activeTrigger).includes(true)\n  }\n\n  _getConfig(config) {\n    const dataAttributes = Manipulator.getDataAttributes(this._element)\n\n    for (const dataAttribute of Object.keys(dataAttributes)) {\n      if (DISALLOWED_ATTRIBUTES.has(dataAttribute)) {\n        delete dataAttributes[dataAttribute]\n      }\n    }\n\n    config = {\n      ...dataAttributes,\n      ...(typeof config === 'object' && config ? config : {})\n    }\n    config = this._mergeConfigObj(config)\n    config = this._configAfterMerge(config)\n    this._typeCheckConfig(config)\n    return config\n  }\n\n  _configAfterMerge(config) {\n    config.container = config.container === false ? document.body : getElement(config.container)\n\n    if (typeof config.delay === 'number') {\n      config.delay = {\n        show: config.delay,\n        hide: config.delay\n      }\n    }\n\n    if (typeof config.title === 'number') {\n      config.title = config.title.toString()\n    }\n\n    if (typeof config.content === 'number') {\n      config.content = config.content.toString()\n    }\n\n    return config\n  }\n\n  _getDelegateConfig() {\n    const config = {}\n\n    for (const [key, value] of Object.entries(this._config)) {\n      if (this.constructor.Default[key] !== value) {\n        config[key] = value\n      }\n    }\n\n    config.selector = false\n    config.trigger = 'manual'\n\n    // In the future can be replaced with:\n    // const keysWithDifferentValues = Object.entries(this._config).filter(entry => this.constructor.Default[entry[0]] !== this._config[entry[0]])\n    // `Object.fromEntries(keysWithDifferentValues)`\n    return config\n  }\n\n  _disposePopper() {\n    if (this._popper) {\n      this._popper.destroy()\n      this._popper = null\n    }\n\n    if (this.tip) {\n      this.tip.remove()\n      this.tip = null\n    }\n  }\n\n  // Static\n  static jQueryInterface(config) {\n    return this.each(function () {\n      const data = Tooltip.getOrCreateInstance(this, config)\n\n      if (typeof config !== 'string') {\n        return\n      }\n\n      if (typeof data[config] === 'undefined') {\n        throw new TypeError(`No method named \"${config}\"`)\n      }\n\n      data[config]()\n    })\n  }\n}\n\n/**\n * jQuery\n */\n\ndefineJQueryPlugin(Tooltip)\n\nexport default Tooltip\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap popover.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport Tooltip from './tooltip.js'\nimport { defineJQueryPlugin } from './util/index.js'\n\n/**\n * Constants\n */\n\nconst NAME = 'popover'\n\nconst SELECTOR_TITLE = '.popover-header'\nconst SELECTOR_CONTENT = '.popover-body'\n\nconst Default = {\n  ...Tooltip.Default,\n  content: '',\n  offset: [0, 8],\n  placement: 'right',\n  template: '<div class=\"popover\" role=\"tooltip\">' +\n    '<div class=\"popover-arrow\"></div>' +\n    '<h3 class=\"popover-header\"></h3>' +\n    '<div class=\"popover-body\"></div>' +\n    '</div>',\n  trigger: 'click'\n}\n\nconst DefaultType = {\n  ...Tooltip.DefaultType,\n  content: '(null|string|element|function)'\n}\n\n/**\n * Class definition\n */\n\nclass Popover extends Tooltip {\n  // Getters\n  static get Default() {\n    return Default\n  }\n\n  static get DefaultType() {\n    return DefaultType\n  }\n\n  static get NAME() {\n    return NAME\n  }\n\n  // Overrides\n  _isWithContent() {\n    return this._getTitle() || this._getContent()\n  }\n\n  // Private\n  _getContentForTemplate() {\n    return {\n      [SELECTOR_TITLE]: this._getTitle(),\n      [SELECTOR_CONTENT]: this._getContent()\n    }\n  }\n\n  _getContent() {\n    return this._resolvePossibleFunction(this._config.content)\n  }\n\n  // Static\n  static jQueryInterface(config) {\n    return this.each(function () {\n      const data = Popover.getOrCreateInstance(this, config)\n\n      if (typeof config !== 'string') {\n        return\n      }\n\n      if (typeof data[config] === 'undefined') {\n        throw new TypeError(`No method named \"${config}\"`)\n      }\n\n      data[config]()\n    })\n  }\n}\n\n/**\n * jQuery\n */\n\ndefineJQueryPlugin(Popover)\n\nexport default Popover\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap scrollspy.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport BaseComponent from './base-component.js'\nimport EventHandler from './dom/event-handler.js'\nimport SelectorEngine from './dom/selector-engine.js'\nimport { defineJQueryPlugin, getElement, isDisabled, isVisible } from './util/index.js'\n\n/**\n * Constants\n */\n\nconst NAME = 'scrollspy'\nconst DATA_KEY = 'bs.scrollspy'\nconst EVENT_KEY = `.${DATA_KEY}`\nconst DATA_API_KEY = '.data-api'\n\nconst EVENT_ACTIVATE = `activate${EVENT_KEY}`\nconst EVENT_CLICK = `click${EVENT_KEY}`\nconst EVENT_LOAD_DATA_API = `load${EVENT_KEY}${DATA_API_KEY}`\n\nconst CLASS_NAME_DROPDOWN_ITEM = 'dropdown-item'\nconst CLASS_NAME_ACTIVE = 'active'\n\nconst SELECTOR_DATA_SPY = '[data-bs-spy=\"scroll\"]'\nconst SELECTOR_TARGET_LINKS = '[href]'\nconst SELECTOR_NAV_LIST_GROUP = '.nav, .list-group'\nconst SELECTOR_NAV_LINKS = '.nav-link'\nconst SELECTOR_NAV_ITEMS = '.nav-item'\nconst SELECTOR_LIST_ITEMS = '.list-group-item'\nconst SELECTOR_LINK_ITEMS = `${SELECTOR_NAV_LINKS}, ${SELECTOR_NAV_ITEMS} > ${SELECTOR_NAV_LINKS}, ${SELECTOR_LIST_ITEMS}`\nconst SELECTOR_DROPDOWN = '.dropdown'\nconst SELECTOR_DROPDOWN_TOGGLE = '.dropdown-toggle'\n\nconst Default = {\n  offset: null, // TODO: v6 @deprecated, keep it for backwards compatibility reasons\n  rootMargin: '0px 0px -25%',\n  smoothScroll: false,\n  target: null,\n  threshold: [0.1, 0.5, 1]\n}\n\nconst DefaultType = {\n  offset: '(number|null)', // TODO v6 @deprecated, keep it for backwards compatibility reasons\n  rootMargin: 'string',\n  smoothScroll: 'boolean',\n  target: 'element',\n  threshold: 'array'\n}\n\n/**\n * Class definition\n */\n\nclass ScrollSpy extends BaseComponent {\n  constructor(element, config) {\n    super(element, config)\n\n    // this._element is the observablesContainer and config.target the menu links wrapper\n    this._targetLinks = new Map()\n    this._observableSections = new Map()\n    this._rootElement = getComputedStyle(this._element).overflowY === 'visible' ? null : this._element\n    this._activeTarget = null\n    this._observer = null\n    this._previousScrollData = {\n      visibleEntryTop: 0,\n      parentScrollTop: 0\n    }\n    this.refresh() // initialize\n  }\n\n  // Getters\n  static get Default() {\n    return Default\n  }\n\n  static get DefaultType() {\n    return DefaultType\n  }\n\n  static get NAME() {\n    return NAME\n  }\n\n  // Public\n  refresh() {\n    this._initializeTargetsAndObservables()\n    this._maybeEnableSmoothScroll()\n\n    if (this._observer) {\n      this._observer.disconnect()\n    } else {\n      this._observer = this._getNewObserver()\n    }\n\n    for (const section of this._observableSections.values()) {\n      this._observer.observe(section)\n    }\n  }\n\n  dispose() {\n    this._observer.disconnect()\n    super.dispose()\n  }\n\n  // Private\n  _configAfterMerge(config) {\n    // TODO: on v6 target should be given explicitly & remove the {target: 'ss-target'} case\n    config.target = getElement(config.target) || document.body\n\n    // TODO: v6 Only for backwards compatibility reasons. Use rootMargin only\n    config.rootMargin = config.offset ? `${config.offset}px 0px -30%` : config.rootMargin\n\n    if (typeof config.threshold === 'string') {\n      config.threshold = config.threshold.split(',').map(value => Number.parseFloat(value))\n    }\n\n    return config\n  }\n\n  _maybeEnableSmoothScroll() {\n    if (!this._config.smoothScroll) {\n      return\n    }\n\n    // unregister any previous listeners\n    EventHandler.off(this._config.target, EVENT_CLICK)\n\n    EventHandler.on(this._config.target, EVENT_CLICK, SELECTOR_TARGET_LINKS, event => {\n      const observableSection = this._observableSections.get(event.target.hash)\n      if (observableSection) {\n        event.preventDefault()\n        const root = this._rootElement || window\n        const height = observableSection.offsetTop - this._element.offsetTop\n        if (root.scrollTo) {\n          root.scrollTo({ top: height, behavior: 'smooth' })\n          return\n        }\n\n        // Chrome 60 doesn't support `scrollTo`\n        root.scrollTop = height\n      }\n    })\n  }\n\n  _getNewObserver() {\n    const options = {\n      root: this._rootElement,\n      threshold: this._config.threshold,\n      rootMargin: this._config.rootMargin\n    }\n\n    return new IntersectionObserver(entries => this._observerCallback(entries), options)\n  }\n\n  // The logic of selection\n  _observerCallback(entries) {\n    const targetElement = entry => this._targetLinks.get(`#${entry.target.id}`)\n    const activate = entry => {\n      this._previousScrollData.visibleEntryTop = entry.target.offsetTop\n      this._process(targetElement(entry))\n    }\n\n    const parentScrollTop = (this._rootElement || document.documentElement).scrollTop\n    const userScrollsDown = parentScrollTop >= this._previousScrollData.parentScrollTop\n    this._previousScrollData.parentScrollTop = parentScrollTop\n\n    for (const entry of entries) {\n      if (!entry.isIntersecting) {\n        this._activeTarget = null\n        this._clearActiveClass(targetElement(entry))\n\n        continue\n      }\n\n      const entryIsLowerThanPrevious = entry.target.offsetTop >= this._previousScrollData.visibleEntryTop\n      // if we are scrolling down, pick the bigger offsetTop\n      if (userScrollsDown && entryIsLowerThanPrevious) {\n        activate(entry)\n        // if parent isn't scrolled, let's keep the first visible item, breaking the iteration\n        if (!parentScrollTop) {\n          return\n        }\n\n        continue\n      }\n\n      // if we are scrolling up, pick the smallest offsetTop\n      if (!userScrollsDown && !entryIsLowerThanPrevious) {\n        activate(entry)\n      }\n    }\n  }\n\n  _initializeTargetsAndObservables() {\n    this._targetLinks = new Map()\n    this._observableSections = new Map()\n\n    const targetLinks = SelectorEngine.find(SELECTOR_TARGET_LINKS, this._config.target)\n\n    for (const anchor of targetLinks) {\n      // ensure that the anchor has an id and is not disabled\n      if (!anchor.hash || isDisabled(anchor)) {\n        continue\n      }\n\n      const observableSection = SelectorEngine.findOne(decodeURI(anchor.hash), this._element)\n\n      // ensure that the observableSection exists & is visible\n      if (isVisible(observableSection)) {\n        this._targetLinks.set(decodeURI(anchor.hash), anchor)\n        this._observableSections.set(anchor.hash, observableSection)\n      }\n    }\n  }\n\n  _process(target) {\n    if (this._activeTarget === target) {\n      return\n    }\n\n    this._clearActiveClass(this._config.target)\n    this._activeTarget = target\n    target.classList.add(CLASS_NAME_ACTIVE)\n    this._activateParents(target)\n\n    EventHandler.trigger(this._element, EVENT_ACTIVATE, { relatedTarget: target })\n  }\n\n  _activateParents(target) {\n    // Activate dropdown parents\n    if (target.classList.contains(CLASS_NAME_DROPDOWN_ITEM)) {\n      SelectorEngine.findOne(SELECTOR_DROPDOWN_TOGGLE, target.closest(SELECTOR_DROPDOWN))\n        .classList.add(CLASS_NAME_ACTIVE)\n      return\n    }\n\n    for (const listGroup of SelectorEngine.parents(target, SELECTOR_NAV_LIST_GROUP)) {\n      // Set triggered links parents as active\n      // With both <ul> and <nav> markup a parent is the previous sibling of any nav ancestor\n      for (const item of SelectorEngine.prev(listGroup, SELECTOR_LINK_ITEMS)) {\n        item.classList.add(CLASS_NAME_ACTIVE)\n      }\n    }\n  }\n\n  _clearActiveClass(parent) {\n    parent.classList.remove(CLASS_NAME_ACTIVE)\n\n    const activeNodes = SelectorEngine.find(`${SELECTOR_TARGET_LINKS}.${CLASS_NAME_ACTIVE}`, parent)\n    for (const node of activeNodes) {\n      node.classList.remove(CLASS_NAME_ACTIVE)\n    }\n  }\n\n  // Static\n  static jQueryInterface(config) {\n    return this.each(function () {\n      const data = ScrollSpy.getOrCreateInstance(this, config)\n\n      if (typeof config !== 'string') {\n        return\n      }\n\n      if (data[config] === undefined || config.startsWith('_') || config === 'constructor') {\n        throw new TypeError(`No method named \"${config}\"`)\n      }\n\n      data[config]()\n    })\n  }\n}\n\n/**\n * Data API implementation\n */\n\nEventHandler.on(window, EVENT_LOAD_DATA_API, () => {\n  for (const spy of SelectorEngine.find(SELECTOR_DATA_SPY)) {\n    ScrollSpy.getOrCreateInstance(spy)\n  }\n})\n\n/**\n * jQuery\n */\n\ndefineJQueryPlugin(ScrollSpy)\n\nexport default ScrollSpy\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap tab.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport BaseComponent from './base-component.js'\nimport EventHandler from './dom/event-handler.js'\nimport SelectorEngine from './dom/selector-engine.js'\nimport { defineJQueryPlugin, getNextActiveElement, isDisabled } from './util/index.js'\n\n/**\n * Constants\n */\n\nconst NAME = 'tab'\nconst DATA_KEY = 'bs.tab'\nconst EVENT_KEY = `.${DATA_KEY}`\n\nconst EVENT_HIDE = `hide${EVENT_KEY}`\nconst EVENT_HIDDEN = `hidden${EVENT_KEY}`\nconst EVENT_SHOW = `show${EVENT_KEY}`\nconst EVENT_SHOWN = `shown${EVENT_KEY}`\nconst EVENT_CLICK_DATA_API = `click${EVENT_KEY}`\nconst EVENT_KEYDOWN = `keydown${EVENT_KEY}`\nconst EVENT_LOAD_DATA_API = `load${EVENT_KEY}`\n\nconst ARROW_LEFT_KEY = 'ArrowLeft'\nconst ARROW_RIGHT_KEY = 'ArrowRight'\nconst ARROW_UP_KEY = 'ArrowUp'\nconst ARROW_DOWN_KEY = 'ArrowDown'\nconst HOME_KEY = 'Home'\nconst END_KEY = 'End'\n\nconst CLASS_NAME_ACTIVE = 'active'\nconst CLASS_NAME_FADE = 'fade'\nconst CLASS_NAME_SHOW = 'show'\nconst CLASS_DROPDOWN = 'dropdown'\n\nconst SELECTOR_DROPDOWN_TOGGLE = '.dropdown-toggle'\nconst SELECTOR_DROPDOWN_MENU = '.dropdown-menu'\nconst NOT_SELECTOR_DROPDOWN_TOGGLE = ':not(.dropdown-toggle)'\n\nconst SELECTOR_TAB_PANEL = '.list-group, .nav, [role=\"tablist\"]'\nconst SELECTOR_OUTER = '.nav-item, .list-group-item'\nconst SELECTOR_INNER = `.nav-link${NOT_SELECTOR_DROPDOWN_TOGGLE}, .list-group-item${NOT_SELECTOR_DROPDOWN_TOGGLE}, [role=\"tab\"]${NOT_SELECTOR_DROPDOWN_TOGGLE}`\nconst SELECTOR_DATA_TOGGLE = '[data-bs-toggle=\"tab\"], [data-bs-toggle=\"pill\"], [data-bs-toggle=\"list\"]' // TODO: could only be `tab` in v6\nconst SELECTOR_INNER_ELEM = `${SELECTOR_INNER}, ${SELECTOR_DATA_TOGGLE}`\n\nconst SELECTOR_DATA_TOGGLE_ACTIVE = `.${CLASS_NAME_ACTIVE}[data-bs-toggle=\"tab\"], .${CLASS_NAME_ACTIVE}[data-bs-toggle=\"pill\"], .${CLASS_NAME_ACTIVE}[data-bs-toggle=\"list\"]`\n\n/**\n * Class definition\n */\n\nclass Tab extends BaseComponent {\n  constructor(element) {\n    super(element)\n    this._parent = this._element.closest(SELECTOR_TAB_PANEL)\n\n    if (!this._parent) {\n      return\n      // TODO: should throw exception in v6\n      // throw new TypeError(`${element.outerHTML} has not a valid parent ${SELECTOR_INNER_ELEM}`)\n    }\n\n    // Set up initial aria attributes\n    this._setInitialAttributes(this._parent, this._getChildren())\n\n    EventHandler.on(this._element, EVENT_KEYDOWN, event => this._keydown(event))\n  }\n\n  // Getters\n  static get NAME() {\n    return NAME\n  }\n\n  // Public\n  show() { // Shows this elem and deactivate the active sibling if exists\n    const innerElem = this._element\n    if (this._elemIsActive(innerElem)) {\n      return\n    }\n\n    // Search for active tab on same parent to deactivate it\n    const active = this._getActiveElem()\n\n    const hideEvent = active ?\n      EventHandler.trigger(active, EVENT_HIDE, { relatedTarget: innerElem }) :\n      null\n\n    const showEvent = EventHandler.trigger(innerElem, EVENT_SHOW, { relatedTarget: active })\n\n    if (showEvent.defaultPrevented || (hideEvent && hideEvent.defaultPrevented)) {\n      return\n    }\n\n    this._deactivate(active, innerElem)\n    this._activate(innerElem, active)\n  }\n\n  // Private\n  _activate(element, relatedElem) {\n    if (!element) {\n      return\n    }\n\n    element.classList.add(CLASS_NAME_ACTIVE)\n\n    this._activate(SelectorEngine.getElementFromSelector(element)) // Search and activate/show the proper section\n\n    const complete = () => {\n      if (element.getAttribute('role') !== 'tab') {\n        element.classList.add(CLASS_NAME_SHOW)\n        return\n      }\n\n      element.removeAttribute('tabindex')\n      element.setAttribute('aria-selected', true)\n      this._toggleDropDown(element, true)\n      EventHandler.trigger(element, EVENT_SHOWN, {\n        relatedTarget: relatedElem\n      })\n    }\n\n    this._queueCallback(complete, element, element.classList.contains(CLASS_NAME_FADE))\n  }\n\n  _deactivate(element, relatedElem) {\n    if (!element) {\n      return\n    }\n\n    element.classList.remove(CLASS_NAME_ACTIVE)\n    element.blur()\n\n    this._deactivate(SelectorEngine.getElementFromSelector(element)) // Search and deactivate the shown section too\n\n    const complete = () => {\n      if (element.getAttribute('role') !== 'tab') {\n        element.classList.remove(CLASS_NAME_SHOW)\n        return\n      }\n\n      element.setAttribute('aria-selected', false)\n      element.setAttribute('tabindex', '-1')\n      this._toggleDropDown(element, false)\n      EventHandler.trigger(element, EVENT_HIDDEN, { relatedTarget: relatedElem })\n    }\n\n    this._queueCallback(complete, element, element.classList.contains(CLASS_NAME_FADE))\n  }\n\n  _keydown(event) {\n    if (!([ARROW_LEFT_KEY, ARROW_RIGHT_KEY, ARROW_UP_KEY, ARROW_DOWN_KEY, HOME_KEY, END_KEY].includes(event.key))) {\n      return\n    }\n\n    event.stopPropagation()// stopPropagation/preventDefault both added to support up/down keys without scrolling the page\n    event.preventDefault()\n\n    const children = this._getChildren().filter(element => !isDisabled(element))\n    let nextActiveElement\n\n    if ([HOME_KEY, END_KEY].includes(event.key)) {\n      nextActiveElement = children[event.key === HOME_KEY ? 0 : children.length - 1]\n    } else {\n      const isNext = [ARROW_RIGHT_KEY, ARROW_DOWN_KEY].includes(event.key)\n      nextActiveElement = getNextActiveElement(children, event.target, isNext, true)\n    }\n\n    if (nextActiveElement) {\n      nextActiveElement.focus({ preventScroll: true })\n      Tab.getOrCreateInstance(nextActiveElement).show()\n    }\n  }\n\n  _getChildren() { // collection of inner elements\n    return SelectorEngine.find(SELECTOR_INNER_ELEM, this._parent)\n  }\n\n  _getActiveElem() {\n    return this._getChildren().find(child => this._elemIsActive(child)) || null\n  }\n\n  _setInitialAttributes(parent, children) {\n    this._setAttributeIfNotExists(parent, 'role', 'tablist')\n\n    for (const child of children) {\n      this._setInitialAttributesOnChild(child)\n    }\n  }\n\n  _setInitialAttributesOnChild(child) {\n    child = this._getInnerElement(child)\n    const isActive = this._elemIsActive(child)\n    const outerElem = this._getOuterElement(child)\n    child.setAttribute('aria-selected', isActive)\n\n    if (outerElem !== child) {\n      this._setAttributeIfNotExists(outerElem, 'role', 'presentation')\n    }\n\n    if (!isActive) {\n      child.setAttribute('tabindex', '-1')\n    }\n\n    this._setAttributeIfNotExists(child, 'role', 'tab')\n\n    // set attributes to the related panel too\n    this._setInitialAttributesOnTargetPanel(child)\n  }\n\n  _setInitialAttributesOnTargetPanel(child) {\n    const target = SelectorEngine.getElementFromSelector(child)\n\n    if (!target) {\n      return\n    }\n\n    this._setAttributeIfNotExists(target, 'role', 'tabpanel')\n\n    if (child.id) {\n      this._setAttributeIfNotExists(target, 'aria-labelledby', `${child.id}`)\n    }\n  }\n\n  _toggleDropDown(element, open) {\n    const outerElem = this._getOuterElement(element)\n    if (!outerElem.classList.contains(CLASS_DROPDOWN)) {\n      return\n    }\n\n    const toggle = (selector, className) => {\n      const element = SelectorEngine.findOne(selector, outerElem)\n      if (element) {\n        element.classList.toggle(className, open)\n      }\n    }\n\n    toggle(SELECTOR_DROPDOWN_TOGGLE, CLASS_NAME_ACTIVE)\n    toggle(SELECTOR_DROPDOWN_MENU, CLASS_NAME_SHOW)\n    outerElem.setAttribute('aria-expanded', open)\n  }\n\n  _setAttributeIfNotExists(element, attribute, value) {\n    if (!element.hasAttribute(attribute)) {\n      element.setAttribute(attribute, value)\n    }\n  }\n\n  _elemIsActive(elem) {\n    return elem.classList.contains(CLASS_NAME_ACTIVE)\n  }\n\n  // Try to get the inner element (usually the .nav-link)\n  _getInnerElement(elem) {\n    return elem.matches(SELECTOR_INNER_ELEM) ? elem : SelectorEngine.findOne(SELECTOR_INNER_ELEM, elem)\n  }\n\n  // Try to get the outer element (usually the .nav-item)\n  _getOuterElement(elem) {\n    return elem.closest(SELECTOR_OUTER) || elem\n  }\n\n  // Static\n  static jQueryInterface(config) {\n    return this.each(function () {\n      const data = Tab.getOrCreateInstance(this)\n\n      if (typeof config !== 'string') {\n        return\n      }\n\n      if (data[config] === undefined || config.startsWith('_') || config === 'constructor') {\n        throw new TypeError(`No method named \"${config}\"`)\n      }\n\n      data[config]()\n    })\n  }\n}\n\n/**\n * Data API implementation\n */\n\nEventHandler.on(document, EVENT_CLICK_DATA_API, SELECTOR_DATA_TOGGLE, function (event) {\n  if (['A', 'AREA'].includes(this.tagName)) {\n    event.preventDefault()\n  }\n\n  if (isDisabled(this)) {\n    return\n  }\n\n  Tab.getOrCreateInstance(this).show()\n})\n\n/**\n * Initialize on focus\n */\nEventHandler.on(window, EVENT_LOAD_DATA_API, () => {\n  for (const element of SelectorEngine.find(SELECTOR_DATA_TOGGLE_ACTIVE)) {\n    Tab.getOrCreateInstance(element)\n  }\n})\n/**\n * jQuery\n */\n\ndefineJQueryPlugin(Tab)\n\nexport default Tab\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap toast.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport BaseComponent from './base-component.js'\nimport EventHandler from './dom/event-handler.js'\nimport { enableDismissTrigger } from './util/component-functions.js'\nimport { defineJQueryPlugin, reflow } from './util/index.js'\n\n/**\n * Constants\n */\n\nconst NAME = 'toast'\nconst DATA_KEY = 'bs.toast'\nconst EVENT_KEY = `.${DATA_KEY}`\n\nconst EVENT_MOUSEOVER = `mouseover${EVENT_KEY}`\nconst EVENT_MOUSEOUT = `mouseout${EVENT_KEY}`\nconst EVENT_FOCUSIN = `focusin${EVENT_KEY}`\nconst EVENT_FOCUSOUT = `focusout${EVENT_KEY}`\nconst EVENT_HIDE = `hide${EVENT_KEY}`\nconst EVENT_HIDDEN = `hidden${EVENT_KEY}`\nconst EVENT_SHOW = `show${EVENT_KEY}`\nconst EVENT_SHOWN = `shown${EVENT_KEY}`\n\nconst CLASS_NAME_FADE = 'fade'\nconst CLASS_NAME_HIDE = 'hide' // @deprecated - kept here only for backwards compatibility\nconst CLASS_NAME_SHOW = 'show'\nconst CLASS_NAME_SHOWING = 'showing'\n\nconst DefaultType = {\n  animation: 'boolean',\n  autohide: 'boolean',\n  delay: 'number'\n}\n\nconst Default = {\n  animation: true,\n  autohide: true,\n  delay: 5000\n}\n\n/**\n * Class definition\n */\n\nclass Toast extends BaseComponent {\n  constructor(element, config) {\n    super(element, config)\n\n    this._timeout = null\n    this._hasMouseInteraction = false\n    this._hasKeyboardInteraction = false\n    this._setListeners()\n  }\n\n  // Getters\n  static get Default() {\n    return Default\n  }\n\n  static get DefaultType() {\n    return DefaultType\n  }\n\n  static get NAME() {\n    return NAME\n  }\n\n  // Public\n  show() {\n    const showEvent = EventHandler.trigger(this._element, EVENT_SHOW)\n\n    if (showEvent.defaultPrevented) {\n      return\n    }\n\n    this._clearTimeout()\n\n    if (this._config.animation) {\n      this._element.classList.add(CLASS_NAME_FADE)\n    }\n\n    const complete = () => {\n      this._element.classList.remove(CLASS_NAME_SHOWING)\n      EventHandler.trigger(this._element, EVENT_SHOWN)\n\n      this._maybeScheduleHide()\n    }\n\n    this._element.classList.remove(CLASS_NAME_HIDE) // @deprecated\n    reflow(this._element)\n    this._element.classList.add(CLASS_NAME_SHOW, CLASS_NAME_SHOWING)\n\n    this._queueCallback(complete, this._element, this._config.animation)\n  }\n\n  hide() {\n    if (!this.isShown()) {\n      return\n    }\n\n    const hideEvent = EventHandler.trigger(this._element, EVENT_HIDE)\n\n    if (hideEvent.defaultPrevented) {\n      return\n    }\n\n    const complete = () => {\n      this._element.classList.add(CLASS_NAME_HIDE) // @deprecated\n      this._element.classList.remove(CLASS_NAME_SHOWING, CLASS_NAME_SHOW)\n      EventHandler.trigger(this._element, EVENT_HIDDEN)\n    }\n\n    this._element.classList.add(CLASS_NAME_SHOWING)\n    this._queueCallback(complete, this._element, this._config.animation)\n  }\n\n  dispose() {\n    this._clearTimeout()\n\n    if (this.isShown()) {\n      this._element.classList.remove(CLASS_NAME_SHOW)\n    }\n\n    super.dispose()\n  }\n\n  isShown() {\n    return this._element.classList.contains(CLASS_NAME_SHOW)\n  }\n\n  // Private\n\n  _maybeScheduleHide() {\n    if (!this._config.autohide) {\n      return\n    }\n\n    if (this._hasMouseInteraction || this._hasKeyboardInteraction) {\n      return\n    }\n\n    this._timeout = setTimeout(() => {\n      this.hide()\n    }, this._config.delay)\n  }\n\n  _onInteraction(event, isInteracting) {\n    switch (event.type) {\n      case 'mouseover':\n      case 'mouseout': {\n        this._hasMouseInteraction = isInteracting\n        break\n      }\n\n      case 'focusin':\n      case 'focusout': {\n        this._hasKeyboardInteraction = isInteracting\n        break\n      }\n\n      default: {\n        break\n      }\n    }\n\n    if (isInteracting) {\n      this._clearTimeout()\n      return\n    }\n\n    const nextElement = event.relatedTarget\n    if (this._element === nextElement || this._element.contains(nextElement)) {\n      return\n    }\n\n    this._maybeScheduleHide()\n  }\n\n  _setListeners() {\n    EventHandler.on(this._element, EVENT_MOUSEOVER, event => this._onInteraction(event, true))\n    EventHandler.on(this._element, EVENT_MOUSEOUT, event => this._onInteraction(event, false))\n    EventHandler.on(this._element, EVENT_FOCUSIN, event => this._onInteraction(event, true))\n    EventHandler.on(this._element, EVENT_FOCUSOUT, event => this._onInteraction(event, false))\n  }\n\n  _clearTimeout() {\n    clearTimeout(this._timeout)\n    this._timeout = null\n  }\n\n  // Static\n  static jQueryInterface(config) {\n    return this.each(function () {\n      const data = Toast.getOrCreateInstance(this, config)\n\n      if (typeof config === 'string') {\n        if (typeof data[config] === 'undefined') {\n          throw new TypeError(`No method named \"${config}\"`)\n        }\n\n        data[config](this)\n      }\n    })\n  }\n}\n\n/**\n * Data API implementation\n */\n\nenableDismissTrigger(Toast)\n\n/**\n * jQuery\n */\n\ndefineJQueryPlugin(Toast)\n\nexport default Toast\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap index.umd.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport Alert from './src/alert.js'\nimport Button from './src/button.js'\nimport Carousel from './src/carousel.js'\nimport Collapse from './src/collapse.js'\nimport Dropdown from './src/dropdown.js'\nimport Modal from './src/modal.js'\nimport Offcanvas from './src/offcanvas.js'\nimport Popover from './src/popover.js'\nimport ScrollSpy from './src/scrollspy.js'\nimport Tab from './src/tab.js'\nimport Toast from './src/toast.js'\nimport Tooltip from 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\ No newline at end of file
diff --git a/deps/bootstrap-5.3.1/bootstrap.min.css b/deps/bootstrap-5.3.1/bootstrap.min.css
new file mode 100644
index 00000000..0fa31676
--- /dev/null
+++ b/deps/bootstrap-5.3.1/bootstrap.min.css
@@ -0,0 +1,5 @@
+@import url("font.css");:root{--bslib-bootstrap-version: 5;--bslib-preset-name: shiny;--bslib-preset-type: builtin}/*!
+   * Bootstrap  v5.3.1 (https://getbootstrap.com/)
+   * Copyright 2011-2023 The Bootstrap Authors
+   * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)
+   */:root,[data-bs-theme="light"]{--bs-blue: #007bc2;--bs-indigo: #4b00c1;--bs-purple: #74149c;--bs-pink: #bf007f;--bs-red: #c10000;--bs-orange: #f45100;--bs-yellow: #f9b928;--bs-green: #00891a;--bs-teal: #00bf7f;--bs-cyan: #03c7e8;--bs-black: #000;--bs-white: #fff;--bs-gray: #707782;--bs-gray-dark: #343A46;--bs-gray-100: #f8f8f8;--bs-gray-200: #e9ecef;--bs-gray-300: #dee2e6;--bs-gray-400: #cdd4da;--bs-gray-500: #8D959E;--bs-gray-600: #707782;--bs-gray-700: #48505F;--bs-gray-800: #343A46;--bs-gray-900: #1D1F21;--bs-default: #dee2e6;--bs-primary: #007bc2;--bs-secondary: #404040;--bs-success: #00891a;--bs-info: #03c7e8;--bs-warning: #f9b928;--bs-danger: #c10000;--bs-light: #f8f8f8;--bs-dark: #202020;--bs-default-rgb: 222,226,230;--bs-primary-rgb: 0,123,194;--bs-secondary-rgb: 64,64,64;--bs-success-rgb: 0,137,26;--bs-info-rgb: 3,199,232;--bs-warning-rgb: 249,185,40;--bs-danger-rgb: 193,0,0;--bs-light-rgb: 248,248,248;--bs-dark-rgb: 32,32,32;--bs-primary-text-emphasis: #00314e;--bs-secondary-text-emphasis: #1a1a1a;--bs-success-text-emphasis: #00370a;--bs-info-text-emphasis: #01505d;--bs-warning-text-emphasis: #644a10;--bs-danger-text-emphasis: #4d0000;--bs-light-text-emphasis: #48505F;--bs-dark-text-emphasis: #48505F;--bs-primary-bg-subtle: #cce5f3;--bs-secondary-bg-subtle: #d9d9d9;--bs-success-bg-subtle: #cce7d1;--bs-info-bg-subtle: #cdf4fa;--bs-warning-bg-subtle: #fef1d4;--bs-danger-bg-subtle: #f3cccc;--bs-light-bg-subtle: #fcfcfc;--bs-dark-bg-subtle: #cdd4da;--bs-primary-border-subtle: #99cae7;--bs-secondary-border-subtle: #b3b3b3;--bs-success-border-subtle: #99d0a3;--bs-info-border-subtle: #9ae9f6;--bs-warning-border-subtle: #fde3a9;--bs-danger-border-subtle: #e69999;--bs-light-border-subtle: #e9ecef;--bs-dark-border-subtle: #8D959E;--bs-white-rgb: 255,255,255;--bs-black-rgb: 0,0,0;--bs-font-sans-serif: system-ui, -apple-system, "Segoe UI", Roboto, "Helvetica Neue", "Noto Sans", "Liberation Sans", Arial, sans-serif, "Apple Color Emoji", "Segoe UI 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#202020;--bs-btn-bg: transparent;--bs-gradient: none}.btn-link{--bs-btn-font-weight: 400;--bs-btn-color: var(--bs-link-color);--bs-btn-bg: transparent;--bs-btn-border-color: transparent;--bs-btn-hover-color: var(--bs-link-hover-color);--bs-btn-hover-border-color: transparent;--bs-btn-active-color: var(--bs-link-hover-color);--bs-btn-active-border-color: transparent;--bs-btn-disabled-color: #707782;--bs-btn-disabled-border-color: transparent;--bs-btn-box-shadow: 0 0 0 #000;--bs-btn-focus-shadow-rgb: 38,143,203;text-decoration:underline;-webkit-text-decoration:underline;-moz-text-decoration:underline;-ms-text-decoration:underline;-o-text-decoration:underline}.btn-link:focus-visible{color:var(--bs-btn-color)}.btn-link:hover{color:var(--bs-btn-hover-color)}.btn-lg,.btn-group-lg>.btn{--bs-btn-padding-y: .5rem;--bs-btn-padding-x: 1rem;--bs-btn-font-size:1.25rem;--bs-btn-border-radius: var(--bs-border-radius-lg)}.btn-sm,.btn-group-sm>.btn{--bs-btn-padding-y: .25rem;--bs-btn-padding-x: 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10rem;--bs-dropdown-padding-x: 0;--bs-dropdown-padding-y: .5rem;--bs-dropdown-spacer: .125rem;--bs-dropdown-font-size:1rem;--bs-dropdown-color: var(--bs-body-color);--bs-dropdown-bg: var(--bs-body-bg);--bs-dropdown-border-color: var(--bs-border-color-translucent);--bs-dropdown-border-radius: var(--bs-border-radius);--bs-dropdown-border-width: var(--bs-border-width);--bs-dropdown-inner-border-radius: calc(var(--bs-border-radius) - var(--bs-border-width));--bs-dropdown-divider-bg: var(--bs-border-color-translucent);--bs-dropdown-divider-margin-y: .5rem;--bs-dropdown-box-shadow: 0px 1px 2px RGBA(var(--bslib-box-shadow-color-rgb), 0.1),0px 3px 7px RGBA(var(--bslib-box-shadow-color-rgb), 0.1),0px 12px 30px RGBA(var(--bslib-box-shadow-color-rgb), 0.08);--bs-dropdown-link-color: var(--bs-body-color);--bs-dropdown-link-hover-color: var(--bs-body-color);--bs-dropdown-link-hover-bg: var(--bs-tertiary-bg);--bs-dropdown-link-active-color: #fff;--bs-dropdown-link-active-bg: #007bc2;--bs-dropdown-link-disabled-color: var(--bs-tertiary-color);--bs-dropdown-item-padding-x: 1rem;--bs-dropdown-item-padding-y: .25rem;--bs-dropdown-header-color: #707782;--bs-dropdown-header-padding-x: 1rem;--bs-dropdown-header-padding-y: .5rem;position:absolute;z-index:var(--bs-dropdown-zindex);display:none;min-width:var(--bs-dropdown-min-width);padding:var(--bs-dropdown-padding-y) var(--bs-dropdown-padding-x);margin:0;font-size:var(--bs-dropdown-font-size);color:var(--bs-dropdown-color);text-align:left;list-style:none;background-color:var(--bs-dropdown-bg);background-clip:padding-box;border:var(--bs-dropdown-border-width) solid var(--bs-dropdown-border-color);border-radius:var(--bs-dropdown-border-radius)}.dropdown-menu[data-bs-popper]{top:100%;left:0;margin-top:var(--bs-dropdown-spacer)}.dropdown-menu-start{--bs-position: start}.dropdown-menu-start[data-bs-popper]{right:auto;left:0}.dropdown-menu-end{--bs-position: 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1400px){.dropdown-menu-xxl-start{--bs-position: start}.dropdown-menu-xxl-start[data-bs-popper]{right:auto;left:0}.dropdown-menu-xxl-end{--bs-position: end}.dropdown-menu-xxl-end[data-bs-popper]{right:0;left:auto}}.dropup .dropdown-menu[data-bs-popper]{top:auto;bottom:100%;margin-top:0;margin-bottom:var(--bs-dropdown-spacer)}.dropup .dropdown-toggle::after{display:inline-block;margin-left:.255em;vertical-align:.255em;content:"";border-top:0;border-right:.3em solid transparent;border-bottom:.3em solid;border-left:.3em solid transparent}.dropup .dropdown-toggle:empty::after{margin-left:0}.dropend .dropdown-menu[data-bs-popper]{top:0;right:auto;left:100%;margin-top:0;margin-left:var(--bs-dropdown-spacer)}.dropend .dropdown-toggle::after{display:inline-block;margin-left:.255em;vertical-align:.255em;content:"";border-top:.3em solid transparent;border-right:0;border-bottom:.3em solid transparent;border-left:.3em solid}.dropend .dropdown-toggle:empty::after{margin-left:0}.dropend .dropdown-toggle::after{vertical-align:0}.dropstart .dropdown-menu[data-bs-popper]{top:0;right:100%;left:auto;margin-top:0;margin-right:var(--bs-dropdown-spacer)}.dropstart .dropdown-toggle::after{display:inline-block;margin-left:.255em;vertical-align:.255em;content:""}.dropstart .dropdown-toggle::after{display:none}.dropstart .dropdown-toggle::before{display:inline-block;margin-right:.255em;vertical-align:.255em;content:"";border-top:.3em solid transparent;border-right:.3em solid;border-bottom:.3em solid transparent}.dropstart .dropdown-toggle:empty::after{margin-left:0}.dropstart .dropdown-toggle::before{vertical-align:0}.dropdown-divider{height:0;margin:var(--bs-dropdown-divider-margin-y) 0;overflow:hidden;border-top:1px solid var(--bs-dropdown-divider-bg);opacity:1}.dropdown-item{display:block;width:100%;padding:var(--bs-dropdown-item-padding-y) var(--bs-dropdown-item-padding-x);clear:both;font-weight:400;color:var(--bs-dropdown-link-color);text-align:inherit;text-decoration:none;-webkit-text-decoration:none;-moz-text-decoration:none;-ms-text-decoration:none;-o-text-decoration:none;white-space:nowrap;background-color:transparent;border:0;border-radius:var(--bs-dropdown-item-border-radius, 0)}.dropdown-item:hover,.dropdown-item:focus{color:var(--bs-dropdown-link-hover-color);background-color:var(--bs-dropdown-link-hover-bg)}.dropdown-item.active,.dropdown-item:active{color:var(--bs-dropdown-link-active-color);text-decoration:none;background-color:var(--bs-dropdown-link-active-bg)}.dropdown-item.disabled,.dropdown-item:disabled{color:var(--bs-dropdown-link-disabled-color);pointer-events:none;background-color:transparent}.dropdown-menu.show{display:block}.dropdown-header{display:block;padding:var(--bs-dropdown-header-padding-y) var(--bs-dropdown-header-padding-x);margin-bottom:0;font-size:.875rem;color:var(--bs-dropdown-header-color);white-space:nowrap}.dropdown-item-text{display:block;padding:var(--bs-dropdown-item-padding-y) var(--bs-dropdown-item-padding-x);color:var(--bs-dropdown-link-color)}.dropdown-menu-dark{--bs-dropdown-color: #dee2e6;--bs-dropdown-bg: #343A46;--bs-dropdown-border-color: var(--bs-border-color-translucent);--bs-dropdown-box-shadow: ;--bs-dropdown-link-color: #dee2e6;--bs-dropdown-link-hover-color: #fff;--bs-dropdown-divider-bg: var(--bs-border-color-translucent);--bs-dropdown-link-hover-bg: rgba(255,255,255,0.15);--bs-dropdown-link-active-color: #fff;--bs-dropdown-link-active-bg: #007bc2;--bs-dropdown-link-disabled-color: #8D959E;--bs-dropdown-header-color: #8D959E}.btn-group,.btn-group-vertical{position:relative;display:inline-flex;vertical-align:middle}.btn-group>.btn,.btn-group-vertical>.btn{position:relative;flex:1 1 auto;-webkit-flex:1 1 auto}.btn-group>.btn-check:checked+.btn,.btn-group>.btn-check:focus+.btn,.btn-group>.btn:hover,.btn-group>.btn:focus,.btn-group>.btn:active,.btn-group>.btn.active,.btn-group-vertical>.btn-check:checked+.btn,.btn-group-vertical>.btn-check:focus+.btn,.btn-group-vertical>.btn:hover,.btn-group-vertical>.btn:focus,.btn-group-vertical>.btn:active,.btn-group-vertical>.btn.active{z-index:1}.btn-toolbar{display:flex;display:-webkit-flex;flex-wrap:wrap;-webkit-flex-wrap:wrap;justify-content:flex-start;-webkit-justify-content:flex-start}.btn-toolbar .input-group{width:auto}.btn-group{border-radius:var(--bs-border-radius)}.btn-group>:not(.btn-check:first-child)+.btn,.btn-group>.btn-group:not(:first-child){margin-left:calc(var(--bs-border-width) * -1)}.btn-group>.btn:not(:last-child):not(.dropdown-toggle),.btn-group>.btn.dropdown-toggle-split:first-child,.btn-group>.btn-group:not(:last-child)>.btn{border-top-right-radius:0;border-bottom-right-radius:0}.btn-group>.btn:nth-child(n + 3),.btn-group>:not(.btn-check)+.btn,.btn-group>.btn-group:not(:first-child)>.btn{border-top-left-radius:0;border-bottom-left-radius:0}.dropdown-toggle-split{padding-right:1.5em;padding-left:1.5em}.dropdown-toggle-split::after,.dropup .dropdown-toggle-split::after,.dropend .dropdown-toggle-split::after{margin-left:0}.dropstart .dropdown-toggle-split::before{margin-right:0}.btn-sm+.dropdown-toggle-split,.btn-group-sm>.btn+.dropdown-toggle-split{padding-right:.375rem;padding-left:.375rem}.btn-lg+.dropdown-toggle-split,.btn-group-lg>.btn+.dropdown-toggle-split{padding-right:.75rem;padding-left:.75rem}.btn-group-vertical{flex-direction:column;-webkit-flex-direction:column;align-items:flex-start;-webkit-align-items:flex-start;justify-content:center;-webkit-justify-content:center}.btn-group-vertical>.btn,.btn-group-vertical>.btn-group{width:100%}.btn-group-vertical>.btn:not(:first-child),.btn-group-vertical>.btn-group:not(:first-child){margin-top:calc(var(--bs-border-width) * -1)}.btn-group-vertical>.btn:not(:last-child):not(.dropdown-toggle),.btn-group-vertical>.btn-group:not(:last-child)>.btn{border-bottom-right-radius:0;border-bottom-left-radius:0}.btn-group-vertical>.btn~.btn,.btn-group-vertical>.btn-group:not(:first-child)>.btn{border-top-left-radius:0;border-top-right-radius:0}.nav{--bs-nav-link-padding-x: 1rem;--bs-nav-link-padding-y: .5rem;--bs-nav-link-font-weight: ;--bs-nav-link-color: var(--bs-link-color);--bs-nav-link-hover-color: var(--bs-link-hover-color);--bs-nav-link-disabled-color: var(--bs-secondary-color);display:flex;display:-webkit-flex;flex-wrap:wrap;-webkit-flex-wrap:wrap;padding-left:0;margin-bottom:0;list-style:none}.nav-link{display:block;padding:var(--bs-nav-link-padding-y) var(--bs-nav-link-padding-x);font-size:var(--bs-nav-link-font-size);font-weight:var(--bs-nav-link-font-weight);color:var(--bs-nav-link-color);text-decoration:none;-webkit-text-decoration:none;-moz-text-decoration:none;-ms-text-decoration:none;-o-text-decoration:none;background:none;border:0;transition:color 0.15s ease-in-out,background-color 0.15s ease-in-out,border-color 0.15s ease-in-out}@media (prefers-reduced-motion: reduce){.nav-link{transition:none}}.nav-link:hover,.nav-link:focus{color:var(--bs-nav-link-hover-color)}.nav-link:focus-visible{outline:0;box-shadow:0 0 0 .25rem rgba(0,123,194,0.25)}.nav-link.disabled,.nav-link:disabled{color:var(--bs-nav-link-disabled-color);pointer-events:none;cursor:default}.nav-tabs{--bs-nav-tabs-border-width: var(--bs-border-width);--bs-nav-tabs-border-color: var(--bs-border-color);--bs-nav-tabs-border-radius: var(--bs-border-radius);--bs-nav-tabs-link-hover-border-color: var(--bs-secondary-bg) var(--bs-secondary-bg) var(--bs-border-color);--bs-nav-tabs-link-active-color: var(--bs-emphasis-color);--bs-nav-tabs-link-active-bg: var(--bs-body-bg);--bs-nav-tabs-link-active-border-color: var(--bs-border-color) var(--bs-border-color) var(--bs-body-bg);border-bottom:var(--bs-nav-tabs-border-width) solid var(--bs-nav-tabs-border-color)}.nav-tabs .nav-link{margin-bottom:calc(-1 * var(--bs-nav-tabs-border-width));border:var(--bs-nav-tabs-border-width) solid transparent;border-top-left-radius:var(--bs-nav-tabs-border-radius);border-top-right-radius:var(--bs-nav-tabs-border-radius)}.nav-tabs .nav-link:hover,.nav-tabs .nav-link:focus{isolation:isolate;border-color:var(--bs-nav-tabs-link-hover-border-color)}.nav-tabs .nav-link.active,.nav-tabs .nav-item.show .nav-link{color:var(--bs-nav-tabs-link-active-color);background-color:var(--bs-nav-tabs-link-active-bg);border-color:var(--bs-nav-tabs-link-active-border-color)}.nav-tabs .dropdown-menu{margin-top:calc(-1 * var(--bs-nav-tabs-border-width));border-top-left-radius:0;border-top-right-radius:0}.nav-pills{--bs-nav-pills-border-radius: var(--bs-border-radius);--bs-nav-pills-link-active-color: #fff;--bs-nav-pills-link-active-bg: #007bc2}.nav-pills .nav-link{border-radius:var(--bs-nav-pills-border-radius)}.nav-pills .nav-link.active,.nav-pills .show>.nav-link{color:var(--bs-nav-pills-link-active-color);background-color:var(--bs-nav-pills-link-active-bg)}.nav-underline{--bs-nav-underline-gap: 1rem;--bs-nav-underline-border-width: .125rem;--bs-nav-underline-link-active-color: var(--bs-emphasis-color);gap:var(--bs-nav-underline-gap)}.nav-underline .nav-link{padding-right:0;padding-left:0;border-bottom:var(--bs-nav-underline-border-width) solid transparent}.nav-underline .nav-link:hover,.nav-underline .nav-link:focus{border-bottom-color:currentcolor}.nav-underline .nav-link.active,.nav-underline .show>.nav-link{font-weight:700;color:var(--bs-nav-underline-link-active-color);border-bottom-color:currentcolor}.nav-fill>.nav-link,.nav-fill .nav-item{flex:1 1 auto;-webkit-flex:1 1 auto;text-align:center}.nav-justified>.nav-link,.nav-justified .nav-item{flex-basis:0;-webkit-flex-basis:0;flex-grow:1;-webkit-flex-grow:1;text-align:center}.nav-fill .nav-item .nav-link,.nav-justified .nav-item .nav-link{width:100%}.tab-content>.tab-pane{display:none}.tab-content>.active{display:block}.navbar{--bs-navbar-padding-x: .66rem;--bs-navbar-padding-y: .5rem;--bs-navbar-color: rgba(var(--bs-emphasis-color-rgb), 0.65);--bs-navbar-hover-color: rgba(var(--bs-emphasis-color-rgb), 0.8);--bs-navbar-disabled-color: rgba(var(--bs-emphasis-color-rgb), 0.3);--bs-navbar-active-color: rgba(var(--bs-emphasis-color-rgb), 1);--bs-navbar-brand-padding-y: .3125rem;--bs-navbar-brand-margin-end: 1rem;--bs-navbar-brand-font-size: 1.25rem;--bs-navbar-brand-color: rgba(var(--bs-emphasis-color-rgb), 1);--bs-navbar-brand-hover-color: rgba(var(--bs-emphasis-color-rgb), 1);--bs-navbar-nav-link-padding-x: .5rem;--bs-navbar-toggler-padding-y: .25rem;--bs-navbar-toggler-padding-x: .75rem;--bs-navbar-toggler-font-size: 1.25rem;--bs-navbar-toggler-icon-bg: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 30 30'%3e%3cpath stroke='rgba%2829,31,33,0.75%29' stroke-linecap='round' stroke-miterlimit='10' stroke-width='2' d='M4 7h22M4 15h22M4 23h22'/%3e%3c/svg%3e");--bs-navbar-toggler-border-color: rgba(var(--bs-emphasis-color-rgb), 0.15);--bs-navbar-toggler-border-radius: var(--bs-border-radius);--bs-navbar-toggler-focus-width: .25rem;--bs-navbar-toggler-transition: box-shadow 0.15s ease-in-out;position:relative;display:flex;display:-webkit-flex;flex-wrap:wrap;-webkit-flex-wrap:wrap;align-items:center;-webkit-align-items:center;justify-content:space-between;-webkit-justify-content:space-between;padding:var(--bs-navbar-padding-y) 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992px){.navbar-expand-lg{flex-wrap:nowrap;-webkit-flex-wrap:nowrap;justify-content:flex-start;-webkit-justify-content:flex-start}.navbar-expand-lg .navbar-nav{flex-direction:row;-webkit-flex-direction:row}.navbar-expand-lg .navbar-nav .dropdown-menu{position:absolute}.navbar-expand-lg .navbar-nav .nav-link{padding-right:var(--bs-navbar-nav-link-padding-x);padding-left:var(--bs-navbar-nav-link-padding-x)}.navbar-expand-lg .navbar-nav-scroll{overflow:visible}.navbar-expand-lg .navbar-collapse{display:flex !important;display:-webkit-flex !important;flex-basis:auto;-webkit-flex-basis:auto}.navbar-expand-lg .navbar-toggler{display:none}.navbar-expand-lg .offcanvas{position:static;z-index:auto;flex-grow:1;-webkit-flex-grow:1;width:auto !important;height:auto !important;visibility:visible !important;background-color:transparent !important;border:0 !important;transform:none !important;transition:none}.navbar-expand-lg .offcanvas .offcanvas-header{display:none}.navbar-expand-lg .offcanvas 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!important;transform:none !important;transition:none}.navbar-expand-xl .offcanvas .offcanvas-header{display:none}.navbar-expand-xl .offcanvas .offcanvas-body{display:flex;display:-webkit-flex;flex-grow:0;-webkit-flex-grow:0;padding:0;overflow-y:visible}}@media (min-width: 1400px){.navbar-expand-xxl{flex-wrap:nowrap;-webkit-flex-wrap:nowrap;justify-content:flex-start;-webkit-justify-content:flex-start}.navbar-expand-xxl .navbar-nav{flex-direction:row;-webkit-flex-direction:row}.navbar-expand-xxl .navbar-nav .dropdown-menu{position:absolute}.navbar-expand-xxl .navbar-nav .nav-link{padding-right:var(--bs-navbar-nav-link-padding-x);padding-left:var(--bs-navbar-nav-link-padding-x)}.navbar-expand-xxl .navbar-nav-scroll{overflow:visible}.navbar-expand-xxl .navbar-collapse{display:flex !important;display:-webkit-flex !important;flex-basis:auto;-webkit-flex-basis:auto}.navbar-expand-xxl .navbar-toggler{display:none}.navbar-expand-xxl .offcanvas{position:static;z-index:auto;flex-grow:1;-webkit-flex-grow:1;width:auto !important;height:auto !important;visibility:visible !important;background-color:transparent !important;border:0 !important;transform:none !important;transition:none}.navbar-expand-xxl .offcanvas .offcanvas-header{display:none}.navbar-expand-xxl .offcanvas .offcanvas-body{display:flex;display:-webkit-flex;flex-grow:0;-webkit-flex-grow:0;padding:0;overflow-y:visible}}.navbar-expand{flex-wrap:nowrap;-webkit-flex-wrap:nowrap;justify-content:flex-start;-webkit-justify-content:flex-start}.navbar-expand .navbar-nav{flex-direction:row;-webkit-flex-direction:row}.navbar-expand .navbar-nav .dropdown-menu{position:absolute}.navbar-expand .navbar-nav .nav-link{padding-right:var(--bs-navbar-nav-link-padding-x);padding-left:var(--bs-navbar-nav-link-padding-x)}.navbar-expand .navbar-nav-scroll{overflow:visible}.navbar-expand .navbar-collapse{display:flex !important;display:-webkit-flex 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url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%2300314e'%3e%3cpath fill-rule='evenodd' d='M1.646 4.646a.5.5 0 0 1 .708 0L8 10.293l5.646-5.647a.5.5 0 0 1 .708.708l-6 6a.5.5 0 0 1-.708 0l-6-6a.5.5 0 0 1 0-.708z'/%3e%3c/svg%3e");--bs-accordion-btn-focus-border-color: #80bde1;--bs-accordion-btn-focus-box-shadow: 0 0 0 .25rem rgba(0,123,194,0.25);--bs-accordion-body-padding-x: 1.25rem;--bs-accordion-body-padding-y: 1rem;--bs-accordion-active-color: ;--bs-accordion-active-bg: }.accordion-button{position:relative;display:flex;display:-webkit-flex;align-items:center;-webkit-align-items:center;width:100%;padding:var(--bs-accordion-btn-padding-y) var(--bs-accordion-btn-padding-x);font-size:1rem;color:var(--bs-accordion-btn-color);text-align:left;background-color:var(--bs-accordion-btn-bg);border:0;border-radius:0;overflow-anchor:none;transition:var(--bs-accordion-transition)}@media (prefers-reduced-motion: 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reduce){.accordion-button::after{transition:none}}.accordion-button:hover{z-index:2}.accordion-button:focus{z-index:3;border-color:var(--bs-accordion-btn-focus-border-color);outline:0;box-shadow:var(--bs-accordion-btn-focus-box-shadow)}.accordion-header{margin-bottom:0}.accordion-item{color:var(--bs-accordion-color);background-color:var(--bs-accordion-bg);border:var(--bs-accordion-border-width) solid var(--bs-accordion-border-color)}.accordion-item:first-of-type{border-top-left-radius:var(--bs-accordion-border-radius);border-top-right-radius:var(--bs-accordion-border-radius)}.accordion-item:first-of-type .accordion-button{border-top-left-radius:var(--bs-accordion-inner-border-radius);border-top-right-radius:var(--bs-accordion-inner-border-radius)}.accordion-item:not(:first-of-type){border-top:0}.accordion-item:last-of-type{border-bottom-right-radius:var(--bs-accordion-border-radius);border-bottom-left-radius:var(--bs-accordion-border-radius)}.accordion-item:last-of-type .accordion-button.collapsed{border-bottom-right-radius:var(--bs-accordion-inner-border-radius);border-bottom-left-radius:var(--bs-accordion-inner-border-radius)}.accordion-item:last-of-type .accordion-collapse{border-bottom-right-radius:var(--bs-accordion-border-radius);border-bottom-left-radius:var(--bs-accordion-border-radius)}.accordion-body{padding:var(--bs-accordion-body-padding-y) var(--bs-accordion-body-padding-x)}.accordion-flush .accordion-collapse{border-width:0}.accordion-flush .accordion-item{border-right:0;border-left:0;border-radius:0}.accordion-flush .accordion-item:first-child{border-top:0}.accordion-flush .accordion-item:last-child{border-bottom:0}.accordion-flush .accordion-item .accordion-button,.accordion-flush .accordion-item .accordion-button.collapsed{border-radius:0}[data-bs-theme="dark"] .accordion-button::after{--bs-accordion-btn-icon: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%2366b0da'%3e%3cpath fill-rule='evenodd' d='M1.646 4.646a.5.5 0 0 1 .708 0L8 10.293l5.646-5.647a.5.5 0 0 1 .708.708l-6 6a.5.5 0 0 1-.708 0l-6-6a.5.5 0 0 1 0-.708z'/%3e%3c/svg%3e");--bs-accordion-btn-active-icon: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%2366b0da'%3e%3cpath fill-rule='evenodd' d='M1.646 4.646a.5.5 0 0 1 .708 0L8 10.293l5.646-5.647a.5.5 0 0 1 .708.708l-6 6a.5.5 0 0 1-.708 0l-6-6a.5.5 0 0 1 0-.708z'/%3e%3c/svg%3e")}.breadcrumb{--bs-breadcrumb-padding-x: 0;--bs-breadcrumb-padding-y: 0;--bs-breadcrumb-margin-bottom: 1rem;--bs-breadcrumb-bg: ;--bs-breadcrumb-border-radius: ;--bs-breadcrumb-divider-color: var(--bs-secondary-color);--bs-breadcrumb-item-padding-x: .5rem;--bs-breadcrumb-item-active-color: var(--bs-secondary-color);display:flex;display:-webkit-flex;flex-wrap:wrap;-webkit-flex-wrap:wrap;padding:var(--bs-breadcrumb-padding-y) var(--bs-breadcrumb-padding-x);margin-bottom:var(--bs-breadcrumb-margin-bottom);font-size:var(--bs-breadcrumb-font-size);list-style:none;background-color:var(--bs-breadcrumb-bg);border-radius:var(--bs-breadcrumb-border-radius)}.breadcrumb-item+.breadcrumb-item{padding-left:var(--bs-breadcrumb-item-padding-x)}.breadcrumb-item+.breadcrumb-item::before{float:left;padding-right:var(--bs-breadcrumb-item-padding-x);color:var(--bs-breadcrumb-divider-color);content:var(--bs-breadcrumb-divider, "/") /* rtl: var(--bs-breadcrumb-divider, "/") */}.breadcrumb-item.active{color:var(--bs-breadcrumb-item-active-color)}.pagination{--bs-pagination-padding-x: .75rem;--bs-pagination-padding-y: .375rem;--bs-pagination-font-size:1rem;--bs-pagination-color: var(--bs-link-color);--bs-pagination-bg: var(--bs-body-bg);--bs-pagination-border-width: var(--bs-border-width);--bs-pagination-border-color: var(--bs-border-color);--bs-pagination-border-radius: var(--bs-border-radius);--bs-pagination-hover-color: var(--bs-link-hover-color);--bs-pagination-hover-bg: var(--bs-tertiary-bg);--bs-pagination-hover-border-color: var(--bs-border-color);--bs-pagination-focus-color: var(--bs-link-hover-color);--bs-pagination-focus-bg: var(--bs-secondary-bg);--bs-pagination-focus-box-shadow: 0 0 0 .25rem rgba(0,123,194,0.25);--bs-pagination-active-color: #fff;--bs-pagination-active-bg: #007bc2;--bs-pagination-active-border-color: #007bc2;--bs-pagination-disabled-color: var(--bs-secondary-color);--bs-pagination-disabled-bg: var(--bs-secondary-bg);--bs-pagination-disabled-border-color: var(--bs-border-color);display:flex;display:-webkit-flex;padding-left:0;list-style:none}.page-link{position:relative;display:block;padding:var(--bs-pagination-padding-y) var(--bs-pagination-padding-x);font-size:var(--bs-pagination-font-size);color:var(--bs-pagination-color);text-decoration:none;-webkit-text-decoration:none;-moz-text-decoration:none;-ms-text-decoration:none;-o-text-decoration:none;background-color:var(--bs-pagination-bg);border:var(--bs-pagination-border-width) solid var(--bs-pagination-border-color);transition:color 0.15s ease-in-out,background-color 0.15s ease-in-out,border-color 0.15s ease-in-out,box-shadow 0.15s ease-in-out}@media (prefers-reduced-motion: reduce){.page-link{transition:none}}.page-link:hover{z-index:2;color:var(--bs-pagination-hover-color);background-color:var(--bs-pagination-hover-bg);border-color:var(--bs-pagination-hover-border-color)}.page-link:focus{z-index:3;color:var(--bs-pagination-focus-color);background-color:var(--bs-pagination-focus-bg);outline:0;box-shadow:var(--bs-pagination-focus-box-shadow)}.page-link.active,.active>.page-link{z-index:3;color:var(--bs-pagination-active-color);background-color:var(--bs-pagination-active-bg);border-color:var(--bs-pagination-active-border-color)}.page-link.disabled,.disabled>.page-link{color:var(--bs-pagination-disabled-color);pointer-events:none;background-color:var(--bs-pagination-disabled-bg);border-color:var(--bs-pagination-disabled-border-color)}.page-item:not(:first-child) .page-link{margin-left:calc(var(--bs-border-width) * -1)}.page-item:first-child .page-link{border-top-left-radius:var(--bs-pagination-border-radius);border-bottom-left-radius:var(--bs-pagination-border-radius)}.page-item:last-child .page-link{border-top-right-radius:var(--bs-pagination-border-radius);border-bottom-right-radius:var(--bs-pagination-border-radius)}.pagination-lg{--bs-pagination-padding-x: 1.5rem;--bs-pagination-padding-y: .75rem;--bs-pagination-font-size:1.25rem;--bs-pagination-border-radius: var(--bs-border-radius-lg)}.pagination-sm{--bs-pagination-padding-x: .5rem;--bs-pagination-padding-y: .25rem;--bs-pagination-font-size:.875rem;--bs-pagination-border-radius: var(--bs-border-radius-sm)}.badge{--bs-badge-padding-x: .65em;--bs-badge-padding-y: .35em;--bs-badge-font-size:.75em;--bs-badge-font-weight: 700;--bs-badge-color: #fff;--bs-badge-border-radius: var(--bs-border-radius);display:inline-block;padding:var(--bs-badge-padding-y) var(--bs-badge-padding-x);font-size:var(--bs-badge-font-size);font-weight:var(--bs-badge-font-weight);line-height:1;color:var(--bs-badge-color);text-align:center;white-space:nowrap;vertical-align:baseline;border-radius:var(--bs-badge-border-radius)}.badge:empty{display:none}.btn .badge{position:relative;top:-1px}.alert{--bs-alert-bg: transparent;--bs-alert-padding-x: 1rem;--bs-alert-padding-y: 1rem;--bs-alert-margin-bottom: 1rem;--bs-alert-color: inherit;--bs-alert-border-color: transparent;--bs-alert-border: var(--bs-border-width) solid var(--bs-alert-border-color);--bs-alert-border-radius: var(--bs-border-radius);--bs-alert-link-color: inherit;position:relative;padding:var(--bs-alert-padding-y) var(--bs-alert-padding-x);margin-bottom:var(--bs-alert-margin-bottom);color:var(--bs-alert-color);background-color:var(--bs-alert-bg);border:var(--bs-alert-border);border-radius:var(--bs-alert-border-radius)}.alert-heading{color:inherit}.alert-link{font-weight:700;color:var(--bs-alert-link-color)}.alert-dismissible{padding-right:3rem}.alert-dismissible .btn-close{position:absolute;top:0;right:0;z-index:2;padding:1.25rem 1rem}.alert-default{--bs-alert-color: var(--bs-default-text-emphasis);--bs-alert-bg: var(--bs-default-bg-subtle);--bs-alert-border-color: var(--bs-default-border-subtle);--bs-alert-link-color: var(--bs-default-text-emphasis)}.alert-primary{--bs-alert-color: var(--bs-primary-text-emphasis);--bs-alert-bg: var(--bs-primary-bg-subtle);--bs-alert-border-color: var(--bs-primary-border-subtle);--bs-alert-link-color: var(--bs-primary-text-emphasis)}.alert-secondary{--bs-alert-color: var(--bs-secondary-text-emphasis);--bs-alert-bg: var(--bs-secondary-bg-subtle);--bs-alert-border-color: var(--bs-secondary-border-subtle);--bs-alert-link-color: var(--bs-secondary-text-emphasis)}.alert-success{--bs-alert-color: var(--bs-success-text-emphasis);--bs-alert-bg: var(--bs-success-bg-subtle);--bs-alert-border-color: var(--bs-success-border-subtle);--bs-alert-link-color: var(--bs-success-text-emphasis)}.alert-info{--bs-alert-color: var(--bs-info-text-emphasis);--bs-alert-bg: var(--bs-info-bg-subtle);--bs-alert-border-color: var(--bs-info-border-subtle);--bs-alert-link-color: var(--bs-info-text-emphasis)}.alert-warning{--bs-alert-color: var(--bs-warning-text-emphasis);--bs-alert-bg: var(--bs-warning-bg-subtle);--bs-alert-border-color: var(--bs-warning-border-subtle);--bs-alert-link-color: var(--bs-warning-text-emphasis)}.alert-danger{--bs-alert-color: var(--bs-danger-text-emphasis);--bs-alert-bg: var(--bs-danger-bg-subtle);--bs-alert-border-color: var(--bs-danger-border-subtle);--bs-alert-link-color: var(--bs-danger-text-emphasis)}.alert-light{--bs-alert-color: var(--bs-light-text-emphasis);--bs-alert-bg: var(--bs-light-bg-subtle);--bs-alert-border-color: var(--bs-light-border-subtle);--bs-alert-link-color: var(--bs-light-text-emphasis)}.alert-dark{--bs-alert-color: var(--bs-dark-text-emphasis);--bs-alert-bg: var(--bs-dark-bg-subtle);--bs-alert-border-color: var(--bs-dark-border-subtle);--bs-alert-link-color: var(--bs-dark-text-emphasis)}@keyframes progress-bar-stripes{0%{background-position-x:1rem}}.progress,.progress-stacked{--bs-progress-height: 1rem;--bs-progress-font-size:.75rem;--bs-progress-bg: var(--bs-secondary-bg);--bs-progress-border-radius: var(--bs-border-radius);--bs-progress-box-shadow: var(--bs-box-shadow-inset);--bs-progress-bar-color: #fff;--bs-progress-bar-bg: #007bc2;--bs-progress-bar-transition: width 0.6s ease;display:flex;display:-webkit-flex;height:var(--bs-progress-height);overflow:hidden;font-size:var(--bs-progress-font-size);background-color:var(--bs-progress-bg);border-radius:var(--bs-progress-border-radius)}.progress-bar{display:flex;display:-webkit-flex;flex-direction:column;-webkit-flex-direction:column;justify-content:center;-webkit-justify-content:center;overflow:hidden;color:var(--bs-progress-bar-color);text-align:center;white-space:nowrap;background-color:var(--bs-progress-bar-bg);transition:var(--bs-progress-bar-transition)}@media (prefers-reduced-motion: reduce){.progress-bar{transition:none}}.progress-bar-striped{background-image:linear-gradient(45deg, rgba(255,255,255,0.15) 25%, transparent 25%, transparent 50%, rgba(255,255,255,0.15) 50%, rgba(255,255,255,0.15) 75%, transparent 75%, transparent);background-size:var(--bs-progress-height) var(--bs-progress-height)}.progress-stacked>.progress{overflow:visible}.progress-stacked>.progress>.progress-bar{width:100%}.progress-bar-animated{animation:1s linear infinite progress-bar-stripes}@media (prefers-reduced-motion: reduce){.progress-bar-animated{animation:none}}.list-group{--bs-list-group-color: var(--bs-body-color);--bs-list-group-bg: var(--bs-body-bg);--bs-list-group-border-color: var(--bs-border-color);--bs-list-group-border-width: var(--bs-border-width);--bs-list-group-border-radius: var(--bs-border-radius);--bs-list-group-item-padding-x: 1rem;--bs-list-group-item-padding-y: .5rem;--bs-list-group-action-color: var(--bs-secondary-color);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-tertiary-bg);--bs-list-group-action-active-color: var(--bs-body-color);--bs-list-group-action-active-bg: var(--bs-secondary-bg);--bs-list-group-disabled-color: var(--bs-secondary-color);--bs-list-group-disabled-bg: var(--bs-body-bg);--bs-list-group-active-color: #fff;--bs-list-group-active-bg: #007bc2;--bs-list-group-active-border-color: #007bc2;display:flex;display:-webkit-flex;flex-direction:column;-webkit-flex-direction:column;padding-left:0;margin-bottom:0;border-radius:var(--bs-list-group-border-radius)}.list-group-numbered{list-style-type:none;counter-reset:section}.list-group-numbered>.list-group-item::before{content:counters(section, ".") ". ";counter-increment:section}.list-group-item-action{width:100%;color:var(--bs-list-group-action-color);text-align:inherit}.list-group-item-action:hover,.list-group-item-action:focus{z-index:1;color:var(--bs-list-group-action-hover-color);text-decoration:none;background-color:var(--bs-list-group-action-hover-bg)}.list-group-item-action:active{color:var(--bs-list-group-action-active-color);background-color:var(--bs-list-group-action-active-bg)}.list-group-item{position:relative;display:block;padding:var(--bs-list-group-item-padding-y) var(--bs-list-group-item-padding-x);color:var(--bs-list-group-color);text-decoration:none;-webkit-text-decoration:none;-moz-text-decoration:none;-ms-text-decoration:none;-o-text-decoration:none;background-color:var(--bs-list-group-bg);border:var(--bs-list-group-border-width) solid var(--bs-list-group-border-color)}.list-group-item:first-child{border-top-left-radius:inherit;border-top-right-radius:inherit}.list-group-item:last-child{border-bottom-right-radius:inherit;border-bottom-left-radius:inherit}.list-group-item.disabled,.list-group-item:disabled{color:var(--bs-list-group-disabled-color);pointer-events:none;background-color:var(--bs-list-group-disabled-bg)}.list-group-item.active{z-index:2;color:var(--bs-list-group-active-color);background-color:var(--bs-list-group-active-bg);border-color:var(--bs-list-group-active-border-color)}.list-group-item+.list-group-item{border-top-width:0}.list-group-item+.list-group-item.active{margin-top:calc(-1 * var(--bs-list-group-border-width));border-top-width:var(--bs-list-group-border-width)}.list-group-horizontal{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal>.list-group-item.active{margin-top:0}.list-group-horizontal>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}@media (min-width: 576px){.list-group-horizontal-sm{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-sm>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-sm>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-sm>.list-group-item.active{margin-top:0}.list-group-horizontal-sm>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-sm>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media (min-width: 768px){.list-group-horizontal-md{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-md>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-md>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-md>.list-group-item.active{margin-top:0}.list-group-horizontal-md>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-md>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media (min-width: 992px){.list-group-horizontal-lg{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-lg>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-lg>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-lg>.list-group-item.active{margin-top:0}.list-group-horizontal-lg>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-lg>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media (min-width: 1200px){.list-group-horizontal-xl{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-xl>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-xl>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-xl>.list-group-item.active{margin-top:0}.list-group-horizontal-xl>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-xl>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media (min-width: 1400px){.list-group-horizontal-xxl{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-xxl>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-xxl>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-xxl>.list-group-item.active{margin-top:0}.list-group-horizontal-xxl>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-xxl>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}.list-group-flush{border-radius:0}.list-group-flush>.list-group-item{border-width:0 0 var(--bs-list-group-border-width)}.list-group-flush>.list-group-item:last-child{border-bottom-width:0}.list-group-item-default{--bs-list-group-color: var(--bs-default-text-emphasis);--bs-list-group-bg: var(--bs-default-bg-subtle);--bs-list-group-border-color: var(--bs-default-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-default-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-default-border-subtle);--bs-list-group-active-color: var(--bs-default-bg-subtle);--bs-list-group-active-bg: var(--bs-default-text-emphasis);--bs-list-group-active-border-color: var(--bs-default-text-emphasis)}.list-group-item-primary{--bs-list-group-color: var(--bs-primary-text-emphasis);--bs-list-group-bg: var(--bs-primary-bg-subtle);--bs-list-group-border-color: var(--bs-primary-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-primary-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-primary-border-subtle);--bs-list-group-active-color: var(--bs-primary-bg-subtle);--bs-list-group-active-bg: var(--bs-primary-text-emphasis);--bs-list-group-active-border-color: var(--bs-primary-text-emphasis)}.list-group-item-secondary{--bs-list-group-color: var(--bs-secondary-text-emphasis);--bs-list-group-bg: var(--bs-secondary-bg-subtle);--bs-list-group-border-color: var(--bs-secondary-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-secondary-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-secondary-border-subtle);--bs-list-group-active-color: var(--bs-secondary-bg-subtle);--bs-list-group-active-bg: var(--bs-secondary-text-emphasis);--bs-list-group-active-border-color: var(--bs-secondary-text-emphasis)}.list-group-item-success{--bs-list-group-color: var(--bs-success-text-emphasis);--bs-list-group-bg: var(--bs-success-bg-subtle);--bs-list-group-border-color: var(--bs-success-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-success-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-success-border-subtle);--bs-list-group-active-color: var(--bs-success-bg-subtle);--bs-list-group-active-bg: var(--bs-success-text-emphasis);--bs-list-group-active-border-color: var(--bs-success-text-emphasis)}.list-group-item-info{--bs-list-group-color: var(--bs-info-text-emphasis);--bs-list-group-bg: var(--bs-info-bg-subtle);--bs-list-group-border-color: var(--bs-info-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-info-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-info-border-subtle);--bs-list-group-active-color: var(--bs-info-bg-subtle);--bs-list-group-active-bg: var(--bs-info-text-emphasis);--bs-list-group-active-border-color: var(--bs-info-text-emphasis)}.list-group-item-warning{--bs-list-group-color: var(--bs-warning-text-emphasis);--bs-list-group-bg: var(--bs-warning-bg-subtle);--bs-list-group-border-color: var(--bs-warning-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-warning-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-warning-border-subtle);--bs-list-group-active-color: var(--bs-warning-bg-subtle);--bs-list-group-active-bg: var(--bs-warning-text-emphasis);--bs-list-group-active-border-color: var(--bs-warning-text-emphasis)}.list-group-item-danger{--bs-list-group-color: var(--bs-danger-text-emphasis);--bs-list-group-bg: var(--bs-danger-bg-subtle);--bs-list-group-border-color: var(--bs-danger-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-danger-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-danger-border-subtle);--bs-list-group-active-color: var(--bs-danger-bg-subtle);--bs-list-group-active-bg: var(--bs-danger-text-emphasis);--bs-list-group-active-border-color: var(--bs-danger-text-emphasis)}.list-group-item-light{--bs-list-group-color: var(--bs-light-text-emphasis);--bs-list-group-bg: var(--bs-light-bg-subtle);--bs-list-group-border-color: var(--bs-light-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-light-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-light-border-subtle);--bs-list-group-active-color: var(--bs-light-bg-subtle);--bs-list-group-active-bg: var(--bs-light-text-emphasis);--bs-list-group-active-border-color: var(--bs-light-text-emphasis)}.list-group-item-dark{--bs-list-group-color: var(--bs-dark-text-emphasis);--bs-list-group-bg: var(--bs-dark-bg-subtle);--bs-list-group-border-color: var(--bs-dark-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-dark-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-dark-border-subtle);--bs-list-group-active-color: var(--bs-dark-bg-subtle);--bs-list-group-active-bg: var(--bs-dark-text-emphasis);--bs-list-group-active-border-color: var(--bs-dark-text-emphasis)}.btn-close{--bs-btn-close-color: #000;--bs-btn-close-bg: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%23000'%3e%3cpath d='M.293.293a1 1 0 0 1 1.414 0L8 6.586 14.293.293a1 1 0 1 1 1.414 1.414L9.414 8l6.293 6.293a1 1 0 0 1-1.414 1.414L8 9.414l-6.293 6.293a1 1 0 0 1-1.414-1.414L6.586 8 .293 1.707a1 1 0 0 1 0-1.414z'/%3e%3c/svg%3e");--bs-btn-close-opacity: .5;--bs-btn-close-hover-opacity: .75;--bs-btn-close-focus-shadow: 0 0 0 .25rem rgba(0,123,194,0.25);--bs-btn-close-focus-opacity: 1;--bs-btn-close-disabled-opacity: .25;--bs-btn-close-white-filter: invert(1) grayscale(100%) brightness(200%);box-sizing:content-box;width:1em;height:1em;padding:.25em .25em;color:var(--bs-btn-close-color);background:transparent var(--bs-btn-close-bg) center/1em auto no-repeat;border:0;border-radius:3px;opacity:var(--bs-btn-close-opacity)}.btn-close:hover{color:var(--bs-btn-close-color);text-decoration:none;opacity:var(--bs-btn-close-hover-opacity)}.btn-close:focus{outline:0;box-shadow:var(--bs-btn-close-focus-shadow);opacity:var(--bs-btn-close-focus-opacity)}.btn-close:disabled,.btn-close.disabled{pointer-events:none;user-select:none;-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;opacity:var(--bs-btn-close-disabled-opacity)}.btn-close-white{filter:var(--bs-btn-close-white-filter)}[data-bs-theme="dark"] .btn-close{filter:var(--bs-btn-close-white-filter)}.toast{--bs-toast-zindex: 1090;--bs-toast-padding-x: .75rem;--bs-toast-padding-y: .5rem;--bs-toast-spacing: 1.5rem;--bs-toast-max-width: 350px;--bs-toast-font-size:.875rem;--bs-toast-color: ;--bs-toast-bg: rgba(var(--bs-body-bg-rgb), 0.85);--bs-toast-border-width: var(--bs-border-width);--bs-toast-border-color: var(--bs-border-color-translucent);--bs-toast-border-radius: var(--bs-border-radius);--bs-toast-box-shadow: var(--bs-box-shadow);--bs-toast-header-color: var(--bs-secondary-color);--bs-toast-header-bg: rgba(var(--bs-body-bg-rgb), 0.85);--bs-toast-header-border-color: var(--bs-border-color-translucent);width:var(--bs-toast-max-width);max-width:100%;font-size:var(--bs-toast-font-size);color:var(--bs-toast-color);pointer-events:auto;background-color:var(--bs-toast-bg);background-clip:padding-box;border:var(--bs-toast-border-width) solid var(--bs-toast-border-color);box-shadow:var(--bs-toast-box-shadow);border-radius:var(--bs-toast-border-radius)}.toast.showing{opacity:0}.toast:not(.show){display:none}.toast-container{--bs-toast-zindex: 1090;position:absolute;z-index:var(--bs-toast-zindex);width:max-content;width:-webkit-max-content;width:-moz-max-content;width:-ms-max-content;width:-o-max-content;max-width:100%;pointer-events:none}.toast-container>:not(:last-child){margin-bottom:var(--bs-toast-spacing)}.toast-header{display:flex;display:-webkit-flex;align-items:center;-webkit-align-items:center;padding:var(--bs-toast-padding-y) var(--bs-toast-padding-x);color:var(--bs-toast-header-color);background-color:var(--bs-toast-header-bg);background-clip:padding-box;border-bottom:var(--bs-toast-border-width) solid var(--bs-toast-header-border-color);border-top-left-radius:calc(var(--bs-toast-border-radius) - var(--bs-toast-border-width));border-top-right-radius:calc(var(--bs-toast-border-radius) - var(--bs-toast-border-width))}.toast-header .btn-close{margin-right:calc(-.5 * var(--bs-toast-padding-x));margin-left:var(--bs-toast-padding-x)}.toast-body{padding:var(--bs-toast-padding-x);word-wrap:break-word}.modal{--bs-modal-zindex: 1055;--bs-modal-width: 500px;--bs-modal-padding: 1rem;--bs-modal-margin: .5rem;--bs-modal-color: ;--bs-modal-bg: var(--bs-body-bg);--bs-modal-border-color: var(--bs-border-color-translucent);--bs-modal-border-width: var(--bs-border-width);--bs-modal-border-radius: var(--bs-border-radius-lg);--bs-modal-box-shadow: 0px 1px 2px RGBA(var(--bslib-box-shadow-color-rgb), 0.1),0px 2px 3px RGBA(var(--bslib-box-shadow-color-rgb), 0.1),0px 3px 8px RGBA(var(--bslib-box-shadow-color-rgb), 0.1);--bs-modal-inner-border-radius: calc(var(--bs-border-radius-lg) - (var(--bs-border-width)));--bs-modal-header-padding-x: 1rem;--bs-modal-header-padding-y: 1rem;--bs-modal-header-padding: 1.5rem;--bs-modal-header-border-color: var(--bs-border-color);--bs-modal-header-border-width: none;--bs-modal-title-line-height: 1.5;--bs-modal-footer-gap: .5rem;--bs-modal-footer-bg: ;--bs-modal-footer-border-color: var(--bs-border-color);--bs-modal-footer-border-width: none;position:fixed;top:0;left:0;z-index:var(--bs-modal-zindex);display:none;width:100%;height:100%;overflow-x:hidden;overflow-y:auto;outline:0}.modal-dialog{position:relative;width:auto;margin:var(--bs-modal-margin);pointer-events:none}.modal.fade .modal-dialog{transition:transform 0.3s ease-out;transform:translate(0, -50px)}@media (prefers-reduced-motion: reduce){.modal.fade .modal-dialog{transition:none}}.modal.show .modal-dialog{transform:none}.modal.modal-static .modal-dialog{transform:scale(1.02)}.modal-dialog-scrollable{height:calc(100% - var(--bs-modal-margin) * 2)}.modal-dialog-scrollable .modal-content{max-height:100%;overflow:hidden}.modal-dialog-scrollable .modal-body{overflow-y:auto}.modal-dialog-centered{display:flex;display:-webkit-flex;align-items:center;-webkit-align-items:center;min-height:calc(100% - var(--bs-modal-margin) * 2)}.modal-content{position:relative;display:flex;display:-webkit-flex;flex-direction:column;-webkit-flex-direction:column;width:100%;color:var(--bs-modal-color);pointer-events:auto;background-color:var(--bs-modal-bg);background-clip:padding-box;border:var(--bs-modal-border-width) solid var(--bs-modal-border-color);border-radius:var(--bs-modal-border-radius);outline:0}.modal-backdrop{--bs-backdrop-zindex: 1050;--bs-backdrop-bg: #464646;--bs-backdrop-opacity: .5;position:fixed;top:0;left:0;z-index:var(--bs-backdrop-zindex);width:100vw;height:100vh;background-color:var(--bs-backdrop-bg)}.modal-backdrop.fade{opacity:0}.modal-backdrop.show{opacity:var(--bs-backdrop-opacity)}.modal-header{display:flex;display:-webkit-flex;flex-shrink:0;-webkit-flex-shrink:0;align-items:center;-webkit-align-items:center;justify-content:space-between;-webkit-justify-content:space-between;padding:var(--bs-modal-header-padding);border-bottom:var(--bs-modal-header-border-width) solid var(--bs-modal-header-border-color);border-top-left-radius:var(--bs-modal-inner-border-radius);border-top-right-radius:var(--bs-modal-inner-border-radius)}.modal-header .btn-close{padding:calc(var(--bs-modal-header-padding-y) * .5) calc(var(--bs-modal-header-padding-x) * .5);margin:calc(-.5 * var(--bs-modal-header-padding-y)) calc(-.5 * var(--bs-modal-header-padding-x)) calc(-.5 * var(--bs-modal-header-padding-y)) auto}.modal-title{margin-bottom:0;line-height:var(--bs-modal-title-line-height)}.modal-body{position:relative;flex:1 1 auto;-webkit-flex:1 1 auto;padding:var(--bs-modal-padding)}.modal-footer{display:flex;display:-webkit-flex;flex-shrink:0;-webkit-flex-shrink:0;flex-wrap:wrap;-webkit-flex-wrap:wrap;align-items:center;-webkit-align-items:center;justify-content:flex-end;-webkit-justify-content:flex-end;padding:calc(var(--bs-modal-padding) - var(--bs-modal-footer-gap) * .5);background-color:var(--bs-modal-footer-bg);border-top:var(--bs-modal-footer-border-width) solid 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(max-width: 1199.98px){.modal-fullscreen-xl-down{width:100vw;max-width:none;height:100%;margin:0}.modal-fullscreen-xl-down .modal-content{height:100%;border:0;border-radius:0}.modal-fullscreen-xl-down .modal-header,.modal-fullscreen-xl-down .modal-footer{border-radius:0}.modal-fullscreen-xl-down .modal-body{overflow-y:auto}}@media (max-width: 1399.98px){.modal-fullscreen-xxl-down{width:100vw;max-width:none;height:100%;margin:0}.modal-fullscreen-xxl-down .modal-content{height:100%;border:0;border-radius:0}.modal-fullscreen-xxl-down .modal-header,.modal-fullscreen-xxl-down .modal-footer{border-radius:0}.modal-fullscreen-xxl-down .modal-body{overflow-y:auto}}.tooltip{--bs-tooltip-zindex: 1080;--bs-tooltip-max-width: 200px;--bs-tooltip-padding-x: .5rem;--bs-tooltip-padding-y: .25rem;--bs-tooltip-margin: ;--bs-tooltip-font-size:.875rem;--bs-tooltip-color: var(--bs-body-bg);--bs-tooltip-bg: var(--bs-emphasis-color);--bs-tooltip-border-radius: var(--bs-border-radius);--bs-tooltip-opacity: 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.tooltip-arrow::before{bottom:-1px;border-width:0 calc(var(--bs-tooltip-arrow-width) * .5) var(--bs-tooltip-arrow-height);border-bottom-color:var(--bs-tooltip-bg)}.bs-tooltip-start .tooltip-arrow,.bs-tooltip-auto[data-popper-placement^="left"] .tooltip-arrow{right:calc(-1 * var(--bs-tooltip-arrow-height));width:var(--bs-tooltip-arrow-height);height:var(--bs-tooltip-arrow-width)}.bs-tooltip-start .tooltip-arrow::before,.bs-tooltip-auto[data-popper-placement^="left"] .tooltip-arrow::before{left:-1px;border-width:calc(var(--bs-tooltip-arrow-width) * .5) 0 calc(var(--bs-tooltip-arrow-width) * .5) var(--bs-tooltip-arrow-height);border-left-color:var(--bs-tooltip-bg)}.tooltip-inner{max-width:var(--bs-tooltip-max-width);padding:var(--bs-tooltip-padding-y) var(--bs-tooltip-padding-x);color:var(--bs-tooltip-color);text-align:center;background-color:var(--bs-tooltip-bg);border-radius:var(--bs-tooltip-border-radius)}.popover{--bs-popover-zindex: 1070;--bs-popover-max-width: 276px;--bs-popover-font-size:.875rem;--bs-popover-bg: var(--bs-body-bg);--bs-popover-border-width: var(--bs-border-width);--bs-popover-border-color: var(--bs-border-color-translucent);--bs-popover-border-radius: var(--bs-border-radius-lg);--bs-popover-inner-border-radius: calc(var(--bs-border-radius-lg) - var(--bs-border-width));--bs-popover-box-shadow: 0px 1px 2px RGBA(var(--bslib-box-shadow-color-rgb), 0.1),0px 3px 7px RGBA(var(--bslib-box-shadow-color-rgb), 0.1),0px 12px 30px RGBA(var(--bslib-box-shadow-color-rgb), 0.08);--bs-popover-header-padding-x: 1rem;--bs-popover-header-padding-y: .5rem;--bs-popover-header-font-size:1rem;--bs-popover-header-color: inherit;--bs-popover-header-bg: var(--bs-secondary-bg);--bs-popover-body-padding-x: 1rem;--bs-popover-body-padding-y: 1rem;--bs-popover-body-color: var(--bs-body-color);--bs-popover-arrow-width: 1rem;--bs-popover-arrow-height: .5rem;--bs-popover-arrow-border: 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#fff;background-color:var(--bslib-color-bg);color:var(--bslib-color-fg)}.text-indigo{--bslib-color-fg: #4b00c1;color:var(--bslib-color-fg)}.bg-purple{--bslib-color-bg: #74149c;--bslib-color-fg: #fff;background-color:var(--bslib-color-bg);color:var(--bslib-color-fg)}.text-purple{--bslib-color-fg: #74149c;color:var(--bslib-color-fg)}.bg-pink{--bslib-color-bg: #bf007f;--bslib-color-fg: #fff;background-color:var(--bslib-color-bg);color:var(--bslib-color-fg)}.text-pink{--bslib-color-fg: #bf007f;color:var(--bslib-color-fg)}.bg-red{--bslib-color-bg: #c10000;--bslib-color-fg: #fff;background-color:var(--bslib-color-bg);color:var(--bslib-color-fg)}.text-red{--bslib-color-fg: #c10000;color:var(--bslib-color-fg)}.bg-orange{--bslib-color-bg: #f45100;--bslib-color-fg: #000;background-color:var(--bslib-color-bg);color:var(--bslib-color-fg)}.text-orange{--bslib-color-fg: #f45100;color:var(--bslib-color-fg)}.bg-yellow{--bslib-color-bg: #f9b928;--bslib-color-fg: #000;background-color:var(--bslib-color-bg);color:var(--bslib-color-fg)}.text-yellow{--bslib-color-fg: #f9b928;color:var(--bslib-color-fg)}.bg-green{--bslib-color-bg: #00891a;--bslib-color-fg: #fff;background-color:var(--bslib-color-bg);color:var(--bslib-color-fg)}.text-green{--bslib-color-fg: #00891a;color:var(--bslib-color-fg)}.bg-teal{--bslib-color-bg: #00bf7f;--bslib-color-fg: #000;background-color:var(--bslib-color-bg);color:var(--bslib-color-fg)}.text-teal{--bslib-color-fg: #00bf7f;color:var(--bslib-color-fg)}.bg-cyan{--bslib-color-bg: #03c7e8;--bslib-color-fg: #000;background-color:var(--bslib-color-bg);color:var(--bslib-color-fg)}.text-cyan{--bslib-color-fg: #03c7e8;color:var(--bslib-color-fg)}.text-default{--bslib-color-fg: #dee2e6}.bg-default{--bslib-color-bg: #dee2e6;--bslib-color-fg: #000}.text-primary{--bslib-color-fg: #007bc2}.bg-primary{--bslib-color-bg: #007bc2;--bslib-color-fg: #fff}.text-secondary{--bslib-color-fg: #404040}.bg-secondary{--bslib-color-bg: #404040;--bslib-color-fg: #fff}.text-success{--bslib-color-fg: #00891a}.bg-success{--bslib-color-bg: #00891a;--bslib-color-fg: #fff}.text-info{--bslib-color-fg: #03c7e8}.bg-info{--bslib-color-bg: #03c7e8;--bslib-color-fg: #000}.text-warning{--bslib-color-fg: #f9b928}.bg-warning{--bslib-color-bg: #f9b928;--bslib-color-fg: #000}.text-danger{--bslib-color-fg: #c10000}.bg-danger{--bslib-color-bg: #c10000;--bslib-color-fg: #fff}.text-light{--bslib-color-fg: #f8f8f8}.bg-light{--bslib-color-bg: #f8f8f8;--bslib-color-fg: #000}.text-dark{--bslib-color-fg: #202020}.bg-dark{--bslib-color-bg: #202020;--bslib-color-fg: #fff}.bg-gradient-blue-indigo{--bslib-color-fg: #fff;--bslib-color-bg: #1e4ac2;background:linear-gradient(var(--bg-gradient-deg, 140deg), #007bc2 var(--bg-gradient-start, 36%), #4b00c1 var(--bg-gradient-end, 180%)) #1e4ac2;color:#fff}.bg-gradient-blue-purple{--bslib-color-fg: #fff;--bslib-color-bg: #2e52b3;background:linear-gradient(var(--bg-gradient-deg, 140deg), #007bc2 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li{margin-bottom:0.5rem}aside .dev-status .list-unstyled li{margin-bottom:0.1rem}@media (max-width: 575.98px){aside{margin:0.5rem;width:calc(100vw - 1rem);background-color:#f8f8f8;border-color:#dee2e6;border-radius:3px}aside h2:first-child,aside .h2:first-child{margin-top:1rem}}body{position:relative}#toc>.nav{margin-bottom:1rem}#toc>.nav a.nav-link{color:inherit;padding:0.25rem 0.5rem;margin-bottom:2px;border-radius:3px;border:0 solid #dee2e6}#toc>.nav a.nav-link:hover,#toc>.nav a.nav-link:focus{background-color:rgba(0,123,194,0.1);color:#000}#toc>.nav a.nav-link.active{background-color:#e8e9e9;color:#000}#toc>.nav .nav a.nav-link{margin-left:0.5rem}#toc>.nav .nav{display:none !important}#toc>.nav a.active+.nav{display:flex !important}footer{margin:1rem 0 1rem 0;font-size:.875em;border-top:1px solid #dee2e6;background:rgba(0,0,0,0);color:#4a4c4d;display:flex;column-gap:1rem}@media (max-width: 575.98px){footer{flex-direction:column}}@media (min-width: 576px){footer .pkgdown-footer-right{text-align:right}}footer div{flex:1 1 auto}html,body{height:100%}body>.container{min-height:100%;display:flex;flex-direction:column}body>.container .row{flex:1 0 auto}::selection{background-color:#cce5f3}main img{max-width:100%;height:auto}main table{display:block;overflow:auto}body{font-display:fallback}.page-header{border-bottom:1px solid #dee2e6;padding-bottom:0.5rem;margin-bottom:0.5rem;margin-top:1.5rem}dd{margin-left:1.5rem}summary{margin-bottom:0.5rem}details{margin-bottom:1rem}.html-widget{margin-bottom:1rem}a.anchor{display:none;margin-left:5px;width:Min(0.9em, 20px);height:Min(0.9em, 20px);background-image:url(../../link.svg);background-repeat:no-repeat;background-size:Min(0.9em, 20px) Min(0.9em, 20px);background-position:center center}h2:hover .anchor,.h2:hover .anchor,h3:hover .anchor,.h3:hover .anchor,h4:hover .anchor,.h4:hover .anchor,h5:hover .anchor,.h5:hover .anchor,h6:hover .anchor,.h6:hover 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div.csl-entry{margin-left:2em;text-indent:-2em}div.csl-left-margin{min-width:2em;float:left}div.csl-right-inline{margin-left:2em;padding-left:1em}div.csl-indent{margin-left:2em}pre,pre code{word-wrap:normal}code{overflow-wrap:break-word}.hasCopyButton{position:relative}.btn-copy-ex{position:absolute;right:5px;top:5px;visibility:hidden}.hasCopyButton:hover button.btn-copy-ex{visibility:visible}pre{padding:1rem 0.5rem}@media (max-width: 575.98px){div>div>pre{margin-left:calc(var(--bs-gutter-x) * -.5);margin-right:calc(var(--bs-gutter-x) * -.5);border-radius:0;padding-left:1rem;padding-right:1rem}.btn-copy-ex{right:calc(var(--bs-gutter-x) * -.5 + 5px)}}code a:any-link{color:inherit;text-decoration-color:#707782}pre code{padding:0;background:transparent}pre code .error,pre code .warning{font-weight:bolder}pre .img img,pre .r-plt img{margin:5px 0;background-color:#fff}@media print{code a:link:after,code 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diff --git a/deps/bootstrap-5.3.1/font.css b/deps/bootstrap-5.3.1/font.css
new file mode 100644
index 00000000..b74f3e13
--- /dev/null
+++ b/deps/bootstrap-5.3.1/font.css
@@ -0,0 +1,124 @@
+@font-face {
+  font-family: 'Open Sans';
+  font-style: italic;
+  font-weight: 300;
+  font-stretch: normal;
+  font-display: swap;
+  src: url(fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk5hkaVQ.woff) format('woff');
+}
+@font-face {
+  font-family: 'Open Sans';
+  font-style: italic;
+  font-weight: 400;
+  font-stretch: normal;
+  font-display: swap;
+  src: url(fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk8ZkaVQ.woff) format('woff');
+}
+@font-face {
+  font-family: 'Open Sans';
+  font-style: italic;
+  font-weight: 500;
+  font-stretch: normal;
+  font-display: swap;
+  src: url(fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk_RkaVQ.woff) format('woff');
+}
+@font-face {
+  font-family: 'Open Sans';
+  font-style: italic;
+  font-weight: 600;
+  font-stretch: normal;
+  font-display: swap;
+  src: url(fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0RkxhjaVQ.woff) format('woff');
+}
+@font-face {
+  font-family: 'Open Sans';
+  font-style: italic;
+  font-weight: 700;
+  font-stretch: normal;
+  font-display: swap;
+  src: url(fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0RkyFjaVQ.woff) format('woff');
+}
+@font-face {
+  font-family: 'Open Sans';
+  font-style: italic;
+  font-weight: 800;
+  font-stretch: normal;
+  font-display: swap;
+  src: url(fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk0ZjaVQ.woff) format('woff');
+}
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 300;
+  font-stretch: normal;
+  font-display: swap;
+  src: url(fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsiH0C4k.woff) format('woff');
+}
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 400;
+  font-stretch: normal;
+  font-display: swap;
+  src: url(fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsjZ0C4k.woff) format('woff');
+}
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 500;
+  font-stretch: normal;
+  font-display: swap;
+  src: url(fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsjr0C4k.woff) format('woff');
+}
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 600;
+  font-stretch: normal;
+  font-display: swap;
+  src: url(fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsgH1y4k.woff) format('woff');
+}
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 700;
+  font-stretch: normal;
+  font-display: swap;
+  src: url(fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsg-1y4k.woff) format('woff');
+}
+@font-face {
+  font-family: 'Open Sans';
+  font-style: normal;
+  font-weight: 800;
+  font-stretch: normal;
+  font-display: swap;
+  src: url(fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgshZ1y4k.woff) format('woff');
+}
+@font-face {
+  font-family: 'Source Code Pro';
+  font-style: italic;
+  font-weight: 400;
+  font-display: swap;
+  src: url(fonts/HI_jiYsKILxRpg3hIP6sJ7fM7PqlOPHYvDP_W9O7GQTTbI1rSg.woff) format('woff');
+}
+@font-face {
+  font-family: 'Source Code Pro';
+  font-style: italic;
+  font-weight: 600;
+  font-display: swap;
+  src: url(fonts/HI_jiYsKILxRpg3hIP6sJ7fM7PqlOPHYvDP_W9O7GQTTsoprSg.woff) format('woff');
+}
+@font-face {
+  font-family: 'Source Code Pro';
+  font-style: normal;
+  font-weight: 400;
+  font-display: swap;
+  src: url(fonts/HI_diYsKILxRpg3hIP6sJ7fM7PqPMcMnZFqUwX28DMyQhM0.woff) format('woff');
+}
+@font-face {
+  font-family: 'Source Code Pro';
+  font-style: normal;
+  font-weight: 600;
+  font-display: swap;
+  src: url(fonts/HI_diYsKILxRpg3hIP6sJ7fM7PqPMcMnZFqUwX28DBKXhM0.woff) format('woff');
+}
diff --git a/deps/bootstrap-5.3.1/fonts/1Ptxg8zYS_SKggPN4iEgvnHyvveLxVs9pbCIPrc.woff b/deps/bootstrap-5.3.1/fonts/1Ptxg8zYS_SKggPN4iEgvnHyvveLxVs9pbCIPrc.woff
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diff --git a/deps/bootstrap-5.3.1/fonts/q5uGsou0JOdh94bfvQlr.woff b/deps/bootstrap-5.3.1/fonts/q5uGsou0JOdh94bfvQlr.woff
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diff --git a/deps/data-deps.txt b/deps/data-deps.txt
index 21592b52..693b82d1 100644
--- a/deps/data-deps.txt
+++ b/deps/data-deps.txt
@@ -1,4 +1,4 @@
 <script src="deps/jquery-3.6.0/jquery-3.6.0.min.js"></script>
 <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no" />
-<link href="deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet" />
-<script src="deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script>
+<link href="deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet" />
+<script src="deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script>
diff --git a/index.html b/index.html
index 9cdf3bcb..070a0581 100644
--- a/index.html
+++ b/index.html
@@ -19,8 +19,8 @@
   demographic history [Chen et al. (2009) &lt;doi:10.1101/gr.083634.108&gt;].">
 <title>Breeding Program Simulations • AlphaSimR</title>
 <script src="deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
-<link href="deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet">
-<script src="deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
+<link href="deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
 <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
 <!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="pkgdown.js"></script><meta property="og:title" content="Breeding Program Simulations">
 <meta property="og:description" content="The successor to the AlphaSim software for breeding program 
@@ -48,7 +48,7 @@
     
     <a class="navbar-brand me-2" href="index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/news/index.html b/news/index.html
index 32e27ba3..33a6a4ff 100644
--- a/news/index.html
+++ b/news/index.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Changelog • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Changelog"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Changelog • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Changelog"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body>
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -51,6 +51,10 @@
       <small>Source: <a href="https://github.com/gaynorr/AlphaSimR/blob/HEAD/NEWS.md" class="external-link"><code>NEWS.md</code></a></small>
     </div>
 
+    <div class="section level2">
+<h2 class="pkg-version" data-toc-text="1.5.3" id="alphasimr-153">AlphaSimR 1.5.3<a class="anchor" aria-label="anchor" href="#alphasimr-153"></a></h2>
+<p>*fixed bug in <code>SimParam$restrSegSites</code> with excluding sites at end of chromosome</p>
+</div>
     <div class="section level2">
 <h2 class="pkg-version" data-toc-text="1.5.2" id="alphasimr-152">AlphaSimR 1.5.2<a class="anchor" aria-label="anchor" href="#alphasimr-152"></a></h2><p class="text-muted">CRAN release: 2023-11-01</p>
 <p>*fix SimParam examples for CRAN</p>
diff --git a/pkgdown.yml b/pkgdown.yml
index e13ccbf0..845c2edd 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -4,7 +4,7 @@ pkgdown_sha: ~
 articles:
   intro: intro.html
   traits: traits.html
-last_built: 2023-11-01T17:42Z
+last_built: 2023-11-30T23:25Z
 urls:
   reference: https://gaynorr.github.io/AlphaSimR/reference
   article: https://gaynorr.github.io/AlphaSimR/articles
diff --git a/reference/AlphaSimR-package.html b/reference/AlphaSimR-package.html
index a8fff685..39c88bfe 100644
--- a/reference/AlphaSimR-package.html
+++ b/reference/AlphaSimR-package.html
@@ -13,7 +13,7 @@
 demographic history [Chen et al. (2009) &amp;lt;doi:10.1101/gr.083634.108&amp;gt;].
 Please see the introductory vignette for instructions for using this package. 
 The vignette can be viewed using the following command: 
-vignette(&quot;intro&quot;,package=&quot;AlphaSimR&quot;)"><title>AlphaSimR: Breeding Program Simulations — AlphaSimR-package • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="AlphaSimR: Breeding Program Simulations — AlphaSimR-package"><meta property="og:description" content="The successor to the 'AlphaSim' software for breeding program 
+vignette(&quot;intro&quot;,package=&quot;AlphaSimR&quot;)"><title>AlphaSimR: Breeding Program Simulations — AlphaSimR-package • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="AlphaSimR: Breeding Program Simulations — AlphaSimR-package"><meta property="og:description" content="The successor to the 'AlphaSim' software for breeding program 
 simulation [Faux et al. (2016) &amp;lt;doi:10.3835/plantgenome2016.02.0013&amp;gt;]. 
 Used for stochastic simulations of breeding programs to the level of DNA 
 sequence for every individual. Contained is a wide range of functions for 
@@ -38,7 +38,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/HybridPop-class.html b/reference/HybridPop-class.html
index 5fbcc822..490a4ea2 100644
--- a/reference/HybridPop-class.html
+++ b/reference/HybridPop-class.html
@@ -1,6 +1,6 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="A lightweight version of Pop-class for hybrid lines.
-Memory is saved by not storing genotypic data."><title>Hybrid population — HybridPop-class • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Hybrid population — HybridPop-class"><meta property="og:description" content="A lightweight version of Pop-class for hybrid lines.
+Memory is saved by not storing genotypic data."><title>Hybrid population — HybridPop-class • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Hybrid population — HybridPop-class"><meta property="og:description" content="A lightweight version of Pop-class for hybrid lines.
 Memory is saved by not storing genotypic data."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/LociMap-class.html b/reference/LociMap-class.html
index d00a03ef..5cd9ce14 100644
--- a/reference/LociMap-class.html
+++ b/reference/LociMap-class.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="used for both SNPs and QTLs"><title>Loci metadata — LociMap-class • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Loci metadata — LociMap-class"><meta property="og:description" content="used for both SNPs and QTLs"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="used for both SNPs and QTLs"><title>Loci metadata — LociMap-class • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Loci metadata — LociMap-class"><meta property="og:description" content="used for both SNPs and QTLs"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body>
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/MapPop-class.html b/reference/MapPop-class.html
index 5ec89764..0ba5c4ec 100644
--- a/reference/MapPop-class.html
+++ b/reference/MapPop-class.html
@@ -2,7 +2,7 @@
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Extends RawPop-class to add a genetic map.
 This is the first object created in a simulation. It is used
 for creating initial populations and setting traits in the
-SimParam."><title>Raw population with genetic map — MapPop-class • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Raw population with genetic map — MapPop-class"><meta property="og:description" content="Extends RawPop-class to add a genetic map.
+SimParam."><title>Raw population with genetic map — MapPop-class • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Raw population with genetic map — MapPop-class"><meta property="og:description" content="Extends RawPop-class to add a genetic map.
 This is the first object created in a simulation. It is used
 for creating initial populations and setting traits in the
 SimParam."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
@@ -16,7 +16,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/MultiPop-class.html b/reference/MultiPop-class.html
index 262a4cea..ba64af9b 100644
--- a/reference/MultiPop-class.html
+++ b/reference/MultiPop-class.html
@@ -1,6 +1,6 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="The mega-population represents a population of populations.
-It is designed to behave like a list of populations."><title>Multi-Population — MultiPop-class • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Multi-Population — MultiPop-class"><meta property="og:description" content="The mega-population represents a population of populations.
+It is designed to behave like a list of populations."><title>Multi-Population — MultiPop-class • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Multi-Population — MultiPop-class"><meta property="og:description" content="The mega-population represents a population of populations.
 It is designed to behave like a list of populations."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/NamedMapPop-class.html b/reference/NamedMapPop-class.html
index fa0b24aa..f819cf83 100644
--- a/reference/NamedMapPop-class.html
+++ b/reference/NamedMapPop-class.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Extends MapPop-class to add id, mother and father."><title>Raw population with genetic map and id — NamedMapPop-class • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Raw population with genetic map and id — NamedMapPop-class"><meta property="og:description" content="Extends MapPop-class to add id, mother and father."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Extends MapPop-class to add id, mother and father."><title>Raw population with genetic map and id — NamedMapPop-class • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Raw population with genetic map and id — NamedMapPop-class"><meta property="og:description" content="Extends MapPop-class to add id, mother and father."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body>
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/Pop-class.html b/reference/Pop-class.html
index b4be0247..1619a734 100644
--- a/reference/Pop-class.html
+++ b/reference/Pop-class.html
@@ -1,6 +1,6 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Extends RawPop-class to add sex, genetic values,
-phenotypes, and pedigrees."><title>Population — Pop-class • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Population — Pop-class"><meta property="og:description" content="Extends RawPop-class to add sex, genetic values,
+phenotypes, and pedigrees."><title>Population — Pop-class • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Population — Pop-class"><meta property="og:description" content="Extends RawPop-class to add sex, genetic values,
 phenotypes, and pedigrees."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/RRBLUP.html b/reference/RRBLUP.html
index b42567ef..908cc727 100644
--- a/reference/RRBLUP.html
+++ b/reference/RRBLUP.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Fits an RR-BLUP model for genomic predictions."><title>RR-BLUP Model — RRBLUP • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="RR-BLUP Model — RRBLUP"><meta property="og:description" content="Fits an RR-BLUP model for genomic predictions."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Fits an RR-BLUP model for genomic predictions."><title>RR-BLUP Model — RRBLUP • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="RR-BLUP Model — RRBLUP"><meta property="og:description" content="Fits an RR-BLUP model for genomic predictions."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body>
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -134,7 +134,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="co">#Evaluate accuracy</span></span></span>
 <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/cor.html" class="external-link">cor</a></span><span class="op">(</span><span class="fu"><a href="gv.html">gv</a></span><span class="op">(</span><span class="va">pop</span><span class="op">)</span>, <span class="fu"><a href="ebv.html">ebv</a></span><span class="op">(</span><span class="va">pop</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>        est_GV_Trait1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Trait1     0.6206319</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Trait1     0.7377476</span>
 <span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
diff --git a/reference/RRBLUP2.html b/reference/RRBLUP2.html
index c63ed5cd..e48f621f 100644
--- a/reference/RRBLUP2.html
+++ b/reference/RRBLUP2.html
@@ -2,7 +2,7 @@
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Fits an RR-BLUP model for genomic predictions. This implementation is 
 meant for situations where RRBLUP is too slow. Note that 
 RRBLUP2 is only faster in certain situations, see details below. Most 
-users should use RRBLUP."><title>RR-BLUP Model 2 — RRBLUP2 • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="RR-BLUP Model 2 — RRBLUP2"><meta property="og:description" content="Fits an RR-BLUP model for genomic predictions. This implementation is 
+users should use RRBLUP."><title>RR-BLUP Model 2 — RRBLUP2 • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="RR-BLUP Model 2 — RRBLUP2"><meta property="og:description" content="Fits an RR-BLUP model for genomic predictions. This implementation is 
 meant for situations where RRBLUP is too slow. Note that 
 RRBLUP2 is only faster in certain situations, see details below. Most 
 users should use RRBLUP."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
@@ -16,7 +16,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -193,7 +193,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="co">#Evaluate accuracy</span></span></span>
 <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/cor.html" class="external-link">cor</a></span><span class="op">(</span><span class="fu"><a href="gv.html">gv</a></span><span class="op">(</span><span class="va">pop</span><span class="op">)</span>, <span class="fu"><a href="ebv.html">ebv</a></span><span class="op">(</span><span class="va">pop</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>        est_GV_Trait1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Trait1     0.4048304</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Trait1     0.7056706</span>
 <span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
diff --git a/reference/RRBLUPMemUse.html b/reference/RRBLUPMemUse.html
index f9d00c4c..700792b3 100644
--- a/reference/RRBLUPMemUse.html
+++ b/reference/RRBLUPMemUse.html
@@ -1,7 +1,7 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Estimates the amount of RAM needed to run the RRBLUP
 and its related functions for a given training population size. 
-Note that this function may underestimate total usage."><title>RRBLUP Memory Usage — RRBLUPMemUse • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="RRBLUP Memory Usage — RRBLUPMemUse"><meta property="og:description" content="Estimates the amount of RAM needed to run the RRBLUP
+Note that this function may underestimate total usage."><title>RRBLUP Memory Usage — RRBLUPMemUse • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="RRBLUP Memory Usage — RRBLUPMemUse"><meta property="og:description" content="Estimates the amount of RAM needed to run the RRBLUP
 and its related functions for a given training population size. 
 Note that this function may underestimate total usage."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/RRBLUP_D.html b/reference/RRBLUP_D.html
index 2ac642c8..33189ade 100644
--- a/reference/RRBLUP_D.html
+++ b/reference/RRBLUP_D.html
@@ -1,6 +1,6 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Fits an RR-BLUP model for genomic predictions that includes 
-dominance effects."><title>RR-BLUP Model with Dominance — RRBLUP_D • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="RR-BLUP Model with Dominance — RRBLUP_D"><meta property="og:description" content="Fits an RR-BLUP model for genomic predictions that includes 
+dominance effects."><title>RR-BLUP Model with Dominance — RRBLUP_D • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="RR-BLUP Model with Dominance — RRBLUP_D"><meta property="og:description" content="Fits an RR-BLUP model for genomic predictions that includes 
 dominance effects."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -138,7 +138,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="co">#Evaluate accuracy</span></span></span>
 <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/cor.html" class="external-link">cor</a></span><span class="op">(</span><span class="fu"><a href="gv.html">gv</a></span><span class="op">(</span><span class="va">pop</span><span class="op">)</span>, <span class="fu"><a href="ebv.html">ebv</a></span><span class="op">(</span><span class="va">pop</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>        est_GV_Trait1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Trait1     0.3385086</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Trait1     0.7802633</span>
 <span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
diff --git a/reference/RRBLUP_D2.html b/reference/RRBLUP_D2.html
index 21415a3f..f71be2a9 100644
--- a/reference/RRBLUP_D2.html
+++ b/reference/RRBLUP_D2.html
@@ -3,7 +3,7 @@
 dominance effects. This implementation is meant for situations where 
 RRBLUP_D is too slow. Note that RRBLUP_D2 
 is only faster in certain situations. Most users should use 
-RRBLUP_D."><title>RR-BLUP with Dominance Model 2 — RRBLUP_D2 • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="RR-BLUP with Dominance Model 2 — RRBLUP_D2"><meta property="og:description" content="Fits an RR-BLUP model for genomic predictions that includes 
+RRBLUP_D."><title>RR-BLUP with Dominance Model 2 — RRBLUP_D2 • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="RR-BLUP with Dominance Model 2 — RRBLUP_D2"><meta property="og:description" content="Fits an RR-BLUP model for genomic predictions that includes 
 dominance effects. This implementation is meant for situations where 
 RRBLUP_D is too slow. Note that RRBLUP_D2 
 is only faster in certain situations. Most users should use 
@@ -18,7 +18,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -175,7 +175,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="co">#Evaluate accuracy</span></span></span>
 <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/cor.html" class="external-link">cor</a></span><span class="op">(</span><span class="fu"><a href="gv.html">gv</a></span><span class="op">(</span><span class="va">pop</span><span class="op">)</span>, <span class="fu"><a href="ebv.html">ebv</a></span><span class="op">(</span><span class="va">pop</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>        est_GV_Trait1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Trait1     0.5351522</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Trait1     0.8385404</span>
 <span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
diff --git a/reference/RRBLUP_GCA.html b/reference/RRBLUP_GCA.html
index 8e0c2a34..5c736042 100644
--- a/reference/RRBLUP_GCA.html
+++ b/reference/RRBLUP_GCA.html
@@ -2,7 +2,7 @@
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Fits an RR-BLUP model that estimates seperate marker effects for
 females and males. Useful for predicting GCA of parents
 in single cross hybrids. Can also predict performance of specific 
-single cross hybrids."><title>RR-BLUP GCA Model — RRBLUP_GCA • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="RR-BLUP GCA Model — RRBLUP_GCA"><meta property="og:description" content="Fits an RR-BLUP model that estimates seperate marker effects for
+single cross hybrids."><title>RR-BLUP GCA Model — RRBLUP_GCA • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="RR-BLUP GCA Model — RRBLUP_GCA"><meta property="og:description" content="Fits an RR-BLUP model that estimates seperate marker effects for
 females and males. Useful for predicting GCA of parents
 in single cross hybrids. Can also predict performance of specific 
 single cross hybrids."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
@@ -16,7 +16,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -142,7 +142,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="co">#Evaluate accuracy</span></span></span>
 <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/cor.html" class="external-link">cor</a></span><span class="op">(</span><span class="fu"><a href="gv.html">gv</a></span><span class="op">(</span><span class="va">pop</span><span class="op">)</span>, <span class="fu"><a href="ebv.html">ebv</a></span><span class="op">(</span><span class="va">pop</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>        est_GV_Trait1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Trait1     0.8030224</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Trait1     0.4269091</span>
 <span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
diff --git a/reference/RRBLUP_GCA2.html b/reference/RRBLUP_GCA2.html
index d68bf04b..59d1e18f 100644
--- a/reference/RRBLUP_GCA2.html
+++ b/reference/RRBLUP_GCA2.html
@@ -3,7 +3,7 @@
 females and males. This implementation is meant for situations where 
 RRBLUP_GCA is too slow. Note that RRBLUP_GCA2 
 is only faster in certain situations. Most users should use 
-RRBLUP_GCA."><title>RR-BLUP GCA Model 2 — RRBLUP_GCA2 • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="RR-BLUP GCA Model 2 — RRBLUP_GCA2"><meta property="og:description" content="Fits an RR-BLUP model that estimates seperate marker effects for
+RRBLUP_GCA."><title>RR-BLUP GCA Model 2 — RRBLUP_GCA2 • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="RR-BLUP GCA Model 2 — RRBLUP_GCA2"><meta property="og:description" content="Fits an RR-BLUP model that estimates seperate marker effects for
 females and males. This implementation is meant for situations where 
 RRBLUP_GCA is too slow. Note that RRBLUP_GCA2 
 is only faster in certain situations. Most users should use 
@@ -18,7 +18,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -174,7 +174,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="co">#Evaluate accuracy</span></span></span>
 <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/cor.html" class="external-link">cor</a></span><span class="op">(</span><span class="fu"><a href="gv.html">gv</a></span><span class="op">(</span><span class="va">pop</span><span class="op">)</span>, <span class="fu"><a href="ebv.html">ebv</a></span><span class="op">(</span><span class="va">pop</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>        est_GV_Trait1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Trait1     0.6225819</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Trait1     0.7978478</span>
 <span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
diff --git a/reference/RRBLUP_SCA.html b/reference/RRBLUP_SCA.html
index 910ed145..fc9e3934 100644
--- a/reference/RRBLUP_SCA.html
+++ b/reference/RRBLUP_SCA.html
@@ -1,7 +1,7 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="An extention of RRBLUP_GCA that adds dominance effects. 
 Note that we have not seen any consistent benefit of this model over 
-RRBLUP_GCA."><title>RR-BLUP SCA Model — RRBLUP_SCA • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="RR-BLUP SCA Model — RRBLUP_SCA"><meta property="og:description" content="An extention of RRBLUP_GCA that adds dominance effects. 
+RRBLUP_GCA."><title>RR-BLUP SCA Model — RRBLUP_SCA • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="RR-BLUP SCA Model — RRBLUP_SCA"><meta property="og:description" content="An extention of RRBLUP_GCA that adds dominance effects. 
 Note that we have not seen any consistent benefit of this model over 
 RRBLUP_GCA."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/RRBLUP_SCA2.html b/reference/RRBLUP_SCA2.html
index c3c39a54..4494039b 100644
--- a/reference/RRBLUP_SCA2.html
+++ b/reference/RRBLUP_SCA2.html
@@ -3,7 +3,7 @@
 females and males and a dominance effect. This implementation is meant 
 for situations where RRBLUP_SCA is too slow. Note that 
 RRBLUP_SCA2 is only faster in certain situations. Most users should use 
-RRBLUP_SCA."><title>RR-BLUP SCA Model 2 — RRBLUP_SCA2 • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="RR-BLUP SCA Model 2 — RRBLUP_SCA2"><meta property="og:description" content="Fits an RR-BLUP model that estimates seperate additive effects for
+RRBLUP_SCA."><title>RR-BLUP SCA Model 2 — RRBLUP_SCA2 • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="RR-BLUP SCA Model 2 — RRBLUP_SCA2"><meta property="og:description" content="Fits an RR-BLUP model that estimates seperate additive effects for
 females and males and a dominance effect. This implementation is meant 
 for situations where RRBLUP_SCA is too slow. Note that 
 RRBLUP_SCA2 is only faster in certain situations. Most users should use 
@@ -18,7 +18,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -180,7 +180,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="co">#Evaluate accuracy</span></span></span>
 <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/cor.html" class="external-link">cor</a></span><span class="op">(</span><span class="fu"><a href="gv.html">gv</a></span><span class="op">(</span><span class="va">pop</span><span class="op">)</span>, <span class="fu"><a href="ebv.html">ebv</a></span><span class="op">(</span><span class="va">pop</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>        est_GV_Trait1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Trait1     0.5958648</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Trait1     0.6495195</span>
 <span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
diff --git a/reference/RRsol-class.html b/reference/RRsol-class.html
index f2f79537..25afea74 100644
--- a/reference/RRsol-class.html
+++ b/reference/RRsol-class.html
@@ -1,6 +1,6 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Contains output from AlphaSimR's genomic 
-selection functions."><title>RR-BLUP Solution — RRsol-class • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="RR-BLUP Solution — RRsol-class"><meta property="og:description" content="Contains output from AlphaSimR's genomic 
+selection functions."><title>RR-BLUP Solution — RRsol-class • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="RR-BLUP Solution — RRsol-class"><meta property="og:description" content="Contains output from AlphaSimR's genomic 
 selection functions."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/RawPop-class.html b/reference/RawPop-class.html
index 59b4e323..82455efe 100644
--- a/reference/RawPop-class.html
+++ b/reference/RawPop-class.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="The raw population class contains only genotype data."><title>Raw Population — RawPop-class • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Raw Population — RawPop-class"><meta property="og:description" content="The raw population class contains only genotype data."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="The raw population class contains only genotype data."><title>Raw Population — RawPop-class • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Raw Population — RawPop-class"><meta property="og:description" content="The raw population class contains only genotype data."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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 <![endif]--></head><body>
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/Rplot002.png b/reference/Rplot002.png
index f8dcaad8..6db0b877 100644
Binary files a/reference/Rplot002.png and b/reference/Rplot002.png differ
diff --git a/reference/Rplot003.png b/reference/Rplot003.png
index cba74f4a..4a4368cc 100644
Binary files a/reference/Rplot003.png and b/reference/Rplot003.png differ
diff --git a/reference/SimParam.html b/reference/SimParam.html
index 65f4e1b5..6aed0a89 100644
--- a/reference/SimParam.html
+++ b/reference/SimParam.html
@@ -1,6 +1,6 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Container for global simulation parameters. Saving this object
-as SP will allow it to be accessed by function defaults."><title>Simulation parameters — SimParam • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Simulation parameters — SimParam"><meta property="og:description" content="Container for global simulation parameters. Saving this object
+as SP will allow it to be accessed by function defaults."><title>Simulation parameters — SimParam • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Simulation parameters — SimParam"><meta property="og:description" content="Container for global simulation parameters. Saving this object
 as SP will allow it to be accessed by function defaults."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -2158,10 +2158,10 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="va">SP</span><span class="op">$</span><span class="va">nThreads</span> <span class="op">=</span> <span class="fl">1L</span></span></span>
 <span class="r-in"><span><span class="va">SP</span><span class="op">$</span><span class="fu">altAddTraitAD</span><span class="op">(</span>nQtlPerChr<span class="op">=</span><span class="fl">10</span>, mean<span class="op">=</span><span class="fl">0</span>, varA<span class="op">=</span><span class="fl">1</span>, varD<span class="op">=</span><span class="fl">0.05</span>, inbrDepr<span class="op">=</span><span class="fl">0.2</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> A new trait called Trait1 was added. </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>    varD = 0.0500001 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>    inbrDepr = 0.2000003 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>    meanDD = 0.01138151 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>    varDD = 0.03436831 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>    varD = 0.01267706 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>    inbrDepr = 0.249998 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>    meanDD = 0.1500681 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>    varDD = 0 </span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co">## ------------------------------------------------</span></span></span>
 <span class="r-in"><span><span class="co">## Method `SimParam$addTraitAG`</span></span></span>
@@ -2279,7 +2279,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="va">pop</span> <span class="op">=</span> <span class="fu"><a href="newPop.html">newPop</a></span><span class="op">(</span><span class="va">founderPop</span>, simParam<span class="op">=</span><span class="va">SP</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="fu"><a href="meanG.html">meanG</a></span><span class="op">(</span><span class="va">pop</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>       Trait1 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 6.661338e-17 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3.330669e-17 </span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co">#Change mean to 1</span></span></span>
 <span class="r-in"><span><span class="va">SP</span><span class="op">$</span><span class="fu">rescaleTraits</span><span class="op">(</span>mean<span class="op">=</span><span class="fl">1</span><span class="op">)</span></span></span>
diff --git a/reference/TraitA-class.html b/reference/TraitA-class.html
index 46d856c6..83164fc1 100644
--- a/reference/TraitA-class.html
+++ b/reference/TraitA-class.html
@@ -1,6 +1,6 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Extends LociMap-class
-to model additive traits"><title>Additive trait — TraitA-class • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Additive trait — TraitA-class"><meta property="og:description" content="Extends LociMap-class
+to model additive traits"><title>Additive trait — TraitA-class • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Additive trait — TraitA-class"><meta property="og:description" content="Extends LociMap-class
 to model additive traits"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/TraitA2-class.html b/reference/TraitA2-class.html
index 6160d532..80acb5db 100644
--- a/reference/TraitA2-class.html
+++ b/reference/TraitA2-class.html
@@ -1,7 +1,7 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Extends TraitA-class
 to model seperate additive effects for parent of
-origin. Used exclusively for genomic selection."><title>Sex specific additive trait — TraitA2-class • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Sex specific additive trait — TraitA2-class"><meta property="og:description" content="Extends TraitA-class
+origin. Used exclusively for genomic selection."><title>Sex specific additive trait — TraitA2-class • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Sex specific additive trait — TraitA2-class"><meta property="og:description" content="Extends TraitA-class
 to model seperate additive effects for parent of
 origin. Used exclusively for genomic selection."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/TraitA2D-class.html b/reference/TraitA2D-class.html
index 283ce62d..5a13f6a7 100644
--- a/reference/TraitA2D-class.html
+++ b/reference/TraitA2D-class.html
@@ -1,6 +1,6 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Extends TraitA2-class
-to add dominance"><title>Sex specific additive and dominance trait — TraitA2D-class • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Sex specific additive and dominance trait — TraitA2D-class"><meta property="og:description" content="Extends TraitA2-class
+to add dominance"><title>Sex specific additive and dominance trait — TraitA2D-class • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Sex specific additive and dominance trait — TraitA2D-class"><meta property="og:description" content="Extends TraitA2-class
 to add dominance"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/TraitAD-class.html b/reference/TraitAD-class.html
index 0fa46c97..4f8be851 100644
--- a/reference/TraitAD-class.html
+++ b/reference/TraitAD-class.html
@@ -1,6 +1,6 @@
 <!DOCTYPE html>
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-to add dominance"><title>Additive and dominance trait — TraitAD-class • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Additive and dominance trait — TraitAD-class"><meta property="og:description" content="Extends TraitA-class
+to add dominance"><title>Additive and dominance trait — TraitAD-class • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Additive and dominance trait — TraitAD-class"><meta property="og:description" content="Extends TraitA-class
 to add dominance"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/TraitADE-class.html b/reference/TraitADE-class.html
index bbf56e57..55245734 100644
--- a/reference/TraitADE-class.html
+++ b/reference/TraitADE-class.html
@@ -1,6 +1,6 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Extends TraitAD-class
-to add epistasis"><title>Additive, dominance, and epistatic trait — TraitADE-class • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Additive, dominance, and epistatic trait — TraitADE-class"><meta property="og:description" content="Extends TraitAD-class
+to add epistasis"><title>Additive, dominance, and epistatic trait — TraitADE-class • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Additive, dominance, and epistatic trait — TraitADE-class"><meta property="og:description" content="Extends TraitAD-class
 to add epistasis"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/TraitADEG-class.html b/reference/TraitADEG-class.html
index 8ace8efd..975bb0a2 100644
--- a/reference/TraitADEG-class.html
+++ b/reference/TraitADEG-class.html
@@ -1,6 +1,6 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Extends TraitADE-class
-to add GxE effects"><title>Additive, dominance, epistasis, and GxE trait — TraitADEG-class • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Additive, dominance, epistasis, and GxE trait — TraitADEG-class"><meta property="og:description" content="Extends TraitADE-class
+to add GxE effects"><title>Additive, dominance, epistasis, and GxE trait — TraitADEG-class • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Additive, dominance, epistasis, and GxE trait — TraitADEG-class"><meta property="og:description" content="Extends TraitADE-class
 to add GxE effects"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
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diff --git a/reference/TraitADG-class.html b/reference/TraitADG-class.html
index 855dbfe5..69141ded 100644
--- a/reference/TraitADG-class.html
+++ b/reference/TraitADG-class.html
@@ -1,6 +1,6 @@
 <!DOCTYPE html>
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-to add GxE effects"><title>Additive, dominance and GxE trait — TraitADG-class • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Additive, dominance and GxE trait — TraitADG-class"><meta property="og:description" content="Extends TraitAD-class
+to add GxE effects"><title>Additive, dominance and GxE trait — TraitADG-class • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Additive, dominance and GxE trait — TraitADG-class"><meta property="og:description" content="Extends TraitAD-class
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@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/TraitAE-class.html b/reference/TraitAE-class.html
index aeb03a4f..8d134ed4 100644
--- a/reference/TraitAE-class.html
+++ b/reference/TraitAE-class.html
@@ -1,6 +1,6 @@
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-to add epistasis"><title>Additive and epistatic trait — TraitAE-class • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Additive and epistatic trait — TraitAE-class"><meta property="og:description" content="Extends TraitA-class
+to add epistasis"><title>Additive and epistatic trait — TraitAE-class • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Additive and epistatic trait — TraitAE-class"><meta property="og:description" content="Extends TraitA-class
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@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
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diff --git a/reference/TraitAEG-class.html b/reference/TraitAEG-class.html
index 27070302..1757683d 100644
--- a/reference/TraitAEG-class.html
+++ b/reference/TraitAEG-class.html
@@ -1,6 +1,6 @@
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+to add GxE effects"><title>Additive, epistasis and GxE trait — TraitAEG-class • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Additive, epistasis and GxE trait — TraitAEG-class"><meta property="og:description" content="Extends TraitAE-class
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@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/TraitAG-class.html b/reference/TraitAG-class.html
index 92b9682a..8ae7db20 100644
--- a/reference/TraitAG-class.html
+++ b/reference/TraitAG-class.html
@@ -1,6 +1,6 @@
 <!DOCTYPE html>
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-to add GxE effects"><title>Additive and GxE trait — TraitAG-class • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Additive and GxE trait — TraitAG-class"><meta property="og:description" content="Extends TraitA-class
+to add GxE effects"><title>Additive and GxE trait — TraitAG-class • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Additive and GxE trait — TraitAG-class"><meta property="og:description" content="Extends TraitA-class
 to add GxE effects"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/aa.html b/reference/aa.html
index 5f1061e7..18bab3d8 100644
--- a/reference/aa.html
+++ b/reference/aa.html
@@ -1,6 +1,6 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Returns additive-by-additive epistatic
-deviations for all traits"><title>Additive-by-additive epistatic deviations — aa • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Additive-by-additive epistatic deviations — aa"><meta property="og:description" content="Returns additive-by-additive epistatic
+deviations for all traits"><title>Additive-by-additive epistatic deviations — aa • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Additive-by-additive epistatic deviations — aa"><meta property="og:description" content="Returns additive-by-additive epistatic
 deviations for all traits"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/addSegSite.html b/reference/addSegSite.html
index 333d31f6..5fd97e0c 100644
--- a/reference/addSegSite.html
+++ b/reference/addSegSite.html
@@ -1,7 +1,7 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="This function allows for adding a new 
 segregating site with user supplied genotypes to a MapPop. 
-The position of the site is set using a genetic map position."><title>Add segregating site to MapPop — addSegSite • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Add segregating site to MapPop — addSegSite"><meta property="og:description" content="This function allows for adding a new 
+The position of the site is set using a genetic map position."><title>Add segregating site to MapPop — addSegSite • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Add segregating site to MapPop — addSegSite"><meta property="og:description" content="This function allows for adding a new 
 segregating site with user supplied genotypes to a MapPop. 
 The position of the site is set using a genetic map position."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -111,26 +111,26 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="fu"><a href="pullSegSiteHaplo.html">pullSegSiteHaplo</a></span><span class="op">(</span><span class="va">founderPop2</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>      1_1 x 1_2</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1_1    0 1   0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1_1    0 0   0</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 1_2    0 0   1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2_1    1 0   0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2_2    0 1   0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3_1    0 1   0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3_2    0 0   1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4_1    1 1   1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2_1    0 1   0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2_2    0 0   0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3_1    0 1   1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3_2    0 0   0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4_1    0 0   0</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 4_2    0 1   0</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 5_1    1 0   0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 5_2    1 0   1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 6_1    0 0   1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 6_2    0 1   1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 7_1    1 0   1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 7_2    1 1   1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 8_1    0 1   0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 8_2    0 0   1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 9_1    1 1   0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 9_2    0 1   0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 10_1   0 1   1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 10_2   0 0   1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 5_2    1 1   1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 6_1    0 1   0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 6_2    1 1   1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 7_1    0 0   0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 7_2    0 1   0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 8_1    0 0   0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 8_2    0 1   0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 9_1    0 1   1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 9_2    0 1   1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 10_1   0 0   1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 10_2   1 1   0</span>
 <span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
diff --git a/reference/attrition.html b/reference/attrition.html
index 6b5e1380..c7df643a 100644
--- a/reference/attrition.html
+++ b/reference/attrition.html
@@ -1,7 +1,7 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Samples individuals at random to remove from the population. 
 The user supplies a probability for the individuals to be 
-removed from the population."><title>Lose individuals at random — attrition • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Lose individuals at random — attrition"><meta property="og:description" content="Samples individuals at random to remove from the population. 
+removed from the population."><title>Lose individuals at random — attrition • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Lose individuals at random — attrition"><meta property="og:description" content="Samples individuals at random to remove from the population. 
 The user supplies a probability for the individuals to be 
 removed from the population."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/bv.html b/reference/bv.html
index 0ca6112a..47aa59fe 100644
--- a/reference/bv.html
+++ b/reference/bv.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Returns breeding values for all traits"><title>Breeding value — bv • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Breeding value — bv"><meta property="og:description" content="Returns breeding values for all traits"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Returns breeding values for all traits"><title>Breeding value — bv • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Breeding value — bv"><meta property="og:description" content="Returns breeding values for all traits"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body>
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -86,17 +86,17 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="co">#Create population</span></span></span>
 <span class="r-in"><span><span class="va">pop</span> <span class="op">=</span> <span class="fu"><a href="newPop.html">newPop</a></span><span class="op">(</span><span class="va">founderPop</span>, simParam<span class="op">=</span><span class="va">SP</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="fu">bv</span><span class="op">(</span><span class="va">pop</span>, simParam<span class="op">=</span><span class="va">SP</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>            Trait1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1,] -1.52021353</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [2,]  0.04919273</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [3,]  0.36564386</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [4,] -1.29908982</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [5,]  0.67839291</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [6,] -0.54851557</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [7,]  2.01490898</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [8,] -0.36768982</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [9,] -0.28308287</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [10,]  0.91045313</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>           Trait1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1,] -0.5819010</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [2,] -0.6447681</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [3,]  1.1362233</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [4,]  0.1896749</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [5,]  1.1721026</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [6,] -2.2595757</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [7,]  0.9043475</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [8,]  0.3135806</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [9,]  0.3834670</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [10,] -0.6131512</span>
 <span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
diff --git a/reference/cChr.html b/reference/cChr.html
index 88e22e40..e0fd0014 100644
--- a/reference/cChr.html
+++ b/reference/cChr.html
@@ -1,7 +1,7 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Merges the chromosomes of multiple MapPop-class or
 NamedMapPop-class objects.
-Each MapPop must have the same number of chromosomes"><title>Combine MapPop chromosomes — cChr • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Combine MapPop chromosomes — cChr"><meta property="og:description" content="Merges the chromosomes of multiple MapPop-class or
+Each MapPop must have the same number of chromosomes"><title>Combine MapPop chromosomes — cChr • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Combine MapPop chromosomes — cChr"><meta property="og:description" content="Merges the chromosomes of multiple MapPop-class or
 NamedMapPop-class objects.
 Each MapPop must have the same number of chromosomes"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/calcGCA.html b/reference/calcGCA.html
index 46bbf90c..24b9a233 100644
--- a/reference/calcGCA.html
+++ b/reference/calcGCA.html
@@ -1,7 +1,7 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content='Calculate general combining ability of test crosses. Intended for
 output from hybridCross using the "testcross" option, but will work
-for any population.'><title>Calculate GCA — calcGCA • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Calculate GCA — calcGCA"><meta property="og:description" content='Calculate general combining ability of test crosses. Intended for
+for any population.'><title>Calculate GCA — calcGCA • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Calculate GCA — calcGCA"><meta property="og:description" content='Calculate general combining ability of test crosses. Intended for
 output from hybridCross using the "testcross" option, but will work
 for any population.'><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/dd.html b/reference/dd.html
index 4f2fc435..0c461a13 100644
--- a/reference/dd.html
+++ b/reference/dd.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Returns dominance deviations for all traits"><title>Dominance deviations — dd • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Dominance deviations — dd"><meta property="og:description" content="Returns dominance deviations for all traits"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Returns dominance deviations for all traits"><title>Dominance deviations — dd • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Dominance deviations — dd"><meta property="og:description" content="Returns dominance deviations for all traits"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body>
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -86,17 +86,17 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="co">#Create population</span></span></span>
 <span class="r-in"><span><span class="va">pop</span> <span class="op">=</span> <span class="fu"><a href="newPop.html">newPop</a></span><span class="op">(</span><span class="va">founderPop</span>, simParam<span class="op">=</span><span class="va">SP</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="fu">dd</span><span class="op">(</span><span class="va">pop</span>, simParam<span class="op">=</span><span class="va">SP</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>             Trait1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1,] -0.248419109</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [2,]  0.179293756</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [3,] -0.007379679</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [4,] -0.434840829</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [5,]  0.250492859</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [6,]  0.097297389</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [7,]  0.152831587</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [8,]  0.254442736</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [9,]  0.507650125</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [10,] -0.751368836</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>            Trait1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1,] -0.10503553</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [2,]  0.73076413</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [3,]  0.01139845</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [4,]  0.40533407</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [5,]  0.22873377</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [6,] -0.59229218</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [7,]  0.04563734</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [8,] -1.01899456</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [9,] -0.02762519</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [10,]  0.32207968</span>
 <span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
diff --git a/reference/dot-newPop.html b/reference/dot-newPop.html
index f13e157e..f6e743ed 100644
--- a/reference/dot-newPop.html
+++ b/reference/dot-newPop.html
@@ -1,6 +1,6 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Creates a new Pop-class from an object of
-of the Pop superclass."><title>Create new population (internal) — .newPop • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Create new population (internal) — .newPop"><meta property="og:description" content="Creates a new Pop-class from an object of
+of the Pop superclass."><title>Create new population (internal) — .newPop • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Create new population (internal) — .newPop"><meta property="og:description" content="Creates a new Pop-class from an object of
 of the Pop superclass."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/doubleGenome.html b/reference/doubleGenome.html
index e56aa857..56b70eff 100644
--- a/reference/doubleGenome.html
+++ b/reference/doubleGenome.html
@@ -2,7 +2,7 @@
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Creates new individuals with twice the ploidy. 
 This function was created to model the formation of tetraploid 
 potatoes from diploid potatoes. This function will work on any 
-population."><title>Double the ploidy of individuals — doubleGenome • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Double the ploidy of individuals — doubleGenome"><meta property="og:description" content="Creates new individuals with twice the ploidy. 
+population."><title>Double the ploidy of individuals — doubleGenome • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Double the ploidy of individuals — doubleGenome"><meta property="og:description" content="Creates new individuals with twice the ploidy. 
 This function was created to model the formation of tetraploid 
 potatoes from diploid potatoes. This function will work on any 
 population."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
@@ -16,7 +16,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/ebv.html b/reference/ebv.html
index 3f511b57..0f0fa8d4 100644
--- a/reference/ebv.html
+++ b/reference/ebv.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="A wrapper for accessing the ebv slot"><title>Estimated breeding value — ebv • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Estimated breeding value — ebv"><meta property="og:description" content="A wrapper for accessing the ebv slot"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="A wrapper for accessing the ebv slot"><title>Estimated breeding value — ebv • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Estimated breeding value — ebv"><meta property="og:description" content="A wrapper for accessing the ebv slot"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body>
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -84,16 +84,16 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="va">pop</span><span class="op">@</span><span class="va">ebv</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/matrix.html" class="external-link">matrix</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="va">pop</span><span class="op">@</span><span class="va">nInd</span><span class="op">)</span>, nrow<span class="op">=</span><span class="va">pop</span><span class="op">@</span><span class="va">nInd</span>, ncol<span class="op">=</span><span class="fl">1</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="fu">ebv</span><span class="op">(</span><span class="va">pop</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>             [,1]</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1,] -0.8976515</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [2,]  0.2214317</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [3,] -1.6471820</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [4,] -0.3329894</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [5,] -0.1626929</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [6,] -1.0593087</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [7,] -0.1943854</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [8,] -0.1747776</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [9,] -0.1671519</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [10,]  0.4216361</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1,]  0.3040397</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [2,] -1.0463369</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [3,]  0.5035516</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [4,] -0.3157750</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [5,]  0.1527558</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [6,]  0.3604446</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [7,] -1.3172457</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [8,]  1.9060921</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [9,] -0.2842742</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [10,]  0.4744226</span>
 <span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
diff --git a/reference/editGenome.html b/reference/editGenome.html
index 66d3f574..7449fcff 100644
--- a/reference/editGenome.html
+++ b/reference/editGenome.html
@@ -1,7 +1,7 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Edits selected loci of selected individuals to a homozygous 
 state for either the 1 or 0 allele. The gv slot is recalculated to 
-reflect the any changes due to editing, but other slots remain the same."><title>Edit genome — editGenome • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Edit genome — editGenome"><meta property="og:description" content="Edits selected loci of selected individuals to a homozygous 
+reflect the any changes due to editing, but other slots remain the same."><title>Edit genome — editGenome • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Edit genome — editGenome"><meta property="og:description" content="Edits selected loci of selected individuals to a homozygous 
 state for either the 1 or 0 allele. The gv slot is recalculated to 
 reflect the any changes due to editing, but other slots remain the same."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/editGenomeTopQtl.html b/reference/editGenomeTopQtl.html
index 3e4e75ee..e7645ee9 100644
--- a/reference/editGenomeTopQtl.html
+++ b/reference/editGenomeTopQtl.html
@@ -1,7 +1,7 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Edits the top QTL (with the largest additive effect) to a homozygous 
 state for the allele increasing. Only nonfixed QTL are edited The gv slot is
-recalculated to reflect the any changes due to editing, but other slots remain the same."><title>Edit genome - the top QTL — editGenomeTopQtl • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Edit genome - the top QTL — editGenomeTopQtl"><meta property="og:description" content="Edits the top QTL (with the largest additive effect) to a homozygous 
+recalculated to reflect the any changes due to editing, but other slots remain the same."><title>Edit genome - the top QTL — editGenomeTopQtl • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Edit genome - the top QTL — editGenomeTopQtl"><meta property="og:description" content="Edits the top QTL (with the largest additive effect) to a homozygous 
 state for the allele increasing. Only nonfixed QTL are edited The gv slot is
 recalculated to reflect the any changes due to editing, but other slots remain the same."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/fastRRBLUP.html b/reference/fastRRBLUP.html
index 7547d67f..ae2aabfa 100644
--- a/reference/fastRRBLUP.html
+++ b/reference/fastRRBLUP.html
@@ -3,7 +3,7 @@
 components. This implementation is meant as a fast and low memory 
 alternative to RRBLUP or RRBLUP2. Unlike 
 the those functions, the fastRRBLUP does not fit fixed effects (other 
-than the intercept) or account for unequal replication."><title>Fast RR-BLUP — fastRRBLUP • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Fast RR-BLUP — fastRRBLUP"><meta property="og:description" content="Solves an RR-BLUP model for genomic predictions given known variance 
+than the intercept) or account for unequal replication."><title>Fast RR-BLUP — fastRRBLUP • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Fast RR-BLUP — fastRRBLUP"><meta property="og:description" content="Solves an RR-BLUP model for genomic predictions given known variance 
 components. This implementation is meant as a fast and low memory 
 alternative to RRBLUP or RRBLUP2. Unlike 
 the those functions, the fastRRBLUP does not fit fixed effects (other 
@@ -18,7 +18,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -158,7 +158,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="co">#Evaluate accuracy</span></span></span>
 <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/cor.html" class="external-link">cor</a></span><span class="op">(</span><span class="fu"><a href="gv.html">gv</a></span><span class="op">(</span><span class="va">pop</span><span class="op">)</span>, <span class="fu"><a href="ebv.html">ebv</a></span><span class="op">(</span><span class="va">pop</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>        est_GV_Trait1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Trait1     0.8010933</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Trait1     0.8202796</span>
 <span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
diff --git a/reference/genParam.html b/reference/genParam.html
index 640ffc08..3665fe49 100644
--- a/reference/genParam.html
+++ b/reference/genParam.html
@@ -1,6 +1,6 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Calculates genetic and genic additive and dominance variances
-for an object of Pop-class"><title>Sumarize genetic parameters — genParam • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Sumarize genetic parameters — genParam"><meta property="og:description" content="Calculates genetic and genic additive and dominance variances
+for an object of Pop-class"><title>Sumarize genetic parameters — genParam • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Sumarize genetic parameters — genParam"><meta property="og:description" content="Calculates genetic and genic additive and dominance variances
 for an object of Pop-class"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/genicVarA.html b/reference/genicVarA.html
index dccfbf62..43e7abdf 100644
--- a/reference/genicVarA.html
+++ b/reference/genicVarA.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Returns additive genic variance for all traits"><title>Additive genic variance — genicVarA • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Additive genic variance — genicVarA"><meta property="og:description" content="Returns additive genic variance for all traits"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Returns additive genic variance for all traits"><title>Additive genic variance — genicVarA • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Additive genic variance — genicVarA"><meta property="og:description" content="Returns additive genic variance for all traits"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body>
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -87,7 +87,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="va">pop</span> <span class="op">=</span> <span class="fu"><a href="newPop.html">newPop</a></span><span class="op">(</span><span class="va">founderPop</span>, simParam<span class="op">=</span><span class="va">SP</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="fu">genicVarA</span><span class="op">(</span><span class="va">pop</span>, simParam<span class="op">=</span><span class="va">SP</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    Trait1 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 0.8569866 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 0.7557754 </span>
 <span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
diff --git a/reference/genicVarAA.html b/reference/genicVarAA.html
index aca1ad2e..6b81a7eb 100644
--- a/reference/genicVarAA.html
+++ b/reference/genicVarAA.html
@@ -1,6 +1,6 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Returns additive-by-additive epistatic
-genic variance for all traits"><title>Additive-by-additive genic variance — genicVarAA • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Additive-by-additive genic variance — genicVarAA"><meta property="og:description" content="Returns additive-by-additive epistatic
+genic variance for all traits"><title>Additive-by-additive genic variance — genicVarAA • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Additive-by-additive genic variance — genicVarAA"><meta property="og:description" content="Returns additive-by-additive epistatic
 genic variance for all traits"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/genicVarD.html b/reference/genicVarD.html
index dddb68bb..2d951300 100644
--- a/reference/genicVarD.html
+++ b/reference/genicVarD.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Returns dominance genic variance for all traits"><title>Dominance genic variance — genicVarD • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Dominance genic variance — genicVarD"><meta property="og:description" content="Returns dominance genic variance for all traits"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Returns dominance genic variance for all traits"><title>Dominance genic variance — genicVarD • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Dominance genic variance — genicVarD"><meta property="og:description" content="Returns dominance genic variance for all traits"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body>
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -87,7 +87,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="va">pop</span> <span class="op">=</span> <span class="fu"><a href="newPop.html">newPop</a></span><span class="op">(</span><span class="va">founderPop</span>, simParam<span class="op">=</span><span class="va">SP</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="fu">genicVarD</span><span class="op">(</span><span class="va">pop</span>, simParam<span class="op">=</span><span class="va">SP</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    Trait1 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 0.1472531 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 0.1549891 </span>
 <span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
diff --git a/reference/genicVarG.html b/reference/genicVarG.html
index 99ed3cf5..538c9d3b 100644
--- a/reference/genicVarG.html
+++ b/reference/genicVarG.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Returns total genic variance for all traits"><title>Total genic variance — genicVarG • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Total genic variance — genicVarG"><meta property="og:description" content="Returns total genic variance for all traits"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Returns total genic variance for all traits"><title>Total genic variance — genicVarG • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Total genic variance — genicVarG"><meta property="og:description" content="Returns total genic variance for all traits"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body>
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -86,8 +86,8 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="co">#Create population</span></span></span>
 <span class="r-in"><span><span class="va">pop</span> <span class="op">=</span> <span class="fu"><a href="newPop.html">newPop</a></span><span class="op">(</span><span class="va">founderPop</span>, simParam<span class="op">=</span><span class="va">SP</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="fu">genicVarG</span><span class="op">(</span><span class="va">pop</span>, simParam<span class="op">=</span><span class="va">SP</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>    Trait1 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 0.5949148 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   Trait1 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1.714605 </span>
 <span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
diff --git a/reference/getGenMap.html b/reference/getGenMap.html
index dd5affe9..03e28fc3 100644
--- a/reference/getGenMap.html
+++ b/reference/getGenMap.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Retrieves the genetic map for all loci."><title>Get genetic map — getGenMap • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Get genetic map — getGenMap"><meta property="og:description" content="Retrieves the genetic map for all loci."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
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diff --git a/reference/getMisc.html b/reference/getMisc.html
index 82b8594b..cc95cb5f 100644
--- a/reference/getMisc.html
+++ b/reference/getMisc.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Get miscelaneous information in a population"><title>Get miscelaneous information in a population — getMisc • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Get miscelaneous information in a population — getMisc"><meta property="og:description" content="Get miscelaneous information in a population"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Get miscelaneous information in a population"><title>Get miscelaneous information in a population — getMisc • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Get miscelaneous information in a population — getMisc"><meta property="og:description" content="Get miscelaneous information in a population"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/getNumThreads.html b/reference/getNumThreads.html
index 50a05227..d970516a 100644
--- a/reference/getNumThreads.html
+++ b/reference/getNumThreads.html
@@ -1,6 +1,6 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Gets the number of available threads by calling the OpenMP function
-omp_get_max_threads()"><title>Number of available threads — getNumThreads • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Number of available threads — getNumThreads"><meta property="og:description" content="Gets the number of available threads by calling the OpenMP function
+omp_get_max_threads()"><title>Number of available threads — getNumThreads • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Number of available threads — getNumThreads"><meta property="og:description" content="Gets the number of available threads by calling the OpenMP function
 omp_get_max_threads()"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -74,7 +74,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
     <div class="section level2">
     <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">getNumThreads</span><span class="op">(</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 4</span>
 <span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
diff --git a/reference/getPed.html b/reference/getPed.html
index 90e10aca..826ab50e 100644
--- a/reference/getPed.html
+++ b/reference/getPed.html
@@ -1,7 +1,7 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Returns the population's pedigree as stored in the 
 id, mother and father slots. NULL is returned if the 
-input population lacks the required."><title>Get pedigree — getPed • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Get pedigree — getPed"><meta property="og:description" content="Returns the population's pedigree as stored in the 
+input population lacks the required."><title>Get pedigree — getPed • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Get pedigree — getPed"><meta property="og:description" content="Returns the population's pedigree as stored in the 
 id, mother and father slots. NULL is returned if the 
 input population lacks the required."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/getQtlMap.html b/reference/getQtlMap.html
index 6afcd264..8b43c376 100644
--- a/reference/getQtlMap.html
+++ b/reference/getQtlMap.html
@@ -1,6 +1,6 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Retrieves the genetic map for the 
-QTL of a given trait."><title>Get QTL genetic map — getQtlMap • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Get QTL genetic map — getQtlMap"><meta property="og:description" content="Retrieves the genetic map for the 
+QTL of a given trait."><title>Get QTL genetic map — getQtlMap • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Get QTL genetic map — getQtlMap"><meta property="og:description" content="Retrieves the genetic map for the 
 QTL of a given trait."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -113,10 +113,10 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="co">#Pull SNP map</span></span></span>
 <span class="r-in"><span><span class="fu">getQtlMap</span><span class="op">(</span>trait<span class="op">=</span><span class="fl">1</span>, simParam<span class="op">=</span><span class="va">SP</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>        id chr site       pos</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1_2   1_2   1    2 0.1111111</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1_1   1_1   1    1 0.0000000</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 1_3   1_3   1    3 0.2222222</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1_6   1_6   1    6 0.5555556</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 1_7   1_7   1    7 0.6666667</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1_9   1_9   1    9 0.8888889</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 1_10 1_10   1   10 1.0000000</span>
 <span class="r-in"><span></span></span>
 </code></pre></div>
diff --git a/reference/getSnpMap.html b/reference/getSnpMap.html
index d9bd0e5c..d265d58a 100644
--- a/reference/getSnpMap.html
+++ b/reference/getSnpMap.html
@@ -1,6 +1,6 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Retrieves the genetic map for a 
-given SNP chip."><title>Get SNP genetic map — getSnpMap • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Get SNP genetic map — getSnpMap"><meta property="og:description" content="Retrieves the genetic map for a 
+given SNP chip."><title>Get SNP genetic map — getSnpMap • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Get SNP genetic map — getSnpMap"><meta property="og:description" content="Retrieves the genetic map for a 
 given SNP chip."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -113,12 +113,12 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co">#Pull SNP map</span></span></span>
 <span class="r-in"><span><span class="fu">getSnpMap</span><span class="op">(</span>snpChip<span class="op">=</span><span class="fl">1</span>, simParam<span class="op">=</span><span class="va">SP</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>        id chr site       pos</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1_1   1_1   1    1 0.0000000</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1_4   1_4   1    4 0.3333333</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1_5   1_5   1    5 0.4444444</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1_8   1_8   1    8 0.7777778</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1_10 1_10   1   10 1.0000000</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>      id chr site       pos</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1_1 1_1   1    1 0.0000000</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1_2 1_2   1    2 0.1111111</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1_5 1_5   1    5 0.4444444</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1_8 1_8   1    8 0.7777778</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1_9 1_9   1    9 0.8888889</span>
 <span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
diff --git a/reference/gv.html b/reference/gv.html
index c1ff2364..2fef82e2 100644
--- a/reference/gv.html
+++ b/reference/gv.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="A wrapper for accessing the gv slot"><title>Genetic value — gv • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Genetic value — gv"><meta property="og:description" content="A wrapper for accessing the gv slot"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="A wrapper for accessing the gv slot"><title>Genetic value — gv • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Genetic value — gv"><meta property="og:description" content="A wrapper for accessing the gv slot"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body>
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -83,16 +83,16 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="va">pop</span> <span class="op">=</span> <span class="fu"><a href="newPop.html">newPop</a></span><span class="op">(</span><span class="va">founderPop</span>, simParam<span class="op">=</span><span class="va">SP</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="fu">gv</span><span class="op">(</span><span class="va">pop</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>            Trait1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1,] -2.41548806</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [2,]  0.90689241</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [3,] -1.80278854</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [4,] -0.01096506</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [5,]  0.66019369</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [6,]  1.05091577</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [7,]  0.48108102</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [8,]  0.69332057</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [9,] -0.39240571</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [10,]  0.82924390</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1,]  0.71484047</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [2,] -0.07815592</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [3,]  1.37265706</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [4,]  0.13208771</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [5,]  0.95704027</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [6,]  0.82209630</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [7,] -1.25105844</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [8,] -0.47357585</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [9,] -2.04039868</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [10,] -0.15553291</span>
 <span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
diff --git a/reference/hybridCross.html b/reference/hybridCross.html
index dbfdd6fa..a0d5ba42 100644
--- a/reference/hybridCross.html
+++ b/reference/hybridCross.html
@@ -4,7 +4,7 @@
 of HybridPop-class. Note that the HybridPop-class
 should only be used if the parents were created using the makeDH
 function or newPop using inbred founders. The id for
-new individuals is [mother_id]_[father_id]"><title>Hybrid crossing — hybridCross • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Hybrid crossing — hybridCross"><meta property="og:description" content="A convience function for hybrid plant breeding simulations. Allows for
+new individuals is [mother_id]_[father_id]"><title>Hybrid crossing — hybridCross • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Hybrid crossing — hybridCross"><meta property="og:description" content="A convience function for hybrid plant breeding simulations. Allows for
 easy specification of a test cross scheme and/or creation of an object
 of HybridPop-class. Note that the HybridPop-class
 should only be used if the parents were created using the makeDH
@@ -20,7 +20,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/importGenMap.html b/reference/importGenMap.html
index 08367e48..038c279c 100644
--- a/reference/importGenMap.html
+++ b/reference/importGenMap.html
@@ -1,7 +1,7 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Formats a genetic map stored in a data.frame to
 AlphaSimR's internal format. Map positions must be 
-in Morgans."><title>Import genetic map — importGenMap • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Import genetic map — importGenMap"><meta property="og:description" content="Formats a genetic map stored in a data.frame to
+in Morgans."><title>Import genetic map — importGenMap • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Import genetic map — importGenMap"><meta property="og:description" content="Formats a genetic map stored in a data.frame to
 AlphaSimR's internal format. Map positions must be 
 in Morgans."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/importHaplo.html b/reference/importHaplo.html
index 2ca57829..fdc84b32 100644
--- a/reference/importHaplo.html
+++ b/reference/importHaplo.html
@@ -3,7 +3,7 @@
 AlphaSimR population that can be used to 
 initialize a simulation. This function serves 
 as wrapper for newMapPop that 
-utilizes a more user friendly input format."><title>Import haplotypes — importHaplo • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Import haplotypes — importHaplo"><meta property="og:description" content="Formats haplotype in a matrix format to an 
+utilizes a more user friendly input format."><title>Import haplotypes — importHaplo • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Import haplotypes — importHaplo"><meta property="og:description" content="Formats haplotype in a matrix format to an 
 AlphaSimR population that can be used to 
 initialize a simulation. This function serves 
 as wrapper for newMapPop that 
@@ -18,7 +18,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/importInbredGeno.html b/reference/importInbredGeno.html
index 8dd5d4c7..6ddd9536 100644
--- a/reference/importInbredGeno.html
+++ b/reference/importInbredGeno.html
@@ -7,7 +7,7 @@
 but will be coerced to the nearest homozygote. Pedigree 
 information is optional and when provided will be 
 passed to the population for easier identification 
-in the simulation."><title>Import inbred, diploid genotypes — importInbredGeno • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Import inbred, diploid genotypes — importInbredGeno"><meta property="og:description" content="Formats the genotypes from inbred, diploid lines 
+in the simulation."><title>Import inbred, diploid genotypes — importInbredGeno • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Import inbred, diploid genotypes — importInbredGeno"><meta property="og:description" content="Formats the genotypes from inbred, diploid lines 
 to an AlphaSimR population that can be used to 
 initialize a simulation. An attempt is made to 
 automatically detect 0,1,2 or -1,0,1 genotype coding. 
@@ -26,7 +26,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/index.html b/reference/index.html
index a60df4ca..e75b2921 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Function reference • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Function reference"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Function reference • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Function reference"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body>
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/isFemale.html b/reference/isFemale.html
index 887b987d..9a047c85 100644
--- a/reference/isFemale.html
+++ b/reference/isFemale.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Test if individuals of a population are female or male"><title>Test if individuals of a population are female or male — isFemale • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Test if individuals of a population are female or male — isFemale"><meta property="og:description" content="Test if individuals of a population are female or male"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Test if individuals of a population are female or male"><title>Test if individuals of a population are female or male — isFemale • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Test if individuals of a population are female or male — isFemale"><meta property="og:description" content="Test if individuals of a population are female or male"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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 <![endif]--></head><body>
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/isPop.html b/reference/isPop.html
index 3e7b854c..56ca5157 100644
--- a/reference/isPop.html
+++ b/reference/isPop.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Utilify function to test if object is of a Population class"><title>Test if object is of a Population class — isPop • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Test if object is of a Population class — isPop"><meta property="og:description" content="Utilify function to test if object is of a Population class"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Utilify function to test if object is of a Population class"><title>Test if object is of a Population class — isPop • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Test if object is of a Population class — isPop"><meta property="og:description" content="Utilify function to test if object is of a Population class"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body>
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/makeCross.html b/reference/makeCross.html
index 349425e6..59993372 100644
--- a/reference/makeCross.html
+++ b/reference/makeCross.html
@@ -1,6 +1,6 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Makes crosses within a population using a user supplied
-crossing plan."><title>Make designed crosses — makeCross • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Make designed crosses — makeCross"><meta property="og:description" content="Makes crosses within a population using a user supplied
+crossing plan."><title>Make designed crosses — makeCross • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Make designed crosses — makeCross"><meta property="og:description" content="Makes crosses within a population using a user supplied
 crossing plan."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/makeCross2.html b/reference/makeCross2.html
index b1c582d7..30974c90 100644
--- a/reference/makeCross2.html
+++ b/reference/makeCross2.html
@@ -1,6 +1,6 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Makes crosses between two populations using a user supplied
-crossing plan."><title>Make designed crosses — makeCross2 • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Make designed crosses — makeCross2"><meta property="og:description" content="Makes crosses between two populations using a user supplied
+crossing plan."><title>Make designed crosses — makeCross2 • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Make designed crosses — makeCross2"><meta property="og:description" content="Makes crosses between two populations using a user supplied
 crossing plan."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/makeDH.html b/reference/makeDH.html
index 5eba2f1a..855693c7 100644
--- a/reference/makeDH.html
+++ b/reference/makeDH.html
@@ -1,7 +1,7 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Creates DH lines from each individual in a population.
 Only works with diploid individuals. For polyploids, use
-reduceGenome and doubleGenome."><title>Generates DH lines — makeDH • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Generates DH lines — makeDH"><meta property="og:description" content="Creates DH lines from each individual in a population.
+reduceGenome and doubleGenome."><title>Generates DH lines — makeDH • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Generates DH lines — makeDH"><meta property="og:description" content="Creates DH lines from each individual in a population.
 Only works with diploid individuals. For polyploids, use
 reduceGenome and doubleGenome."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/meanG.html b/reference/meanG.html
index 64a75107..5181c61a 100644
--- a/reference/meanG.html
+++ b/reference/meanG.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Returns the mean genetic values for all traits"><title>Mean genetic values — meanG • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Mean genetic values — meanG"><meta property="og:description" content="Returns the mean genetic values for all traits"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Returns the mean genetic values for all traits"><title>Mean genetic values — meanG • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Mean genetic values — meanG"><meta property="og:description" content="Returns the mean genetic values for all traits"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body>
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -82,8 +82,8 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="co">#Create population</span></span></span>
 <span class="r-in"><span><span class="va">pop</span> <span class="op">=</span> <span class="fu"><a href="newPop.html">newPop</a></span><span class="op">(</span><span class="va">founderPop</span>, simParam<span class="op">=</span><span class="va">SP</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="fu">meanG</span><span class="op">(</span><span class="va">pop</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>        Trait1 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> -1.110223e-17 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>       Trait1 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 6.245005e-17 </span>
 <span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
diff --git a/reference/meanP.html b/reference/meanP.html
index 8655ed44..d7674c0b 100644
--- a/reference/meanP.html
+++ b/reference/meanP.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Returns the mean phenotypic values for all traits"><title>Mean phenotypic values — meanP • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Mean phenotypic values — meanP"><meta property="og:description" content="Returns the mean phenotypic values for all traits"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Returns the mean phenotypic values for all traits"><title>Mean phenotypic values — meanP • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Mean phenotypic values — meanP"><meta property="og:description" content="Returns the mean phenotypic values for all traits"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body>
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -82,8 +82,8 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="co">#Create population</span></span></span>
 <span class="r-in"><span><span class="va">pop</span> <span class="op">=</span> <span class="fu"><a href="newPop.html">newPop</a></span><span class="op">(</span><span class="va">founderPop</span>, simParam<span class="op">=</span><span class="va">SP</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="fu">meanP</span><span class="op">(</span><span class="va">pop</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>      Trait1 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> -0.06565018 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>     Trait1 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> -0.5176546 </span>
 <span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
diff --git a/reference/mergeGenome.html b/reference/mergeGenome.html
index 07dd54af..56371ef7 100644
--- a/reference/mergeGenome.html
+++ b/reference/mergeGenome.html
@@ -1,7 +1,7 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="This function is designed to model the pairing of gametes. The male
 and female individuals are treated as gametes, so the ploidy of newly 
-created individuals will be the sum of it parents."><title>Combine genomes of individuals — mergeGenome • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Combine genomes of individuals — mergeGenome"><meta property="og:description" content="This function is designed to model the pairing of gametes. The male
+created individuals will be the sum of it parents."><title>Combine genomes of individuals — mergeGenome • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Combine genomes of individuals — mergeGenome"><meta property="og:description" content="This function is designed to model the pairing of gametes. The male
 and female individuals are treated as gametes, so the ploidy of newly 
 created individuals will be the sum of it parents."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/mergePops.html b/reference/mergePops.html
index 1d7e7966..90b23afb 100644
--- a/reference/mergePops.html
+++ b/reference/mergePops.html
@@ -1,6 +1,6 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Rapidly merges a list of populations into a
-single population"><title>Merge list of populations — mergePops • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Merge list of populations — mergePops"><meta property="og:description" content="Rapidly merges a list of populations into a
+single population"><title>Merge list of populations — mergePops • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Merge list of populations — mergePops"><meta property="og:description" content="Rapidly merges a list of populations into a
 single population"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/mutate.html b/reference/mutate.html
index dcc7e538..50050a4d 100644
--- a/reference/mutate.html
+++ b/reference/mutate.html
@@ -4,7 +4,7 @@
 or EBVs are kept. Thus, the user will need to run 
 setPheno and/or setEBV 
 to generate new phenotypes or EBVs that reflect 
-changes introduced by the new mutations."><title>Add Random Mutations — mutate • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Add Random Mutations — mutate"><meta property="og:description" content="Adds random mutations to individuals in a 
+changes introduced by the new mutations."><title>Add Random Mutations — mutate • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Add Random Mutations — mutate"><meta property="og:description" content="Adds random mutations to individuals in a 
 population. Note that any existing phenotypes 
 or EBVs are kept. Thus, the user will need to run 
 setPheno and/or setEBV 
@@ -20,7 +20,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/nInd.html b/reference/nInd.html
index 29f7beb8..c9d7c5e6 100644
--- a/reference/nInd.html
+++ b/reference/nInd.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="A wrapper for accessing the nInd slot"><title>Number of individuals — nInd • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Number of individuals — nInd"><meta property="og:description" content="A wrapper for accessing the nInd slot"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="A wrapper for accessing the nInd slot"><title>Number of individuals — nInd • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Number of individuals — nInd"><meta property="og:description" content="A wrapper for accessing the nInd slot"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body>
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/newEmptyPop.html b/reference/newEmptyPop.html
index b89c0e13..859779f1 100644
--- a/reference/newEmptyPop.html
+++ b/reference/newEmptyPop.html
@@ -1,6 +1,6 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Creates an empty Pop-class object with user
-defined ploidy and other parameters taken from simParam."><title>Creates an empty population — newEmptyPop • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Creates an empty population — newEmptyPop"><meta property="og:description" content="Creates an empty Pop-class object with user
+defined ploidy and other parameters taken from simParam."><title>Creates an empty population — newEmptyPop • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Creates an empty population — newEmptyPop"><meta property="og:description" content="Creates an empty Pop-class object with user
 defined ploidy and other parameters taken from simParam."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/newMapPop.html b/reference/newMapPop.html
index 8117067b..b38a3e0b 100644
--- a/reference/newMapPop.html
+++ b/reference/newMapPop.html
@@ -1,6 +1,6 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Creates a new MapPop-class from user supplied 
-genetic maps and haplotypes."><title>New MapPop — newMapPop • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="New MapPop — newMapPop"><meta property="og:description" content="Creates a new MapPop-class from user supplied 
+genetic maps and haplotypes."><title>New MapPop — newMapPop • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="New MapPop — newMapPop"><meta property="og:description" content="Creates a new MapPop-class from user supplied 
 genetic maps and haplotypes."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/newMultiPop.html b/reference/newMultiPop.html
index 5e8d2150..1dec63cd 100644
--- a/reference/newMultiPop.html
+++ b/reference/newMultiPop.html
@@ -1,7 +1,7 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Creates a new MultiPop-class from one or more
 Pop-class and/or MultiPop-class
-objects."><title>Create new Multi Population — newMultiPop • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Create new Multi Population — newMultiPop"><meta property="og:description" content="Creates a new MultiPop-class from one or more
+objects."><title>Create new Multi Population — newMultiPop • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Create new Multi Population — newMultiPop"><meta property="og:description" content="Creates a new MultiPop-class from one or more
 Pop-class and/or MultiPop-class
 objects."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/newPop.html b/reference/newPop.html
index 4a9081a4..4b0b45f3 100644
--- a/reference/newPop.html
+++ b/reference/newPop.html
@@ -3,7 +3,7 @@
 MapPop-class or NamedMapPop-class.
 The function is intended for us with output from functions such
 as runMacs, newMapPop, or
-quickHaplo."><title>Create new population — newPop • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Create new population — newPop"><meta property="og:description" content="Creates an initial Pop-class from an object of
+quickHaplo."><title>Create new population — newPop • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Create new population — newPop"><meta property="og:description" content="Creates an initial Pop-class from an object of
 MapPop-class or NamedMapPop-class.
 The function is intended for us with output from functions such
 as runMacs, newMapPop, or
@@ -18,7 +18,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/pedigreeCross.html b/reference/pedigreeCross.html
index abfaa040..28ec204c 100644
--- a/reference/pedigreeCross.html
+++ b/reference/pedigreeCross.html
@@ -5,7 +5,7 @@
 the value of matchID. If matchID is TRUE, the IDs in the user
 supplied pedigree are matched against founderNames. If matchID
 is FALSE, founder individuals in the user supplied pedigree are
-randomly sampled from founderPop."><title>Pedigree cross — pedigreeCross • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Pedigree cross — pedigreeCross"><meta property="og:description" content="Creates a Pop-class from a generic
+randomly sampled from founderPop."><title>Pedigree cross — pedigreeCross • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Pedigree cross — pedigreeCross"><meta property="og:description" content="Creates a Pop-class from a generic
 pedigree and a set of founder individuals.
 The way in which the user supplied pedigree is used depends on
 the value of matchID. If matchID is TRUE, the IDs in the user
@@ -22,7 +22,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/pheno.html b/reference/pheno.html
index 0e4b809a..82bb1323 100644
--- a/reference/pheno.html
+++ b/reference/pheno.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="A wrapper for accessing the pheno slot"><title>Phenotype — pheno • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Phenotype — pheno"><meta property="og:description" content="A wrapper for accessing the pheno slot"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="A wrapper for accessing the pheno slot"><title>Phenotype — pheno • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Phenotype — pheno"><meta property="og:description" content="A wrapper for accessing the pheno slot"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body>
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -83,16 +83,16 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="va">pop</span> <span class="op">=</span> <span class="fu"><a href="newPop.html">newPop</a></span><span class="op">(</span><span class="va">founderPop</span>, simParam<span class="op">=</span><span class="va">SP</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="fu">pheno</span><span class="op">(</span><span class="va">pop</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>            Trait1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1,]  1.75233273</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [2,]  0.04779009</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [3,] -0.47833216</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [4,]  0.91171314</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [5,] -0.31582165</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [6,] -2.15293640</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [7,] -0.21603999</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [8,] -0.24092177</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [9,] -1.76981196</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [10,] -0.83956663</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1,]  1.67656264</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [2,]  0.06400970</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [3,]  0.10327339</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [4,]  0.34523187</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [5,] -2.79961555</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [6,] -1.65236691</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [7,]  1.48035829</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [8,] -0.06125746</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [9,] -0.23027332</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [10,] -0.87406848</span>
 <span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
diff --git a/reference/popVar.html b/reference/popVar.html
index 71154362..4f28e4f3 100644
--- a/reference/popVar.html
+++ b/reference/popVar.html
@@ -2,7 +2,7 @@
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Calculates the population variance matrix as 
 opposed to the sample variance matrix calculated 
 by var. i.e. divides by n instead 
-of n-1"><title>Population variance — popVar • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Population variance — popVar"><meta property="og:description" content="Calculates the population variance matrix as 
+of n-1"><title>Population variance — popVar • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Population variance — popVar"><meta property="og:description" content="Calculates the population variance matrix as 
 opposed to the sample variance matrix calculated 
 by var. i.e. divides by n instead 
 of n-1"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
@@ -16,7 +16,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/pullIbdHaplo.html b/reference/pullIbdHaplo.html
index 327374a7..6ef10c8d 100644
--- a/reference/pullIbdHaplo.html
+++ b/reference/pullIbdHaplo.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Retrieves IBD haplotype data"><title>Pull IBD haplotypes — pullIbdHaplo • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Pull IBD haplotypes — pullIbdHaplo"><meta property="og:description" content="Retrieves IBD haplotype data"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Retrieves IBD haplotype data"><title>Pull IBD haplotypes — pullIbdHaplo • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Pull IBD haplotypes — pullIbdHaplo"><meta property="og:description" content="Retrieves IBD haplotype data"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body>
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/pullMarkerGeno.html b/reference/pullMarkerGeno.html
index 5d51ec3c..9ac09149 100644
--- a/reference/pullMarkerGeno.html
+++ b/reference/pullMarkerGeno.html
@@ -1,6 +1,6 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Retrieves genotype data for user
-specified loci"><title>Pull marker genotypes — pullMarkerGeno • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Pull marker genotypes — pullMarkerGeno"><meta property="og:description" content="Retrieves genotype data for user
+specified loci"><title>Pull marker genotypes — pullMarkerGeno • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Pull marker genotypes — pullMarkerGeno"><meta property="og:description" content="Retrieves genotype data for user
 specified loci"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -110,15 +110,15 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="co">#Marker name is consistent with default naming in AlphaSimR.</span></span></span>
 <span class="r-in"><span><span class="fu">pullMarkerGeno</span><span class="op">(</span><span class="va">pop</span>, markers<span class="op">=</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"1_1"</span>,<span class="st">"1_2"</span><span class="op">)</span>, simParam<span class="op">=</span><span class="va">SP</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    1_1 1_2</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1    2   0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1    0   0</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 2    0   1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3    1   1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4    1   0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3    1   2</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4    2   2</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 5    1   1</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 6    1   1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 7    1   1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 8    2   0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 9    2   2</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 7    0   2</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 8    0   1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 9    2   0</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 10   1   1</span>
 <span class="r-in"><span></span></span>
 </code></pre></div>
diff --git a/reference/pullMarkerHaplo.html b/reference/pullMarkerHaplo.html
index 5a5fe7b5..53eb8dd7 100644
--- a/reference/pullMarkerHaplo.html
+++ b/reference/pullMarkerHaplo.html
@@ -1,6 +1,6 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Retrieves haplotype data for user
-specified loci"><title>Pull marker haplotypes — pullMarkerHaplo • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Pull marker haplotypes — pullMarkerHaplo"><meta property="og:description" content="Retrieves haplotype data for user
+specified loci"><title>Pull marker haplotypes — pullMarkerHaplo • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Pull marker haplotypes — pullMarkerHaplo"><meta property="og:description" content="Retrieves haplotype data for user
 specified loci"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -117,25 +117,25 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="co">#Marker name is consistent with default naming in AlphaSimR.</span></span></span>
 <span class="r-in"><span><span class="fu">pullMarkerHaplo</span><span class="op">(</span><span class="va">pop</span>, markers<span class="op">=</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"1_1"</span>,<span class="st">"1_2"</span><span class="op">)</span>, simParam<span class="op">=</span><span class="va">SP</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>      1_1 1_2</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1_1    1   0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1_1    0   1</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 1_2    0   0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2_1    0   1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2_2    1   0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3_1    0   0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2_1    1   1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2_2    0   1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3_1    1   1</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 3_2    0   0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4_1    0   0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4_1    1   1</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 4_2    1   1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 5_1    1   1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 5_1    0   1</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 5_2    0   0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 6_1    0   1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 6_1    1   1</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 6_2    0   1</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 7_1    0   0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 7_2    0   1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 8_1    1   1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 7_2    1   0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 8_1    1   0</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 8_2    1   1</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 9_1    0   0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 9_2    0   1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 10_1   1   0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 9_2    1   1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 10_1   0   0</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 10_2   0   0</span>
 <span class="r-in"><span></span></span>
 </code></pre></div>
diff --git a/reference/pullQtlGeno.html b/reference/pullQtlGeno.html
index eee9f467..1bb0c59a 100644
--- a/reference/pullQtlGeno.html
+++ b/reference/pullQtlGeno.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Retrieves QTL genotype data"><title>Pull QTL genotypes — pullQtlGeno • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Pull QTL genotypes — pullQtlGeno"><meta property="og:description" content="Retrieves QTL genotype data"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Retrieves QTL genotype data"><title>Pull QTL genotypes — pullQtlGeno • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Pull QTL genotypes — pullQtlGeno"><meta property="og:description" content="Retrieves QTL genotype data"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body>
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -106,17 +106,17 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="co">#Create population</span></span></span>
 <span class="r-in"><span><span class="va">pop</span> <span class="op">=</span> <span class="fu"><a href="newPop.html">newPop</a></span><span class="op">(</span><span class="va">founderPop</span>, simParam<span class="op">=</span><span class="va">SP</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="fu">pullQtlGeno</span><span class="op">(</span><span class="va">pop</span>, simParam<span class="op">=</span><span class="va">SP</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>    1_1 1_2 1_3 1_4 1_5 1_7 1_8 1_10 1_11 1_15</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1    1   1   0   1   1   0   2    1    1    2</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2    0   1   2   1   0   1   1    0    0    2</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3    2   1   2   2   2   1   1    0    0    0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4    0   1   0   1   1   1   1    0    2    1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 5    1   2   2   1   2   1   2    1    1    0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 6    1   1   2   2   0   2   0    1    1    0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 7    1   0   1   2   1   1   1    1    0    1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 8    0   1   1   1   1   0   1    2    2    1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 9    2   1   1   1   0   0   1    2    0    0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 10   2   1   0   1   0   1   1    1    1    0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>    1_2 1_3 1_4 1_6 1_7 1_10 1_11 1_13 1_14 1_15</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1    0   1   0   2   2    0    0    2    1    2</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2    1   0   0   2   0    0    1    2    0    0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3    2   1   1   2   2    1    1    0    1    1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4    2   0   2   1   0    2    1    1    1    1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 5    2   0   1   2   0    0    0    2    0    1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 6    1   2   1   1   1    1    1    0    1    1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 7    0   0   2   0   0    0    1    1    0    2</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 8    1   0   1   1   0    1    1    1    1    1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 9    1   2   2   0   1    1    1    1    2    1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 10   0   1   0   0   1    2    1    1    1    1</span>
 <span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
diff --git a/reference/pullQtlHaplo.html b/reference/pullQtlHaplo.html
index ae6f49c0..4b4f6408 100644
--- a/reference/pullQtlHaplo.html
+++ b/reference/pullQtlHaplo.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Retrieves QTL haplotype data"><title>Pull QTL haplotypes — pullQtlHaplo • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Pull QTL haplotypes — pullQtlHaplo"><meta property="og:description" content="Retrieves QTL haplotype data"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Retrieves QTL haplotype data"><title>Pull QTL haplotypes — pullQtlHaplo • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Pull QTL haplotypes — pullQtlHaplo"><meta property="og:description" content="Retrieves QTL haplotype data"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body>
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -119,27 +119,27 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="co">#Create population</span></span></span>
 <span class="r-in"><span><span class="va">pop</span> <span class="op">=</span> <span class="fu"><a href="newPop.html">newPop</a></span><span class="op">(</span><span class="va">founderPop</span>, simParam<span class="op">=</span><span class="va">SP</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="fu">pullQtlHaplo</span><span class="op">(</span><span class="va">pop</span>, simParam<span class="op">=</span><span class="va">SP</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>      1_2 1_3 1_4 1_8 1_9 1_11 1_12 1_13 1_14 1_15</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1_1    0   0   0   1   1    0    1    1    0    1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1_2    0   1   1   0   1    1    1    1    0    1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2_1    1   1   1   1   1    0    0    1    1    1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2_2    0   0   1   0   1    1    1    1    0    1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3_1    0   0   0   1   1    1    0    0    1    1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3_2    1   0   0   1   1    0    0    1    0    0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4_1    1   1   0   1   0    0    1    0    0    0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4_2    0   0   0   1   0    1    1    0    1    1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 5_1    0   0   0   0   0    0    0    0    0    0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 5_2    1   1   1   0   1    0    0    0    0    0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 6_1    0   1   0   1   0    0    0    0    1    0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 6_2    0   1   1   1   1    0    0    1    1    0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 7_1    0   0   1   1   0    0    1    0    1    0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 7_2    0   0   1   0   1    1    1    1    1    1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 8_1    1   1   1   1   1    0    1    0    1    0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 8_2    0   1   1   0   0    0    1    1    1    1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 9_1    1   0   0   1   1    1    0    0    1    0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 9_2    1   0   0   1   0    0    1    0    0    0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 10_1   0   1   1   0   1    0    1    0    1    1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 10_2   1   1   0   1   1    0    1    0    0    1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>      1_1 1_2 1_3 1_4 1_7 1_9 1_11 1_12 1_13 1_15</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1_1    1   1   0   1   1   1    0    0    0    1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1_2    1   0   0   1   0   1    0    1    1    0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2_1    1   1   1   0   1   1    0    0    1    1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2_2    0   1   0   1   1   0    0    0    1    0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3_1    1   1   1   1   0   1    0    0    1    1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3_2    1   0   1   0   0   1    1    0    1    0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4_1    1   0   0   0   1   0    0    0    1    0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4_2    0   0   0   0   0   1    1    1    0    0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 5_1    0   0   1   0   1   0    0    1    1    1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 5_2    1   0   1   1   1   0    1    1    0    0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 6_1    0   1   0   0   1   1    0    0    1    0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 6_2    0   1   0   1   1   1    1    1    0    1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 7_1    0   0   0   0   1   1    1    1    1    0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 7_2    1   1   1   0   0   0    0    1    1    0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 8_1    1   0   0   1   0   1    1    0    0    1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 8_2    1   1   1   0   0   1    1    1    1    0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 9_1    0   0   1   0   1   0    1    1    1    0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 9_2    0   0   0   1   1   0    0    0    0    1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 10_1   1   1   1   0   0   1    0    0    0    0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 10_2   1   0   0   0   1   0    1    0    1    0</span>
 <span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
diff --git a/reference/pullSegSiteGeno.html b/reference/pullSegSiteGeno.html
index dfe17ac3..5c169ac9 100644
--- a/reference/pullSegSiteGeno.html
+++ b/reference/pullSegSiteGeno.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Retrieves genotype data for all segregating sites"><title>Pull segregating site genotypes — pullSegSiteGeno • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Pull segregating site genotypes — pullSegSiteGeno"><meta property="og:description" content="Retrieves genotype data for all segregating sites"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Retrieves genotype data for all segregating sites"><title>Pull segregating site genotypes — pullSegSiteGeno • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Pull segregating site genotypes — pullSegSiteGeno"><meta property="og:description" content="Retrieves genotype data for all segregating sites"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body>
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -103,16 +103,16 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="va">pop</span> <span class="op">=</span> <span class="fu"><a href="newPop.html">newPop</a></span><span class="op">(</span><span class="va">founderPop</span>, simParam<span class="op">=</span><span class="va">SP</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="fu">pullSegSiteGeno</span><span class="op">(</span><span class="va">pop</span>, simParam<span class="op">=</span><span class="va">SP</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    1_1 1_2 1_3 1_4 1_5 1_6 1_7 1_8 1_9 1_10 1_11 1_12 1_13 1_14 1_15</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1    1   1   2   1   2   0   2   1   1    2    1    2    0    0    2</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2    1   1   0   1   1   1   2   2   0    2    2    0    0    2    0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3    2   0   2   2   1   1   2   0   0    0    1    0    0    1    1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4    0   1   1   2   0   0   1   1   0    2    0    0    1    0    1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 5    2   1   0   1   1   1   0   2   2    1    0    2    1    1    1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 6    1   2   1   1   1   1   2   0   1    1    1    1    0    2    1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 7    1   1   1   1   2   1   0   1   0    0    2    1    2    0    0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 8    1   1   0   1   1   1   1   0   2    2    2    2    2    2    1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 9    0   0   0   0   0   1   2   0   1    1    0    0    2    1    1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 10   0   1   1   0   2   1   2   2   1    1    0    0    1    2    1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1    2   1   2   2   0   2   2   0   1    1    1    0    1    1    1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2    1   1   2   0   1   1   0   0   1    0    1    0    1    0    1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3    0   1   2   0   2   1   1   2   1    1    1    1    2    0    0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4    1   1   1   2   2   2   1   1   2    1    1    1    1    1    2</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 5    2   0   1   2   1   1   0   1   1    0    1    0    2    1    1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 6    1   0   2   2   1   1   1   1   1    0    2    1    0    1    2</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 7    0   0   1   0   1   1   1   0   0    1    2    2    2    2    2</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 8    0   2   1   0   1   1   1   2   0    2    2    1    1    0    1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 9    2   1   1   0   1   1   0   0   1    2    1    2    0    1    0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 10   1   1   1   2   0   1   1   1   1    2    2    1    0    1    0</span>
 <span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
diff --git a/reference/pullSegSiteHaplo.html b/reference/pullSegSiteHaplo.html
index 7db0fd0f..1be89f0f 100644
--- a/reference/pullSegSiteHaplo.html
+++ b/reference/pullSegSiteHaplo.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Retrieves haplotype data for all segregating sites"><title>Pull seg site haplotypes — pullSegSiteHaplo • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Pull seg site haplotypes — pullSegSiteHaplo"><meta property="og:description" content="Retrieves haplotype data for all segregating sites"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Retrieves haplotype data for all segregating sites"><title>Pull seg site haplotypes — pullSegSiteHaplo • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Pull seg site haplotypes — pullSegSiteHaplo"><meta property="og:description" content="Retrieves haplotype data for all segregating sites"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body>
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -116,26 +116,26 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="va">pop</span> <span class="op">=</span> <span class="fu"><a href="newPop.html">newPop</a></span><span class="op">(</span><span class="va">founderPop</span>, simParam<span class="op">=</span><span class="va">SP</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="fu">pullSegSiteHaplo</span><span class="op">(</span><span class="va">pop</span>, simParam<span class="op">=</span><span class="va">SP</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>      1_1 1_2 1_3 1_4 1_5 1_6 1_7 1_8 1_9 1_10 1_11 1_12 1_13 1_14 1_15</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1_1    1   0   0   0   0   0   0   0   0    0    0    1    1    0    1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1_2    0   1   1   1   1   0   1   1   1    1    0    0    1    0    0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2_1    1   1   1   1   0   0   0   1   1    0    0    1    0    0    1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2_2    1   1   0   1   0   1   0   0   0    1    0    0    0    1    0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3_1    1   1   1   0   0   0   0   0   0    1    0    0    0    0    1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3_2    0   1   0   1   0   1   0   1   0    1    0    1    0    0    0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4_1    0   0   0   0   0   1   1   1   0    0    0    1    0    1    1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4_2    0   0   1   0   0   0   1   0   0    1    0    0    1    1    0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 5_1    1   1   1   1   0   0   1   0   0    1    0    1    0    1    0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 5_2    1   1   0   0   1   0   1   1   0    0    0    0    0    1    1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 6_1    0   1   0   1   0   0   0   0   0    1    0    1    1    0    0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 6_2    0   1   0   0   0   0   0   0   1    0    1    1    1    0    0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 7_1    1   1   1   0   1   1   0   1   1    0    0    1    1    1    1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 7_2    1   0   0   1   1   0   1   1   1    1    0    0    0    0    1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 8_1    0   1   0   1   1   1   1   0   0    1    1    1    0    1    1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 8_2    1   1   1   1   1   1   1   1   0    0    1    0    1    0    0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 9_1    0   0   1   1   1   0   1   1   1    1    0    1    0    1    0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 9_2    1   0   0   1   0   1   0   0   0    0    1    0    1    1    0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 10_1   0   1   1   0   1   0   1   0   0    1    0    0    1    0    0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 10_2   0   0   0   1   0   1   0   1   1    0    1    1    1    0    1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1_1    1   0   0   1   1   1   1   0   1    1    0    0    0    1    1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1_2    1   1   1   0   1   0   0   0   0    1    0    0    1    1    0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2_1    0   0   0   0   0   1   1   0   0    1    0    0    0    0    0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2_2    0   0   1   0   0   1   1   0   1    0    0    0    1    0    0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3_1    1   1   0   0   0   0   1   0   0    0    0    0    0    1    0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3_2    1   0   0   1   1   1   1   0   1    1    1    1    0    0    1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4_1    1   1   0   0   1   1   0   0   1    1    1    0    0    0    0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4_2    1   0   1   0   1   1   0   0   0    1    0    1    1    1    0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 5_1    1   1   0   0   0   0   0   1   1    0    1    1    1    1    0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 5_2    1   0   1   0   1   1   0   1   0    0    1    1    1    1    1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 6_1    1   0   1   0   1   1   0   0   0    1    0    0    0    0    1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 6_2    0   0   1   0   0   1   0   0   1    0    0    1    0    0    1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 7_1    1   1   1   0   1   1   1   0   1    0    0    0    1    0    0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 7_2    0   1   0   1   1   0   0   0   1    0    1    1    1    0    1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 8_1    0   0   1   1   0   1   0   1   1    0    0    1    1    1    1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 8_2    0   1   0   0   0   1   1   1   1    1    1    0    1    0    1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 9_1    0   0   0   1   0   1   1   1   0    0    1    0    0    1    0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 9_2    1   0   1   0   0   1   1   0   0    1    0    0    1    1    1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 10_1   1   0   0   1   1   0   0   0   0    0    0    0    1    0    0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 10_2   0   1   1   0   0   0   1   1   1    0    1    0    0    1    1</span>
 <span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
diff --git a/reference/pullSnpGeno.html b/reference/pullSnpGeno.html
index 6c9f2a1d..3819042d 100644
--- a/reference/pullSnpGeno.html
+++ b/reference/pullSnpGeno.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Retrieves SNP genotype data"><title>Pull SNP genotypes — pullSnpGeno • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Pull SNP genotypes — pullSnpGeno"><meta property="og:description" content="Retrieves SNP genotype data"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Retrieves SNP genotype data"><title>Pull SNP genotypes — pullSnpGeno • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Pull SNP genotypes — pullSnpGeno"><meta property="og:description" content="Retrieves SNP genotype data"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body>
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -106,17 +106,17 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="co">#Create population</span></span></span>
 <span class="r-in"><span><span class="va">pop</span> <span class="op">=</span> <span class="fu"><a href="newPop.html">newPop</a></span><span class="op">(</span><span class="va">founderPop</span>, simParam<span class="op">=</span><span class="va">SP</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="fu">pullSnpGeno</span><span class="op">(</span><span class="va">pop</span>, simParam<span class="op">=</span><span class="va">SP</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>    1_1 1_3 1_7 1_9 1_14</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1    2   1   1   2    1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2    1   0   1   2    1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3    1   1   0   0    0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4    0   2   1   2    1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 5    1   2   0   1    2</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 6    0   1   1   0    0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 7    0   0   1   1    2</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 8    0   2   2   1    1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 9    2   2   2   1    1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 10   1   1   1   2    1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>    1_3 1_6 1_7 1_9 1_10</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1    2   0   0   2    0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2    2   1   2   2    2</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3    1   0   0   2    1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4    1   2   0   2    1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 5    0   1   2   1    1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 6    2   1   0   1    2</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 7    1   1   0   0    0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 8    0   2   0   1    0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 9    2   1   2   0    1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 10   0   1   1   2    2</span>
 <span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
diff --git a/reference/pullSnpHaplo.html b/reference/pullSnpHaplo.html
index cdbb6e8e..614acc0d 100644
--- a/reference/pullSnpHaplo.html
+++ b/reference/pullSnpHaplo.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Retrieves SNP haplotype data"><title>Pull SNP haplotypes — pullSnpHaplo • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Pull SNP haplotypes — pullSnpHaplo"><meta property="og:description" content="Retrieves SNP haplotype data"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Retrieves SNP haplotype data"><title>Pull SNP haplotypes — pullSnpHaplo • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Pull SNP haplotypes — pullSnpHaplo"><meta property="og:description" content="Retrieves SNP haplotype data"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body>
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -119,27 +119,27 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="co">#Create population</span></span></span>
 <span class="r-in"><span><span class="va">pop</span> <span class="op">=</span> <span class="fu"><a href="newPop.html">newPop</a></span><span class="op">(</span><span class="va">founderPop</span>, simParam<span class="op">=</span><span class="va">SP</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="fu">pullSnpHaplo</span><span class="op">(</span><span class="va">pop</span>, simParam<span class="op">=</span><span class="va">SP</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>      1_3 1_4 1_8 1_11 1_14</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1_1    0   0   0    1    0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1_2    1   1   0    1    1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2_1    1   0   0    0    1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2_2    0   1   1    0    1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3_1    1   0   1    1    0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3_2    1   0   0    1    0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4_1    1   1   0    0    0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4_2    1   0   0    0    1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 5_1    1   1   1    0    1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 5_2    1   0   0    0    1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 6_1    0   1   0    1    0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 6_2    0   1   0    0    1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 7_1    1   1   1    0    0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 7_2    0   1   0    0    1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 8_1    1   0   1    1    1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 8_2    0   0   0    1    1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 9_1    1   0   0    0    1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 9_2    1   0   1    1    1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 10_1   0   0   0    1    0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 10_2   0   1   1    0    1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>      1_1 1_2 1_4 1_7 1_10</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1_1    1   1   1   0    1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1_2    0   0   0   0    1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2_1    1   0   1   0    0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2_2    1   1   0   0    1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3_1    1   1   1   0    0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3_2    0   1   0   1    0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4_1    1   0   0   1    1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4_2    0   1   0   1    0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 5_1    0   1   1   1    0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 5_2    0   1   1   0    1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 6_1    0   0   1   1    0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 6_2    1   0   1   0    1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 7_1    1   1   1   0    0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 7_2    0   1   0   0    0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 8_1    1   0   1   1    0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 8_2    1   1   1   1    1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 9_1    0   0   0   1    0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 9_2    1   1   0   0    1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 10_1   0   1   0   1    0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 10_2   1   0   0   1    1</span>
 <span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
diff --git a/reference/quickHaplo.html b/reference/quickHaplo.html
index a3e2dd8f..e38969c5 100644
--- a/reference/quickHaplo.html
+++ b/reference/quickHaplo.html
@@ -1,7 +1,7 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Rapidly simulates founder haplotypes by randomly 
 sampling 0s and 1s. This is equivalent to having all loci with 
-allele frequency 0.5 and being in linkage equilibrium."><title>Quick founder haplotype simulation — quickHaplo • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Quick founder haplotype simulation — quickHaplo"><meta property="og:description" content="Rapidly simulates founder haplotypes by randomly 
+allele frequency 0.5 and being in linkage equilibrium."><title>Quick founder haplotype simulation — quickHaplo • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Quick founder haplotype simulation — quickHaplo"><meta property="og:description" content="Rapidly simulates founder haplotypes by randomly 
 sampling 0s and 1s. This is equivalent to having all loci with 
 allele frequency 0.5 and being in linkage equilibrium."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/randCross.html b/reference/randCross.html
index 548fef8d..623f8aeb 100644
--- a/reference/randCross.html
+++ b/reference/randCross.html
@@ -1,6 +1,6 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="A wrapper for makeCross that randomly
-selects parental combinations for all possible combinantions."><title>Make random crosses — randCross • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Make random crosses — randCross"><meta property="og:description" content="A wrapper for makeCross that randomly
+selects parental combinations for all possible combinantions."><title>Make random crosses — randCross • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Make random crosses — randCross"><meta property="og:description" content="A wrapper for makeCross that randomly
 selects parental combinations for all possible combinantions."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/randCross2.html b/reference/randCross2.html
index d6ca6071..6f220144 100644
--- a/reference/randCross2.html
+++ b/reference/randCross2.html
@@ -1,7 +1,7 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="A wrapper for makeCross2 that randomly
 selects parental combinations for all possible combinantions between
-two populations."><title>Make random crosses — randCross2 • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Make random crosses — randCross2"><meta property="og:description" content="A wrapper for makeCross2 that randomly
+two populations."><title>Make random crosses — randCross2 • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Make random crosses — randCross2"><meta property="og:description" content="A wrapper for makeCross2 that randomly
 selects parental combinations for all possible combinantions between
 two populations."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/reduceGenome.html b/reference/reduceGenome.html
index a445124e..c122632b 100644
--- a/reference/reduceGenome.html
+++ b/reference/reduceGenome.html
@@ -4,7 +4,7 @@
 tetraploid potatoes. It can be used on any population with an 
 even ploidy level. The newly created individuals will have half 
 the ploidy level of the originals. The reduction can occur with 
-or without genetic recombination."><title>Create individuals with reduced ploidy — reduceGenome • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Create individuals with reduced ploidy — reduceGenome"><meta property="og:description" content="Creates new individuals from gametes. This function 
+or without genetic recombination."><title>Create individuals with reduced ploidy — reduceGenome • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Create individuals with reduced ploidy — reduceGenome"><meta property="og:description" content="Creates new individuals from gametes. This function 
 was created to model the creation of diploid potatoes from 
 tetraploid potatoes. It can be used on any population with an 
 even ploidy level. The newly created individuals will have half 
@@ -20,7 +20,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/resetPop.html b/reference/resetPop.html
index cfc14b8f..ab739679 100644
--- a/reference/resetPop.html
+++ b/reference/resetPop.html
@@ -1,6 +1,6 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Recalculates a population's genetic values and
-resets phenotypes and EBVs."><title>Reset population — resetPop • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Reset population — resetPop"><meta property="og:description" content="Recalculates a population's genetic values and
+resets phenotypes and EBVs."><title>Reset population — resetPop • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Reset population — resetPop"><meta property="og:description" content="Recalculates a population's genetic values and
 resets phenotypes and EBVs."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/runMacs.html b/reference/runMacs.html
index 40a93275..87c8eb19 100644
--- a/reference/runMacs.html
+++ b/reference/runMacs.html
@@ -1,7 +1,7 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Uses the MaCS software to produce founder haplotypes 
 (Chen et al. 2009)
-."><title>Create founder haplotypes using MaCS — runMacs • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Create founder haplotypes using MaCS — runMacs"><meta property="og:description" content="Uses the MaCS software to produce founder haplotypes 
+."><title>Create founder haplotypes using MaCS — runMacs • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Create founder haplotypes using MaCS — runMacs"><meta property="og:description" content="Uses the MaCS software to produce founder haplotypes 
 (Chen et al. 2009)
 ."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/runMacs2.html b/reference/runMacs2.html
index bd980201..079a14d1 100644
--- a/reference/runMacs2.html
+++ b/reference/runMacs2.html
@@ -6,7 +6,7 @@
 of an appropriate line for the manualCommand argument in runMacs 
 using user supplied variables, but only allows for a subset of the functionality 
 offered by this argument. The default arguments of this function were chosen to match 
-species="GENERIC" in runMacs.'><title>Alternative wrapper for MaCS — runMacs2 • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Alternative wrapper for MaCS — runMacs2"><meta property="og:description" content='A wrapper function for runMacs. This wrapper is designed 
+species="GENERIC" in runMacs.'><title>Alternative wrapper for MaCS — runMacs2 • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Alternative wrapper for MaCS — runMacs2"><meta property="og:description" content='A wrapper function for runMacs. This wrapper is designed 
 to provide a more intuitive interface for writing custom commands
 in MaCS (Chen et al. 2009)
 . It effectively automates the creation 
@@ -24,7 +24,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/sampleHaplo.html b/reference/sampleHaplo.html
index 509792ac..79a2008b 100644
--- a/reference/sampleHaplo.html
+++ b/reference/sampleHaplo.html
@@ -1,6 +1,6 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Creates a new MapPop-class from an existing 
-MapPop-class by randomly sampling haplotypes."><title>Sample haplotypes from a MapPop — sampleHaplo • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Sample haplotypes from a MapPop — sampleHaplo"><meta property="og:description" content="Creates a new MapPop-class from an existing 
+MapPop-class by randomly sampling haplotypes."><title>Sample haplotypes from a MapPop — sampleHaplo • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Sample haplotypes from a MapPop — sampleHaplo"><meta property="og:description" content="Creates a new MapPop-class from an existing 
 MapPop-class by randomly sampling haplotypes."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/selIndex.html b/reference/selIndex.html
index c37539d7..fd9d0f2e 100644
--- a/reference/selIndex.html
+++ b/reference/selIndex.html
@@ -2,7 +2,7 @@
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Calculates values of a selection index given trait values and 
 weights. This function is intended to be used in combination with 
 selection functions working on populations such as 
-selectInd."><title>Selection index — selIndex • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Selection index — selIndex"><meta property="og:description" content="Calculates values of a selection index given trait values and 
+selectInd."><title>Selection index — selIndex • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Selection index — selIndex"><meta property="og:description" content="Calculates values of a selection index given trait values and 
 weights. This function is intended to be used in combination with 
 selection functions working on populations such as 
 selectInd."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
@@ -16,7 +16,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/selInt.html b/reference/selInt.html
index 93488e01..4c39dd16 100644
--- a/reference/selInt.html
+++ b/reference/selInt.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Calculates the standardized selection intensity"><title>Selection intensity — selInt • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Selection intensity — selInt"><meta property="og:description" content="Calculates the standardized selection intensity"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Calculates the standardized selection intensity"><title>Selection intensity — selInt • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Selection intensity — selInt"><meta property="og:description" content="Calculates the standardized selection intensity"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body>
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/selectCross.html b/reference/selectCross.html
index 89f85c49..971c21c2 100644
--- a/reference/selectCross.html
+++ b/reference/selectCross.html
@@ -5,7 +5,7 @@
 crossing in one function call that minimized the amount
 of intermediate populations created. This reduces RAM usage
 and simplifies code writing. Note that this wrapper does not
-provide the full functionality of either function."><title>Select and randomly cross — selectCross • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Select and randomly cross — selectCross"><meta property="og:description" content="This is a wrapper that combines the functionalities of
+provide the full functionality of either function."><title>Select and randomly cross — selectCross • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Select and randomly cross — selectCross"><meta property="og:description" content="This is a wrapper that combines the functionalities of
 randCross and selectInd. The
 purpose of this wrapper is to combine both selection and
 crossing in one function call that minimized the amount
@@ -22,7 +22,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/selectFam.html b/reference/selectFam.html
index d97ee3c1..0433388e 100644
--- a/reference/selectFam.html
+++ b/reference/selectFam.html
@@ -1,6 +1,6 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Selects a subset of full-sib families from a
-population."><title>Select families — selectFam • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Select families — selectFam"><meta property="og:description" content="Selects a subset of full-sib families from a
+population."><title>Select families — selectFam • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Select families — selectFam"><meta property="og:description" content="Selects a subset of full-sib families from a
 population."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/selectInd-1.png b/reference/selectInd-1.png
index 49adb14d..7549587c 100644
Binary files a/reference/selectInd-1.png and b/reference/selectInd-1.png differ
diff --git a/reference/selectInd-2.png b/reference/selectInd-2.png
index d6314ead..0cc7d247 100644
Binary files a/reference/selectInd-2.png and b/reference/selectInd-2.png differ
diff --git a/reference/selectInd-3.png b/reference/selectInd-3.png
index 8627de0b..baecde19 100644
Binary files a/reference/selectInd-3.png and b/reference/selectInd-3.png differ
diff --git a/reference/selectInd.html b/reference/selectInd.html
index 8def5b40..83ad6457 100644
--- a/reference/selectInd.html
+++ b/reference/selectInd.html
@@ -1,6 +1,6 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Selects a subset of nInd individuals from a
-population."><title>Select individuals — selectInd • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Select individuals — selectInd"><meta property="og:description" content="Selects a subset of nInd individuals from a
+population."><title>Select individuals — selectInd • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Select individuals — selectInd"><meta property="og:description" content="Selects a subset of nInd individuals from a
 population."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/selectOP.html b/reference/selectOP.html
index 6992ce35..812e5470 100644
--- a/reference/selectOP.html
+++ b/reference/selectOP.html
@@ -2,7 +2,7 @@
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="This function models selection in an open pollinating
 plant population. It allows for varying the percentage of
 selfing. The function also provides an option for modeling
-selection as occuring before or after pollination."><title>Select open pollinating plants — selectOP • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Select open pollinating plants — selectOP"><meta property="og:description" content="This function models selection in an open pollinating
+selection as occuring before or after pollination."><title>Select open pollinating plants — selectOP • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Select open pollinating plants — selectOP"><meta property="og:description" content="This function models selection in an open pollinating
 plant population. It allows for varying the percentage of
 selfing. The function also provides an option for modeling
 selection as occuring before or after pollination."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
@@ -16,7 +16,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/selectWithinFam.html b/reference/selectWithinFam.html
index 2009d94f..9fe980e7 100644
--- a/reference/selectWithinFam.html
+++ b/reference/selectWithinFam.html
@@ -1,7 +1,7 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Selects a subset of nInd individuals from each
 full-sib family within a population. Will return all individuals
-from a full-sib family if it has less than or equal to nInd individuals."><title>Select individuals within families — selectWithinFam • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Select individuals within families — selectWithinFam"><meta property="og:description" content="Selects a subset of nInd individuals from each
+from a full-sib family if it has less than or equal to nInd individuals."><title>Select individuals within families — selectWithinFam • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Select individuals within families — selectWithinFam"><meta property="og:description" content="Selects a subset of nInd individuals from each
 full-sib family within a population. Will return all individuals
 from a full-sib family if it has less than or equal to nInd individuals."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/self.html b/reference/self.html
index 820f0cad..98f72556 100644
--- a/reference/self.html
+++ b/reference/self.html
@@ -1,6 +1,6 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content='Creates selfed progeny from each individual in a
-population. Only works when sexes is "no".'><title>Self individuals — self • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Self individuals — self"><meta property="og:description" content='Creates selfed progeny from each individual in a
+population. Only works when sexes is "no".'><title>Self individuals — self • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Self individuals — self"><meta property="og:description" content='Creates selfed progeny from each individual in a
 population. Only works when sexes is "no".'><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/setEBV.html b/reference/setEBV.html
index ccccfbc3..21bcd68e 100644
--- a/reference/setEBV.html
+++ b/reference/setEBV.html
@@ -3,7 +3,7 @@
 slot using output from a genomic selection functions. 
 The genomic estimated values can be either estimated 
 breeding values, estimated genetic values, or 
-estimated general combining values."><title>Set EBV — setEBV • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Set EBV — setEBV"><meta property="og:description" content="Adds genomic estimated values to a populations's EBV 
+estimated general combining values."><title>Set EBV — setEBV • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Set EBV — setEBV"><meta property="og:description" content="Adds genomic estimated values to a populations's EBV 
 slot using output from a genomic selection functions. 
 The genomic estimated values can be either estimated 
 breeding values, estimated genetic values, or 
@@ -18,7 +18,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -144,7 +144,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="co">#Evaluate accuracy</span></span></span>
 <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/cor.html" class="external-link">cor</a></span><span class="op">(</span><span class="fu"><a href="gv.html">gv</a></span><span class="op">(</span><span class="va">pop</span><span class="op">)</span>, <span class="fu"><a href="ebv.html">ebv</a></span><span class="op">(</span><span class="va">pop</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>        est_GV_Trait1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Trait1     0.3229975</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Trait1     0.6280871</span>
 <span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
diff --git a/reference/setMarkerHaplo.html b/reference/setMarkerHaplo.html
index 3b72cee3..b4085f1d 100644
--- a/reference/setMarkerHaplo.html
+++ b/reference/setMarkerHaplo.html
@@ -1,6 +1,6 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Manually sets the haplotypes in a population 
-for all individuals at one or more loci."><title>Set marker haplotypes — setMarkerHaplo • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Set marker haplotypes — setMarkerHaplo"><meta property="og:description" content="Manually sets the haplotypes in a population 
+for all individuals at one or more loci."><title>Set marker haplotypes — setMarkerHaplo • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Set marker haplotypes — setMarkerHaplo"><meta property="og:description" content="Manually sets the haplotypes in a population 
 for all individuals at one or more loci."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/setMisc.html b/reference/setMisc.html
index 10b5fcea..029ca420 100644
--- a/reference/setMisc.html
+++ b/reference/setMisc.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Set miscelaneous information in a population"><title>Set miscelaneous information in a population — setMisc • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Set miscelaneous information in a population — setMisc"><meta property="og:description" content="Set miscelaneous information in a population"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Set miscelaneous information in a population"><title>Set miscelaneous information in a population — setMisc • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Set miscelaneous information in a population — setMisc"><meta property="og:description" content="Set miscelaneous information in a population"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body>
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/setPheno.html b/reference/setPheno.html
index ecefeb2d..92a220ee 100644
--- a/reference/setPheno.html
+++ b/reference/setPheno.html
@@ -1,6 +1,6 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Sets phenotypes for all traits by adding random error
-from a multivariate normal distribution."><title>Set phenotypes — setPheno • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Set phenotypes — setPheno"><meta property="og:description" content="Sets phenotypes for all traits by adding random error
+from a multivariate normal distribution."><title>Set phenotypes — setPheno • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Set phenotypes — setPheno"><meta property="og:description" content="Sets phenotypes for all traits by adding random error
 from a multivariate normal distribution."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/setPhenoGCA.html b/reference/setPhenoGCA.html
index 3dcc11f4..fd3c76c8 100644
--- a/reference/setPhenoGCA.html
+++ b/reference/setPhenoGCA.html
@@ -1,6 +1,6 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Calculates general combining ability from a set of testers and
-returns these values as phenotypes for a population."><title>Set GCA as phenotype — setPhenoGCA • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Set GCA as phenotype — setPhenoGCA"><meta property="og:description" content="Calculates general combining ability from a set of testers and
+returns these values as phenotypes for a population."><title>Set GCA as phenotype — setPhenoGCA • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Set GCA as phenotype — setPhenoGCA"><meta property="og:description" content="Calculates general combining ability from a set of testers and
 returns these values as phenotypes for a population."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/setPhenoProgTest.html b/reference/setPhenoProgTest.html
index 82eb21ea..b133efeb 100644
--- a/reference/setPhenoProgTest.html
+++ b/reference/setPhenoProgTest.html
@@ -2,7 +2,7 @@
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Models a progeny test of individuals in 'pop'. Returns 'pop' with a phenotype
 representing the average performance of their progeny. The phenotype is generated
 by mating individuals in 'pop' to randomly chosen individuals in testPop a
-number of times equal to 'nMatePerInd'."><title>Set progeny test as phenotype — setPhenoProgTest • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Set progeny test as phenotype — setPhenoProgTest"><meta property="og:description" content="Models a progeny test of individuals in 'pop'. Returns 'pop' with a phenotype
+number of times equal to 'nMatePerInd'."><title>Set progeny test as phenotype — setPhenoProgTest • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Set progeny test as phenotype — setPhenoProgTest"><meta property="og:description" content="Models a progeny test of individuals in 'pop'. Returns 'pop' with a phenotype
 representing the average performance of their progeny. The phenotype is generated
 by mating individuals in 'pop' to randomly chosen individuals in testPop a
 number of times equal to 'nMatePerInd'."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
@@ -16,7 +16,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/smithHazel.html b/reference/smithHazel.html
index 5f6ae551..53c4bbf4 100644
--- a/reference/smithHazel.html
+++ b/reference/smithHazel.html
@@ -1,6 +1,6 @@
 <!DOCTYPE html>
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-and phenotypic and genotypic variance-covariance matrices."><title>Calculate Smith-Hazel weights — smithHazel • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Calculate Smith-Hazel weights — smithHazel"><meta property="og:description" content="Calculates weights for Smith-Hazel index given economice weights 
+and phenotypic and genotypic variance-covariance matrices."><title>Calculate Smith-Hazel weights — smithHazel • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Calculate Smith-Hazel weights — smithHazel"><meta property="og:description" content="Calculates weights for Smith-Hazel index given economice weights 
 and phenotypic and genotypic variance-covariance matrices."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/solveMKM.html b/reference/solveMKM.html
index f4eeaf85..a37dc197 100644
--- a/reference/solveMKM.html
+++ b/reference/solveMKM.html
@@ -1,5 +1,5 @@
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 <![endif]--></head><body>
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
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diff --git a/reference/solveMVM.html b/reference/solveMVM.html
index ef780fa8..c4043c28 100644
--- a/reference/solveMVM.html
+++ b/reference/solveMVM.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
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     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
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diff --git a/reference/solveRRBLUP.html b/reference/solveRRBLUP.html
index 48af892d..e81708eb 100644
--- a/reference/solveRRBLUP.html
+++ b/reference/solveRRBLUP.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Solves a univariate mixed model of form \(y=X\beta+Mu+e\)"><title>Solve RR-BLUP — solveRRBLUP • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Solve RR-BLUP — solveRRBLUP"><meta property="og:description" content="Solves a univariate mixed model of form \(y=X\beta+Mu+e\)"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Solves a univariate mixed model of form \(y=X\beta+Mu+e\)"><title>Solve RR-BLUP — solveRRBLUP • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Solve RR-BLUP — solveRRBLUP"><meta property="og:description" content="Solves a univariate mixed model of form \(y=X\beta+Mu+e\)"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/solveRRBLUPMK.html b/reference/solveRRBLUPMK.html
index 79f5295d..05101a6c 100644
--- a/reference/solveRRBLUPMK.html
+++ b/reference/solveRRBLUPMK.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Solves a univariate mixed model with multiple random effects."><title>Solve Multikernel RR-BLUP — solveRRBLUPMK • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Solve Multikernel RR-BLUP — solveRRBLUPMK"><meta property="og:description" content="Solves a univariate mixed model with multiple random effects."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Solves a univariate mixed model with multiple random effects."><title>Solve Multikernel RR-BLUP — solveRRBLUPMK • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Solve Multikernel RR-BLUP — solveRRBLUPMK"><meta property="og:description" content="Solves a univariate mixed model with multiple random effects."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
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diff --git a/reference/solveRRBLUPMV.html b/reference/solveRRBLUPMV.html
index 8d897162..3729ce0e 100644
--- a/reference/solveRRBLUPMV.html
+++ b/reference/solveRRBLUPMV.html
@@ -1,5 +1,5 @@
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-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Solves a multivariate mixed model of form \(Y=X\beta+Mu+e\)"><title>Solve Multivariate RR-BLUP — solveRRBLUPMV • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Solve Multivariate RR-BLUP — solveRRBLUPMV"><meta property="og:description" content="Solves a multivariate mixed model of form \(Y=X\beta+Mu+e\)"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Solves a multivariate mixed model of form \(Y=X\beta+Mu+e\)"><title>Solve Multivariate RR-BLUP — solveRRBLUPMV • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Solve Multivariate RR-BLUP — solveRRBLUPMV"><meta property="og:description" content="Solves a multivariate mixed model of form \(Y=X\beta+Mu+e\)"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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 <![endif]--></head><body>
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/solveRRBLUP_EM.html b/reference/solveRRBLUP_EM.html
index 0d429514..c38db8e7 100644
--- a/reference/solveRRBLUP_EM.html
+++ b/reference/solveRRBLUP_EM.html
@@ -1,6 +1,6 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Solves a univariate mixed model of form \(y=X\beta+Mu+e\) using
-the Expectation-Maximization algorithm."><title>Solve RR-BLUP with EM — solveRRBLUP_EM • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Solve RR-BLUP with EM — solveRRBLUP_EM"><meta property="og:description" content="Solves a univariate mixed model of form \(y=X\beta+Mu+e\) using
+the Expectation-Maximization algorithm."><title>Solve RR-BLUP with EM — solveRRBLUP_EM • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Solve RR-BLUP with EM — solveRRBLUP_EM"><meta property="og:description" content="Solves a univariate mixed model of form \(y=X\beta+Mu+e\) using
 the Expectation-Maximization algorithm."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/solveRRBLUP_EM2.html b/reference/solveRRBLUP_EM2.html
index 3f8c40b3..af81b01d 100644
--- a/reference/solveRRBLUP_EM2.html
+++ b/reference/solveRRBLUP_EM2.html
@@ -1,6 +1,6 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Solves a univariate mixed model of form \(y=X\beta+M_1u_1+M_2u_2+e\) using
-the Expectation-Maximization algorithm."><title>Solve RR-BLUP with EM and 2 random effects — solveRRBLUP_EM2 • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Solve RR-BLUP with EM and 2 random effects — solveRRBLUP_EM2"><meta property="og:description" content="Solves a univariate mixed model of form \(y=X\beta+M_1u_1+M_2u_2+e\) using
+the Expectation-Maximization algorithm."><title>Solve RR-BLUP with EM and 2 random effects — solveRRBLUP_EM2 • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Solve RR-BLUP with EM and 2 random effects — solveRRBLUP_EM2"><meta property="og:description" content="Solves a univariate mixed model of form \(y=X\beta+M_1u_1+M_2u_2+e\) using
 the Expectation-Maximization algorithm."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/solveRRBLUP_EM3.html b/reference/solveRRBLUP_EM3.html
index d85f5bad..1f3e063a 100644
--- a/reference/solveRRBLUP_EM3.html
+++ b/reference/solveRRBLUP_EM3.html
@@ -1,6 +1,6 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Solves a univariate mixed model of form \(y=X\beta+M_1u_1+M_2u_2+M_3u_3+e\) using
-the Expectation-Maximization algorithm."><title>Solve RR-BLUP with EM and 3 random effects — solveRRBLUP_EM3 • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Solve RR-BLUP with EM and 3 random effects — solveRRBLUP_EM3"><meta property="og:description" content="Solves a univariate mixed model of form \(y=X\beta+M_1u_1+M_2u_2+M_3u_3+e\) using
+the Expectation-Maximization algorithm."><title>Solve RR-BLUP with EM and 3 random effects — solveRRBLUP_EM3 • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Solve RR-BLUP with EM and 3 random effects — solveRRBLUP_EM3"><meta property="og:description" content="Solves a univariate mixed model of form \(y=X\beta+M_1u_1+M_2u_2+M_3u_3+e\) using
 the Expectation-Maximization algorithm."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/solveUVM.html b/reference/solveUVM.html
index 78f3d4f9..72d39d09 100644
--- a/reference/solveUVM.html
+++ b/reference/solveUVM.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Solves a univariate mixed model of form \(y=X\beta+Zu+e\)"><title>Solve Univariate Model — solveUVM • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Solve Univariate Model — solveUVM"><meta property="og:description" content="Solves a univariate mixed model of form \(y=X\beta+Zu+e\)"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Solves a univariate mixed model of form \(y=X\beta+Zu+e\)"><title>Solve Univariate Model — solveUVM • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Solve Univariate Model — solveUVM"><meta property="og:description" content="Solves a univariate mixed model of form \(y=X\beta+Zu+e\)"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body>
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/transMat.html b/reference/transMat.html
index df4e36b1..b768bf56 100644
--- a/reference/transMat.html
+++ b/reference/transMat.html
@@ -4,7 +4,7 @@
 sampled from a standard normal distribution to produce
 correlated deviates with an arbitrary correlation 
 of R. If R is not positive semi-definite, the function 
-returns smoothing and returns a warning (see details)."><title>Linear transformation matrix — transMat • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Linear transformation matrix — transMat"><meta property="og:description" content="Creates an m by m linear transformation matrix that 
+returns smoothing and returns a warning (see details)."><title>Linear transformation matrix — transMat • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Linear transformation matrix — transMat"><meta property="og:description" content="Creates an m by m linear transformation matrix that 
 can be applied to n by m uncorrelated deviates 
 sampled from a standard normal distribution to produce
 correlated deviates with an arbitrary correlation 
@@ -20,7 +20,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -114,8 +114,8 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="co"># Measure the sample correlation</span></span></span>
 <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/cor.html" class="external-link">cor</a></span><span class="op">(</span><span class="va">Y</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>           [,1]      [,2]</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [1,] 1.0000000 0.4989095</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [2,] 0.4989095 1.0000000</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1,] 1.0000000 0.5236831</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [2,] 0.5236831 1.0000000</span>
 <span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
diff --git a/reference/usefulness.html b/reference/usefulness.html
index a66d8828..f014649f 100644
--- a/reference/usefulness.html
+++ b/reference/usefulness.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Calculates the usefulness criterion"><title>Usefulness criterion — usefulness • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Usefulness criterion — usefulness"><meta property="og:description" content="Calculates the usefulness criterion"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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 <![endif]--></head><body>
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/varA.html b/reference/varA.html
index c7d90edd..d5c82a54 100644
--- a/reference/varA.html
+++ b/reference/varA.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Returns additive variance for all traits"><title>Additive variance — varA • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Additive variance — varA"><meta property="og:description" content="Returns additive variance for all traits"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Returns additive variance for all traits"><title>Additive variance — varA • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Additive variance — varA"><meta property="og:description" content="Returns additive variance for all traits"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/varAA.html b/reference/varAA.html
index 05676a8a..f01ee273 100644
--- a/reference/varAA.html
+++ b/reference/varAA.html
@@ -1,6 +1,6 @@
 <!DOCTYPE html>
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-variance for all traits"><title>Additive-by-additive epistatic variance — varAA • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Additive-by-additive epistatic variance — varAA"><meta property="og:description" content="Returns additive-by-additive epistatic
+variance for all traits"><title>Additive-by-additive epistatic variance — varAA • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Additive-by-additive epistatic variance — varAA"><meta property="og:description" content="Returns additive-by-additive epistatic
 variance for all traits"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/varD.html b/reference/varD.html
index 8345b28d..7a3c7dcb 100644
--- a/reference/varD.html
+++ b/reference/varD.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Returns dominance variance for all traits"><title>Dominance variance — varD • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Dominance variance — varD"><meta property="og:description" content="Returns dominance variance for all traits"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Returns dominance variance for all traits"><title>Dominance variance — varD • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Dominance variance — varD"><meta property="og:description" content="Returns dominance variance for all traits"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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 <![endif]--></head><body>
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -86,8 +86,8 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="co">#Create population</span></span></span>
 <span class="r-in"><span><span class="va">pop</span> <span class="op">=</span> <span class="fu"><a href="newPop.html">newPop</a></span><span class="op">(</span><span class="va">founderPop</span>, simParam<span class="op">=</span><span class="va">SP</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="fu">varD</span><span class="op">(</span><span class="va">pop</span>, simParam<span class="op">=</span><span class="va">SP</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>           Trait1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Trait1 0.2133749</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>            Trait1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Trait1 0.07623885</span>
 <span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
diff --git a/reference/varG.html b/reference/varG.html
index 88763347..498e76a8 100644
--- a/reference/varG.html
+++ b/reference/varG.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Returns total genetic variance for all traits"><title>Total genetic variance — varG • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Total genetic variance — varG"><meta property="og:description" content="Returns total genetic variance for all traits"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Returns total genetic variance for all traits"><title>Total genetic variance — varG • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Total genetic variance — varG"><meta property="og:description" content="Returns total genetic variance for all traits"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body>
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/varP.html b/reference/varP.html
index ef620b1e..e7344920 100644
--- a/reference/varP.html
+++ b/reference/varP.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Returns phenotypic variance for all traits"><title>Phenotypic variance — varP • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Phenotypic variance — varP"><meta property="og:description" content="Returns phenotypic variance for all traits"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Returns phenotypic variance for all traits"><title>Phenotypic variance — varP • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Phenotypic variance — varP"><meta property="og:description" content="Returns phenotypic variance for all traits"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body>
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -82,8 +82,8 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="co">#Create population</span></span></span>
 <span class="r-in"><span><span class="va">pop</span> <span class="op">=</span> <span class="fu"><a href="newPop.html">newPop</a></span><span class="op">(</span><span class="va">founderPop</span>, simParam<span class="op">=</span><span class="va">SP</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="fu">varP</span><span class="op">(</span><span class="va">pop</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>         Trait1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Trait1 1.86957</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>          Trait1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Trait1 2.106527</span>
 <span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
diff --git a/reference/writePlink.html b/reference/writePlink.html
index 00ea9f2f..8c617fbc 100644
--- a/reference/writePlink.html
+++ b/reference/writePlink.html
@@ -5,7 +5,7 @@
 position as stored in AlphaSimR and not an actual base pair 
 position. This is because AlphaSimR doesn't track base pair 
 positions, only relative positions for the loci used in the 
-simulation."><title>Writes a Pop-class as PLINK files — writePlink • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Writes a Pop-class as PLINK files — writePlink"><meta property="og:description" content="Writes a Pop-class to PLINK PED and MAP files. The arguments 
+simulation."><title>Writes a Pop-class as PLINK files — writePlink • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Writes a Pop-class as PLINK files — writePlink"><meta property="og:description" content="Writes a Pop-class to PLINK PED and MAP files. The arguments 
 for this function were chosen for consistency with 
 RRBLUP2. The base pair coordinate will the locus
 position as stored in AlphaSimR and not an actual base pair 
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     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
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diff --git a/reference/writeRecords.html b/reference/writeRecords.html
index f2ab339d..68a749ae 100644
--- a/reference/writeRecords.html
+++ b/reference/writeRecords.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Saves a population's phenotypic and marker data to a directory."><title>Write data records — writeRecords • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Write data records — writeRecords"><meta property="og:description" content="Saves a population's phenotypic and marker data to a directory."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Saves a population's phenotypic and marker data to a directory."><title>Write data records — writeRecords • AlphaSimR</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Write data records — writeRecords"><meta property="og:description" content="Saves a population's phenotypic and marker data to a directory."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AlphaSimR</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.2</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.5.3</small>
 
     
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diff --git a/search.json b/search.json
index 814fb078..1a9fe1e9 100644
--- a/search.json
+++ b/search.json
@@ -1 +1 @@
-[{"path":"https://gaynorr.github.io/AlphaSimR/articles/intro.html","id":"example-breeding-program","dir":"Articles","previous_headings":"","what":"Example Breeding Program","title":"Introduction to AlphaSimR","text":"simplified animal breeding program modeling 20 discrete generations selection. generation consists 1000 animals, 500 male 500 female. generation, best 25 males selected basis genetic value single polygenic trait mated females produce 1000 replacement animals. quantitative trait selection modeled controlled 10,000 QTL. QTL equally split across 10 chromosome groups 1,000 QTL per chromosome. mean genetic value individuals generation recorded construct plot genetic gain per generation.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/articles/intro.html","id":"creating-founder-haplotypes","dir":"Articles","previous_headings":"","what":"Creating Founder Haplotypes","title":"Introduction to AlphaSimR","text":"first step simulation creating set founder haplotypes. founder haplotypes used form genome genotypes animals first generation. genotypes descendants derived haplotypes using simulated mating genetic recombination. simulation, single line code needed create haplotypes, given . code uses quickHaplo function generate initial haplotypes. quickHaplo function generates haplotypes randomly sampling 1s 0s. approach equivalent modeling population linkage Hardy-Weinberg equilibrium allele frequencies 0.5. approach rapid generate realistic haplotypes. makes approach great prototyping code, ill-suited types simulations. preferred choice simulating realistic haplotypes use runMacs function. runMacs function wrapper MaCS software, coalescent simulation program included within distribution AlphaSimR (Chen, Marjoram, Wall 2009). MaCS software used AlphaSimR simulate bi-allelic genome sequences according population demographic history. runMacs function allows user specify one several predefined population histories supply population history. list currently available population histories can found runMacs help document. alternative choice providing realistic initial haplotypes import newMapPop function. function allows user import haplotypes can generated another software package taken directly real marker data.","code":"founderPop = quickHaplo(nInd=1000, nChr=10, segSites=1000)"},{"path":"https://gaynorr.github.io/AlphaSimR/articles/intro.html","id":"setting-simulation-parameters","dir":"Articles","previous_headings":"","what":"Setting Simulation Parameters","title":"Introduction to AlphaSimR","text":"second step setting global parameters simulation. can done three lines code. first line initializes object containing simulation parameters. object must initialized founder haplotypes created previous step code given . output function object class SimParam saved name SP. name SP almost always used, many AlphaSimR functions use argument called “simParam” default value NULL. leave value NULL, functions search global environment object called SP use function’s argument. means use SP, won’t need specify value “simParam” argument. next line code defines quantitative trait used selection. mentioned previous section, trait controlled 1000 QTL per chromosome. rest function arguments left defaults, include trait mean zero variance one unit. ‘’ end SP$addTraitA indicates trait’s QTL additive effects. traits AlphaSimR include additive effects. Traits may also include combination three additional types effects: dominance (“D”), epistasis (“E”), genotype--environment (“G”). specific combination trait effects requested using function appropriate letter ending. example, trait additive epistasis effects can requested using SP$addTraitAE. following trait types currently offered: “”, “AD”, “AE”, “AG”, “ADE”, “ADG”, “AEG”, “ADEG”. final line code defines sexes determined simulation. Sex systematically assigned (.e. male, female, male, …). Systematic assignment used ensure always equal numbers males females.","code":"SP = SimParam$new(founderPop) SP$addTraitA(nQtlPerChr=1000) SP$setSexes(\"yes_sys\")"},{"path":"https://gaynorr.github.io/AlphaSimR/articles/intro.html","id":"modeling-the-breeding-program","dir":"Articles","previous_headings":"","what":"Modeling the Breeding Program","title":"Introduction to AlphaSimR","text":"now ready start modeling breeding program. begin, need generate initial population animals. step take haplotypes founderPop information SP create object Pop-class. Pop-class object represents population individuals. population important units AlphaSimR, AlphaSimR functions use one populations argument. regard, AlphaSimR can thought modeling discrete populations basic unit. contrasts predecessor, used discrete generations. Populations fixed unit AlphaSimR. Many functions AlphaSimR take population argument, modify population, return modified population. Populations can also used “directly”. example, can pull individuals form new (sub-)populations using [] can merge populations together using c(). functionality particularly useful performing tasks AlphaSimR lacks built-function. However, example breeding program presented easily modeled using built-functions. continuing model breeding program, first think data ’ll need examining results next stage. must expressly request relevant data saved. AlphaSimR designed way increased speed reduced memory usage. example plot generation mean time desired. needed construct plot vector containing mean generation. start vector, mean current generation saved “genMean”. subsequent generation, mean generation added “genMean”. Measuring mean current generation accomplished code . final lines code modeling 20 generations selection mating. AlphaSimR host functions modeling selection mating. example selectCross function used, efficiently combines selection mating single function call. function actually uses two separate function AlphaSimR, selectInd randCross selection mating, respectively. model multiple generations selection, function call placed within loop line code tracking population mean. Using loop makes code easier read avoids needless duplication. loop “pop” overwritten generation. keeps memory usage low keeps code simple. However, user needed retain older populations several alternative approaches adopted. approaches include giving population unique name, storing populations elements list, dynamically growing populations c(). code loop given .","code":"pop = newPop(founderPop) genMean = meanG(pop) for(generation in 1:20){   pop = selectCross(pop=pop, nFemale=500, nMale=25, use=\"gv\", nCrosses=1000)   genMean = c(genMean, meanG(pop)) }"},{"path":"https://gaynorr.github.io/AlphaSimR/articles/intro.html","id":"examining-the-results","dir":"Articles","previous_headings":"","what":"Examining the Results","title":"Introduction to AlphaSimR","text":"last step simulation examining results. example one result: vector population means generation. examine result, code produce basic line plot.","code":"plot(0:20, genMean, xlab=\"Generation\", ylab=\"Mean Genetic Value\", type=\"l\")"},{"path":"https://gaynorr.github.io/AlphaSimR/articles/intro.html","id":"full-code","dir":"Articles","previous_headings":"","what":"Full Code","title":"Introduction to AlphaSimR","text":"","code":"library(AlphaSimR) # Creating Founder Haplotypes founderPop = quickHaplo(nInd=1000, nChr=10, segSites=1000)  # Setting Simulation Parameters SP = SimParam$new(founderPop) SP$addTraitA(nQtlPerChr=1000) SP$setSexes(\"yes_sys\")  # Modeling the Breeding Program pop = newPop(founderPop) genMean = meanG(pop) for(generation in 1:20){   pop = selectCross(pop=pop, nFemale=500, nMale=25, use=\"gv\", nCrosses=1000)   genMean = c(genMean, meanG(pop)) }  # Examining the Results plot(0:20, genMean, xlab=\"Generation\", ylab=\"Mean Genetic Value\", type=\"l\")"},{"path":[]},{"path":"https://gaynorr.github.io/AlphaSimR/articles/traits.html","id":"genotype-dosage-scaling","dir":"Articles","previous_headings":"","what":"Genotype Dosage Scaling","title":"Traits in AlphaSimR","text":"AlphaSimR defines individual’s raw genotype dosage number copies “1” allele locus. Since loci AlphaSimR biallelic alleles “0” “1”, definition raw genotype dosage fully explains individual’s genotype. number copies “0” allele just individual’s ploidy level minus raw genotype dosage. usually rather irrelevant detail, user want model diploid organism whose ploidy level always two. However, AlphaSimR can also used model wide range autopolyploid organisms even allows mixing ploidy levels within simulation. means allowable range raw genotype dosage fixed value software must account fact. AlphaSimR accounts different levels ploidy scaling organism’s genotype dosage accordance ploidy level. primary motivation using scaled dosages unify user inputs. use scaled dosages can also make easier compare simulations different levels ploidy. However, user must use care making comparisons, underlying assumptions used model may valid. use scaled genotype dosages implies individual’s genetic value depends relative ratio alleles independent organism’s ploidy level. traits organisms evidence support assumption least reject , also plenty evidence clearly rejecting assumption traits (Gallais 2003). Thus, direct comparisons possible AlphaSimR always biologically relevant. However, vast majority users won’t running simulation depends assumption, information presented solely purpose understanding functions presented following sections. two types scaled genotype dosages AlphaSimR: additive dominance. explanation given . followed table providing example dosage scaling diploid autotetraploid organisms. scaled additive genotype dosage (\\(x_A\\)) shown equation (2). equation linearly scales relative dosage set values opposing homozygotes -1 1. \\[\\begin{equation} x_A = \\big( x - \\tfrac{ploidy}{2} \\big) \\big( \\tfrac{2}{ploidy} \\big) \\end{equation}\\] scaled dominance genotype dosage (\\(x_D\\)) shown equation (3). equation uses non-linear scaling fit value opposing homozygotes 0 middlemost heterozygote 1. middlemost heterozygote genotype equal ratio “0” “1” alleles. diploid organism, scaled dominance genotype dosage matches classic parameterization dominance. autopolyploid organisms, scaled dominance genotype dosage consistent digenic dominance (discussed later). \\[\\begin{equation} x_D = x \\big( ploidy - x \\big) \\big( \\tfrac{2}{ploidy} \\big)^2 \\end{equation}\\] Table 1 provides example raw scaled genotype dosages diploid autotetraploid organism. diploid tetraploid columns represent raw genotype dosages respective organisms. additive dominance columns represent corresponding scaled genotype dosages. table shows 0, 1 2 genotypes diploid organism treated equivalent 0, 2 4 genotypes autotetraploid organism.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/articles/traits.html","id":"additive-effects","dir":"Articles","previous_headings":"","what":"Additive Effects","title":"Traits in AlphaSimR","text":"\\[\\begin{equation} (x) = \\sum x_A \\end{equation}\\] function additive effects given equation (4). right-hand side summation QTL product additive effect (\\(\\)) scaled additive dosage (\\(x_A\\)). equation equivalent parameterizations classic quantitative trait models. unique aspect additive effects AlphaSimR sampling effects. Additive effects sampled two stages. first stage involves sampling initial values similar methods used stochastic simulation software programs. second stage unique. stage involves scaling magnitude initial values achieve desired genetic variance, either total additive genetic variance. first stage sampling additive effects setting initial values effects. Initial values sampled either standard normal distribution gamma distribution. using gamma distribution, user specifies shape parameter scale parameter set 1. deviates sampled gamma distribution randomly assigned either positive negative sign. Random assignment sign results expected distribution symmetric distribution mean 0. second stage scaling magnitude effects achieve user specified genetic variance. user specified genetic variance can either total additive. scaling procedure involves just additive effect, also dominance epistatic effects trait includes effects well. procedure works first calculating variance founder population using initially sampled effects calculating scaling constant applied effects achieve desired variance founder population. scaling constant equals square-root target genetic variance (total additive) divided square-root initial genetic variance (total additive). Note founder population population user uses initialize simulation parameters object. Scaling magnitude effects allows AlphaSimR build simulations trait values matching real-world counterparts. example, user simulating grain yield plant species likely estimates means variances tons per hectare. user can use create simulation values. primary benefit matching values make interpretation simulation results intuitive. significance results apparent user can work scale familiar . also allows user easily identify potential flaws simulation values move outside range biologically acceptable values.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/articles/traits.html","id":"dominance-effects","dir":"Articles","previous_headings":"","what":"Dominance Effects","title":"Traits in AlphaSimR","text":"\\[\\begin{equation} D(x) = \\sum d x_D \\end{equation}\\] function dominance effects given equation (5). right-hand side equation summation QTL product dominance effect (\\(d\\)) scaled dominance dosage (\\(x_D\\)). equation equivalent parameterization dominance classic quantitative trait models diploid organisms. additive effects, method sampling dominance effects AlphaSimR requires special attention. Dominance effects calculated AlphaSimR using concept dominance degrees. formula calculation given equation (6). equation shows dominance effect (\\(d\\)) locus dominance degree (\\(\\delta\\)) locus times absolute value additive effect (\\(\\)). \\[\\begin{equation} d = \\delta \\left| \\right| \\end{equation}\\] rationale behind using dominance degrees intuitive biological interpretation diploid organisms. example, dominance degree 0 represents dominance additive model. dominance degree 1 corresponds complete dominance. Dominance degrees 0 1 correspond partial dominance, values 1 correspond -dominance. Dominance effects, additive effects, sampled two stages. first stage sampling initial values second stage scaling magnitude values. sampling initial effects involves two user supplied parameters, mean variance normal distribution used sample dominance degrees. dominance degrees used conjunction additive effects calculate dominance effects. scaling procedure performed described additive effects section calculate scaling constant. scaling constant directly applied dominance effects. Note scaling changes value dominance effect, change value dominance degree. means specification dominance degree distribution independent requested genetic variance. Dominance effects become complicated discussing polyploid organisms. polyploids additional heterozygous genotypes. example, autotetraploid organism two homozygous genotypes (0 4) three heterozygous genotypes (1, 2 3). additional heterozygous genotype requires additional dominance parameter obtain fully parameterized model. Several different parameterizations used polyploids full discussion parameterizations outside scope document. Interested readers refer Gallais’s textbook details (2003). AlphaSimR include additional term dominance model polyploids, make use fully parameterized model. Instead, AlphaSimR uses digenic dominance model ploidy levels due use scaled dominance genotype dosages. model chosen provides consistency user interface internal coding regardless ploidy level provides reasonable approximation partial dominance highly polygenic traits. unfortunate side effect dominance model polyploids previously described interpretation dominance degrees breaks. Consider single QTL additive effect 1 dominance degree 1. genotypes genetic values example diploid autotetraploid organism given Table 2. diploid organism, heterozygous genotype equivalent best homozygote, dominance degree 1 indicates complete dominance. However, autotetraploid organism three heterozygous genotypes. value middlemost heterozygous genotype equivalent best homozygote, heterozygous genotype highest value. heterozygous genotype highest value better best homozygote, dominance degree 1 actually represents -dominance autotetraploid.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/articles/traits.html","id":"epistatic-effects","dir":"Articles","previous_headings":"","what":"Epistatic Effects","title":"Traits in AlphaSimR","text":"\\[\\begin{equation} E(x) = \\sum e x_{A_1} x_{A_2} \\end{equation}\\] function epistatic effects given equation (7). summation right-hand side pairs QTLs, AlphaSimR uses simplified model epistasis restricts epistatic interactions pairs loci. QTL must present one one pair, number pairs equal half number QTL. remaining elements right-hand side equation (7) epistatic effects (\\(e\\)), scaled additive dosage first locus pair (\\(x_{A_1}\\)) scaled additive dosage second locus pair (\\(x_{A_2}\\)). epistatic model equation (7) somewhat constrained. model allows epistasis pairs loci models additive--additive epistasis. motivation behind using constrained model maintain computational tractability using large numbers QTL. dominance model, model considered reasonable approximation complicated reality. sampling epistatic effects similar sampling additive effects one additional user specified parameter relative ratio additive--additive epistatic variance. relative ratio refers ratio additive--additive epistatic variance additive variance. parameter sets variance epistatic effects. Specifically, variance effects set value expected achieve desired ratio random mating population whose QTL linkage equilibrium allele frequency 0.5. Note populations, including simulated populations, meet assumptions, observed relative ratio additive additive--additive epistatic variance unlikely match requested ratio. observed additive--additive epistatic variance typically smaller, value maximized allele frequency 0.5. Note unselected bi-parental populations derived inbred parents expected allele frequencies 0.5 segregating alleles. Thus, populations ideal estimating reasonable value relative ratio additive--additive epistatic variance.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/articles/traits.html","id":"genotype-by-environment-effects","dir":"Articles","previous_headings":"","what":"Genotype-by-Environment Effects","title":"Traits in AlphaSimR","text":"\\[\\begin{equation} G(x, w) = w b(x) \\end{equation}\\] \\[\\begin{equation} b(x) = \\mu_G + \\sum g x_A \\end{equation}\\] function genotype--environment effects given equations (8) (9). right-hand side equation (8) contains two parts: environmental covariate (\\(w\\)) genotype specific slope (\\(b(x)\\)). formula genotype specific slope shown equation (9). right-hand side equation includes intercept value (\\(\\mu_G\\)) summation QTL product genotype--environment effect (\\(g\\)) scaled additive dosage (\\(x_A\\)). following paragraphs explain equations model genotype--environment interactions. Initially, explanation cover case population genotype--environment interaction variance, environmental variance. explanation parameters equations changed model genotype--environment interaction variance environmental variance given next section. begin, description variables equations sampled needed. much easier understand formulas come together model genotype--environment interactions understood variables represent. environmental covariate (\\(w\\)) equation (8) represents environmental component genotype--environment interaction. value environmental covariate randomly sampled standard normal distribution. definition, means average value environmental covariate zero variance one. average value environmental covariate considered target environment. Thus, value equation (8) target environment always zero. genotype specific slope equation (9) represents genetic component genotype--environment interaction. astute reader notice equation similar equation additive trait. Indeed, genotype specific slope really just additive trait. term \\(\\mu_G\\) serves similar role \\(\\mu\\) equation (1) summation right-hand side equation (9) similar function additive effects equation (4). Also like additive trait, effects genotype specific slope scaled achieve specific mean variance founder population. case, mean set zero variance set user specified genotype--environment interaction variance. understand environmental covariate genotype specific slope model genotype--environment interactions helps review properties variables. environmental covariate just random variable mean zero variance one. genotype specific slope also random variable, regards founder population, mean zero variance equal genotype--environment variance. means equation (8) just product two random variables. random variables independent, formula variance product given equation . \\[\\begin{equation} Var(w b) = E[w]^2 Var(b) + Var(w) E[b]^2 + Var(w) Var(b) \\end{equation}\\] Equation (10) gives variance product \\(w\\) \\(b\\) equation (8). term \\(Var()\\) indicates variance variable term \\(E[]\\) indicates expectation (mean) variable. founder population, expectations \\(w\\) \\(b\\) zero, first two terms right-hand side equation drop . Equation (10) reduces product two variances. variance \\(w\\) one variance \\(b\\) equals genotype--environment interaction variance, variance equation (8) equals genotype--environment interaction variance equivalent variance genotype specific slopes. must repeated description limited founder population. important point, mean variance genotype specific slope can different populations since genetic control.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/articles/traits.html","id":"adding-environmental-variance","dir":"Articles","previous_headings":"Genotype-by-Environment Effects","what":"Adding Environmental Variance","title":"Traits in AlphaSimR","text":"genotype--environment effects model described altered model founder population non-zero environmental variance. equations remain relevant altered model sampling distributions effects equations changed. Specifically, variance environmental covariate set environmental variance (\\(\\sigma_E^2\\)) genotype specific slope set different mean variance. mean genotype specific slope set one variance set genotype--environment interaction variance divided environmental variance (\\(\\tfrac{\\sigma_{GE}^2}{\\sigma_E^2}\\)). logic behind modifications becomes clear examination equation (10). right-hand side equation (10) contains three terms. first term equals zero, environmental covariate mean zero (.e. \\(E[w] = 0\\)). second term equals environmental variance, mean genotype specific slope equals one variance environmental covariate equals environmental variance (.e. \\(E[b] = 1\\) \\(Var(w) = \\sigma_E^2\\)). Finally, value last term equals genotype--environment interaction variance (.e. \\(Var(w) Var(b) = \\sigma_E^2 \\tfrac{\\sigma_{GE}^2}{\\sigma_E^2} = \\sigma_{GE}^2\\)). examination equation (10) also shows environmental genotype--environment interaction variances populations specific parameters genetic control. example, population higher average genotype specific slope also higher value second term equation (10). population thus higher environmental variance even though environment changed. Likewise, amount genotype--environment interaction variance depends variance genotype specific slope.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/articles/traits.html","id":"relationship-to-finlay-wilkinson-regression","dir":"Articles","previous_headings":"Genotype-by-Environment Effects","what":"Relationship to Finlay-Wilkinson Regression","title":"Traits in AlphaSimR","text":"AlphaSimR’s model genotype--environment effects effectively biological model Finlay-Wilkinson regression. Finlay-Wilkinson regression classic technique analyzing genotype--environment interactions (Finlay Wilkinson 1963). simplest form, individual’s genotype--environment interaction reduced intercept slope. slope Finlay-Wilkinson regression roughly equivalent genotype specific slope equation (9). intercept Finlay-Wilkinson regression roughly equivalent genetic value individual target environment. Initially, similarity two models intentional. model used AlphaSimR originates model used Gaynor et al. (2017). model treated QTL’s additive effect random variable whose value depended value environmental covariate. model roughly equivalent AlphaSimR’s model founder population zero environmental variance. difference models AlphaSimR scales effects exactly achieve desired variance Gaynor et al. model randomly sampled effects expectation sampled effects equaled desired variance. realized later slight change model, described , introduce specified amount environmental variance modifications result model properties matching measured Finlay-Wilkinson regression.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/articles/traits.html","id":"user-interaction","dir":"Articles","previous_headings":"Genotype-by-Environment Effects","what":"User Interaction","title":"Traits in AlphaSimR","text":"AlphaSimR users directly observe set value environmental covariate. Instead, indirectly set value providing randomly sampled p-value environment. AlphaSimR uses p-value calculate appropriate value \\(w\\) level environmental variance. Users note p-values follow uniform distribution range zero one, recommended users randomly generate p-values using R’s built-runif function. p-value 0.5 corresponds \\(w\\) equaling zero equivalent target environment. user supply p-value, AlphaSimR sample one random. Genetic values genetic variances reported AlphaSimR always target environment. Since target environment corresponds \\(w\\) equaling zero, equation (8) effectively ignored calculations. values phenotypes phenotypic variance ever reflect contribution genotype--environment interaction.","code":""},{"path":[]},{"path":"https://gaynorr.github.io/AlphaSimR/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Chris Gaynor. Author, maintainer. Gregor Gorjanc. Contributor. John Hickey. Contributor. Daniel Money. Contributor. David Wilson. Contributor. Thiago Oliveira. Contributor. Audrey Martin. Contributor. Philip Greenspoon. Contributor.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Gaynor RC, Gorjanc G, Hickey JM (2021). “AlphaSimR: R package breeding program simulations.” G3 Gene|Genomes|Genetics, 11(jkaa07). https://doi.org/10.1093/g3journal/jkaa017.","code":"@Article{,   title = {AlphaSimR: an R package for breeding program simulations},   author = {R Chris Gaynor and Gregor Gorjanc and John M Hickey},   journal = {G3 Gene|Genomes|Genetics},   year = {2021},   volume = {11},   number = {jkaa07},   issue = {2},   url = {https://doi.org/10.1093/g3journal/jkaa017}, }"},{"path":"https://gaynorr.github.io/AlphaSimR/index.html","id":"readme","dir":"","previous_headings":"","what":"Breeding Program Simulations","title":"Breeding Program Simulations","text":"successor ‘AlphaSim’ software breeding program simulation (Faux et al., 2016; https://doi.org/10.3835/plantgenome2016.02.0013). Used stochastic simulations breeding programs level DNA sequence every individual. Contained wide range functions modeling common tasks breeding program, selection crossing. functions allow constructing simulations highly complex plant animal breeding programs via scripting R software environment. simulations can used evaluate overall breeding program performance conduct research breeding program design, implementation genomic selection. Included ‘Markovian Coalescent Simulator’ (‘MaCS’) fast simulation biallelic sequences according population demographic history (Chen et al., 2009; https://doi.org/10.1101/gr.083634.108).","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/index.html","id":"publication","dir":"","previous_headings":"","what":"Publication","title":"Breeding Program Simulations","text":"Gaynor, R. Chris, Gregor Gorjanc, John M. Hickey. 2021. AlphaSimR: R package breeding program simulations. G3 Gene|Genomes|Genetics 11(2):jkaa017. https://doi.org/10.1093/g3journal/jkaa017.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/index.html","id":"download","dir":"","previous_headings":"","what":"Download","title":"Breeding Program Simulations","text":"AlphaSimR available CRAN. install use: development version AlphaSimR (potentially unstable) can accessed devel branch GitHub. install use: install vignettes use:","code":"install.packages('AlphaSimR') devtools::install_github(repo=\"gaynorr/AlphaSimR@devel\") devtools::install_github(repo=\"gaynorr/AlphaSimR@devel\", build_vignettes=TRUE)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/AlphaSimR-package.html","id":null,"dir":"Reference","previous_headings":"","what":"AlphaSimR: Breeding Program Simulations — AlphaSimR-package","title":"AlphaSimR: Breeding Program Simulations — AlphaSimR-package","text":"successor 'AlphaSim' software breeding program  simulation [Faux et al. (2016) <doi:10.3835/plantgenome2016.02.0013>].  Used stochastic simulations breeding programs level DNA  sequence every individual. Contained wide range functions  modeling common tasks breeding program, selection crossing.  functions allow constructing simulations highly complex plant  animal breeding programs via scripting R software environment.  simulations can used evaluate overall breeding program performance  conduct research breeding program design, implementation  genomic selection. Included 'Markovian Coalescent Simulator' ('MaCS')  fast simulation biallelic sequences according population  demographic history [Chen et al. (2009) <doi:10.1101/gr.083634.108>]. Please see introductory vignette instructions using package.  vignette can viewed using following command:  vignette(\"intro\",package=\"AlphaSimR\")","code":""},{"path":[]},{"path":"https://gaynorr.github.io/AlphaSimR/reference/AlphaSimR-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"AlphaSimR: Breeding Program Simulations — AlphaSimR-package","text":"Maintainer: Chris Gaynor gaynor.robert@hotmail.com (ORCID) contributors: Gregor Gorjanc (ORCID) [contributor] John Hickey (ORCID) [contributor] Daniel Money (ORCID) [contributor] David Wilson [contributor] Thiago Oliveira (ORCID) [contributor] Audrey Martin (ORCID) [contributor] Philip Greenspoon (ORCID) [contributor]","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/HybridPop-class.html","id":null,"dir":"Reference","previous_headings":"","what":"Hybrid population — HybridPop-class","title":"Hybrid population — HybridPop-class","text":"lightweight version Pop-class hybrid lines. Memory saved storing genotypic data.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/HybridPop-class.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Hybrid population — HybridPop-class","text":"","code":"# S4 method for HybridPop [(x, i)  # S4 method for HybridPop c(x, ...)  isHybridPop(x)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/HybridPop-class.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Hybrid population — HybridPop-class","text":"x 'HybridPop' index individuals ... additional 'HybridPop' objects","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/HybridPop-class.html","id":"methods-by-generic-","dir":"Reference","previous_headings":"","what":"Methods (by generic)","title":"Hybrid population — HybridPop-class","text":"[: Extract HybridPop using index id c(HybridPop): Combine multiple HybridPops","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/HybridPop-class.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Hybrid population — HybridPop-class","text":"isHybridPop(): Test object HybridPop class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/HybridPop-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"Hybrid population — HybridPop-class","text":"nInd number individuals id individual's identifier mother identifier individual's mother father identifier individual's father nTraits number traits gv matrix genetic values. using GxE traits, gv reflects gv p=0.5. Dimensions nInd nTraits. pheno matrix phenotypic values. Dimensions nInd nTraits. gxe list containing GxE slopes GxE traits","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/LociMap-class.html","id":null,"dir":"Reference","previous_headings":"","what":"Loci metadata — LociMap-class","title":"Loci metadata — LociMap-class","text":"used SNPs QTLs","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/LociMap-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"Loci metadata — LociMap-class","text":"nLoci total number loci lociPerChr number loci per chromosome lociLoc physical position loci name optional name LociMap object","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/MapPop-class.html","id":null,"dir":"Reference","previous_headings":"","what":"Raw population with genetic map — MapPop-class","title":"Raw population with genetic map — MapPop-class","text":"Extends RawPop-class add genetic map. first object created simulation. used creating initial populations setting traits SimParam.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/MapPop-class.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Raw population with genetic map — MapPop-class","text":"","code":"# S4 method for MapPop [(x, i)  # S4 method for MapPop c(x, ...)  isMapPop(x)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/MapPop-class.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Raw population with genetic map — MapPop-class","text":"x 'MapPop' object index individuals ... additional 'MapPop' objects","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/MapPop-class.html","id":"methods-by-generic-","dir":"Reference","previous_headings":"","what":"Methods (by generic)","title":"Raw population with genetic map — MapPop-class","text":"[: Extract MapPop index c(MapPop): Combine multiple MapPops","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/MapPop-class.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Raw population with genetic map — MapPop-class","text":"isMapPop(): Test object MapPop class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/MapPop-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"Raw population with genetic map — MapPop-class","text":"genMap list chromosome genetic maps centromere vector centromere positions inbred indicates whether individuals fully inbred","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/MultiPop-class.html","id":null,"dir":"Reference","previous_headings":"","what":"Multi-Population — MultiPop-class","title":"Multi-Population — MultiPop-class","text":"mega-population represents population populations. designed behave like list populations.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/MultiPop-class.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Multi-Population — MultiPop-class","text":"","code":"# S4 method for MultiPop [(x, i)  # S4 method for MultiPop [[(x, i)  # S4 method for MultiPop c(x, ...)  isMultiPop(x)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/MultiPop-class.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Multi-Population — MultiPop-class","text":"x 'MultiPop' object index populations mega-populations ... additional 'MultiPop' 'Pop' objects","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/MultiPop-class.html","id":"methods-by-generic-","dir":"Reference","previous_headings":"","what":"Methods (by generic)","title":"Multi-Population — MultiPop-class","text":"[: Extract MultiPop index [[: Extract Pop index c(MultiPop): Combine multiple MultiPops","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/MultiPop-class.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Multi-Population — MultiPop-class","text":"isMultiPop(): Test object MultiPop class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/MultiPop-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"Multi-Population — MultiPop-class","text":"pops list Pop-class /MultiPop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/NamedMapPop-class.html","id":null,"dir":"Reference","previous_headings":"","what":"Raw population with genetic map and id — NamedMapPop-class","title":"Raw population with genetic map and id — NamedMapPop-class","text":"Extends MapPop-class add id, mother father.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/NamedMapPop-class.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Raw population with genetic map and id — NamedMapPop-class","text":"","code":"# S4 method for NamedMapPop [(x, i)  # S4 method for NamedMapPop c(x, ...)  isNamedMapPop(x)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/NamedMapPop-class.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Raw population with genetic map and id — NamedMapPop-class","text":"x 'NamedMapPop' object index individuals ... additional 'NamedMapPop' objects","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/NamedMapPop-class.html","id":"methods-by-generic-","dir":"Reference","previous_headings":"","what":"Methods (by generic)","title":"Raw population with genetic map and id — NamedMapPop-class","text":"[: Extract NamedMapPop index c(NamedMapPop): Combine multiple NamedMapPops","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/NamedMapPop-class.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Raw population with genetic map and id — NamedMapPop-class","text":"isNamedMapPop(): Test object NamedMapPop class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/NamedMapPop-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"Raw population with genetic map and id — NamedMapPop-class","text":"id individual's identifier mother identifier individual's mother father identifier individual's father","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/Pop-class.html","id":null,"dir":"Reference","previous_headings":"","what":"Population — Pop-class","title":"Population — Pop-class","text":"Extends RawPop-class add sex, genetic values, phenotypes, pedigrees.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/Pop-class.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Population — Pop-class","text":"","code":"# S4 method for Pop [(x, i)  # S4 method for Pop c(x, ...)  # S4 method for Pop show(object)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/Pop-class.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Population — Pop-class","text":"x 'Pop' object index individuals ... additional 'Pop' objects object 'Pop' object","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/Pop-class.html","id":"methods-by-generic-","dir":"Reference","previous_headings":"","what":"Methods (by generic)","title":"Population — Pop-class","text":"[: Extract Pop index id c(Pop): Combine multiple Pops show(Pop): Show population summary","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/Pop-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"Population — Pop-class","text":"id individual's identifier iid individual's internal identifier mother identifier individual's mother father identifier individual's father sex sex individuals: \"M\" males, \"F\" females, \"H\" hermaphrodites nTraits number traits gv matrix genetic values. using GxE traits, gv reflects gv p=0.5. Dimensions nInd nTraits. pheno matrix phenotypic values. Dimensions nInd nTraits. ebv matrix estimated breeding values. Dimensions nInd rows variable number columns. gxe list containing GxE slopes GxE traits fixEff fixed effect relating phenotype. Used genomic selection models otherwise ignored. misc list whose elements correspond individuals population. list normally empty exists solely open slot available uses store extra information individuals. miscPop list length containing optional meta data  population. list empty unless information supplied user. Note list emptied every time population subsetted.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUP.html","id":null,"dir":"Reference","previous_headings":"","what":"RR-BLUP Model — RRBLUP","title":"RR-BLUP Model — RRBLUP","text":"Fits RR-BLUP model genomic predictions.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUP.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"RR-BLUP Model — RRBLUP","text":"","code":"RRBLUP(   pop,   traits = 1,   use = \"pheno\",   snpChip = 1,   useQtl = FALSE,   maxIter = 1000L,   simParam = NULL,   ... )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUP.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"RR-BLUP Model — RRBLUP","text":"pop Pop-class serve training population traits integer indicating trait traits model, vector trait names,  function traits returning single value. use train model using phenotypes \"pheno\", genetic values \"gv\",  estimated breeding values \"ebv\", breeding values \"bv\", randomly \"rand\" snpChip integer indicating SNP chip genotype  use useQtl QTL genotypes used instead SNP chip.  TRUE, snpChip specifies trait's QTL use, thus  QTL may match QTL underlying phenotype supplied traits. maxIter maximum number iterations. used  number traits greater 1. simParam object SimParam ... additional arguments using function  traits","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUP.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"RR-BLUP Model — RRBLUP","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=20)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitA(10) SP$setVarE(h2=0.5) SP$addSnpChip(10)  #Create population pop = newPop(founderPop, simParam=SP)  #Run GS model and set EBV ans = RRBLUP(pop, simParam=SP) pop = setEBV(pop, ans, simParam=SP)  #Evaluate accuracy cor(gv(pop), ebv(pop)) #>        est_GV_Trait1 #> Trait1     0.6206319"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUP2.html","id":null,"dir":"Reference","previous_headings":"","what":"RR-BLUP Model 2 — RRBLUP2","title":"RR-BLUP Model 2 — RRBLUP2","text":"Fits RR-BLUP model genomic predictions. implementation  meant situations RRBLUP slow. Note  RRBLUP2 faster certain situations, see details .  users use RRBLUP.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUP2.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"RR-BLUP Model 2 — RRBLUP2","text":"","code":"RRBLUP2(   pop,   traits = 1,   use = \"pheno\",   snpChip = 1,   useQtl = FALSE,   maxIter = 10,   Vu = NULL,   Ve = NULL,   useEM = TRUE,   tol = 1e-06,   simParam = NULL,   ... )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUP2.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"RR-BLUP Model 2 — RRBLUP2","text":"pop Pop-class serve training population traits integer indicating trait model, trait name, function traits returning single value. Unlike RRBLUP,  univariate models supported. use train model using phenotypes \"pheno\", genetic values \"gv\",  estimated breeding values \"ebv\", breeding values \"bv\", randomly \"rand\" snpChip integer indicating SNP chip genotype  use useQtl QTL genotypes used instead SNP chip.  TRUE, snpChip specifies trait's QTL use, thus  QTL may match QTL underlying phenotype supplied traits. maxIter maximum number iterations. Vu marker effect variance. value NULL,  reasonable starting point chosen automatically. Ve error variance. value NULL,  reasonable starting point chosen automatically. useEM use EM solve variance components. false,  initial values considered true. tol tolerance EM algorithm convergence simParam object SimParam ... additional arguments using function  traits","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUP2.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"RR-BLUP Model 2 — RRBLUP2","text":"RRBLUP2 function works best number markers  large. solves RR-BLUP problem setting  solving Henderson's mixed model equations. Solving equations  involves square matrix dimensions equal number fixed  effects plus number random effects (markers). Whereas RRBLUP  function solves RR-BLUP problem using EMMA approach. approach involves  square matrix dimensions equal number phenotypic records. means  RRBLUP2 function uses less memory RRBLUP number markers  approximately equal smaller number phenotypic records. RRBLUP2 function recommend cases variance components  unknown. uses EM algorithm solve unknown variance components,  generally considerably slower EMMA approach RRBLUP.  number iterations EM algorithm set maxIter. default value  typically small convergence. algorithm fails converge  warning displayed, results given last iteration. results may  \"good enough\". However make claim effect, can generalize  possible use cases. RRBLUP2 function can quickly solve mixed model equations without estimating variance  components. variance components set defining Vu Ve. Estimation components  suppressed setting useEM false. may useful model retrained  multiple times simulation. run RRBLUP function first  time model trained, use variance components output  future runs RRBLUP2 functions. , can make claim general robustness  approach.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUP2.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"RR-BLUP Model 2 — RRBLUP2","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=20)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitA(10) SP$setVarE(h2=0.5) SP$addSnpChip(10)  #Create population pop = newPop(founderPop, simParam=SP)  #Run GS model and set EBV ans = RRBLUP2(pop, simParam=SP) pop = setEBV(pop, ans, simParam=SP)  #Evaluate accuracy cor(gv(pop), ebv(pop)) #>        est_GV_Trait1 #> Trait1     0.4048304"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUPMemUse.html","id":null,"dir":"Reference","previous_headings":"","what":"RRBLUP Memory Usage — RRBLUPMemUse","title":"RRBLUP Memory Usage — RRBLUPMemUse","text":"Estimates amount RAM needed run RRBLUP related functions given training population size.  Note function may underestimate total usage.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUPMemUse.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"RRBLUP Memory Usage — RRBLUPMemUse","text":"","code":"RRBLUPMemUse(nInd, nMarker, model = \"REG\")"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUPMemUse.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"RRBLUP Memory Usage — RRBLUPMemUse","text":"nInd number individuals training population nMarker number markers per individual model either \"REG\", \"GCA\", \"SCA\" RRBLUP  RRBLUP_GCA RRBLUP_SCA respectively.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUPMemUse.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"RRBLUP Memory Usage — RRBLUPMemUse","text":"Returns estimate required gigabytes RAM","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUPMemUse.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"RRBLUP Memory Usage — RRBLUPMemUse","text":"","code":"RRBLUPMemUse(nInd=1000, nMarker=5000) #> [1] 0.06412"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUP_D.html","id":null,"dir":"Reference","previous_headings":"","what":"RR-BLUP Model with Dominance — RRBLUP_D","title":"RR-BLUP Model with Dominance — RRBLUP_D","text":"Fits RR-BLUP model genomic predictions includes  dominance effects.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUP_D.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"RR-BLUP Model with Dominance — RRBLUP_D","text":"","code":"RRBLUP_D(   pop,   traits = 1,   use = \"pheno\",   snpChip = 1,   useQtl = FALSE,   maxIter = 40L,   simParam = NULL,   ... )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUP_D.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"RR-BLUP Model with Dominance — RRBLUP_D","text":"pop Pop-class serve training population traits integer indicating trait model, trait name, function traits returning single value. use train model using phenotypes \"pheno\", genetic values \"gv\",  estimated breeding values \"ebv\", breeding values \"bv\", randomly \"rand\" snpChip integer indicating SNP chip genotype  use useQtl QTL genotypes used instead SNP chip.  TRUE, snpChip specifies trait's QTL use, thus  QTL may match QTL underlying phenotype supplied traits. maxIter maximum number iterations. used  number traits greater 1. simParam object SimParam ... additional arguments using function  traits","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUP_D.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"RR-BLUP Model with Dominance — RRBLUP_D","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=20)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitAD(10, meanDD=0.5) SP$setVarE(h2=0.5) SP$addSnpChip(10)  #Create population pop = newPop(founderPop, simParam=SP)  #Run GS model and set EBV ans = RRBLUP_D(pop, simParam=SP) #> Warning: Reached maxIter without converging pop = setEBV(pop, ans, simParam=SP)  #Evaluate accuracy cor(gv(pop), ebv(pop)) #>        est_GV_Trait1 #> Trait1     0.3385086"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUP_D2.html","id":null,"dir":"Reference","previous_headings":"","what":"RR-BLUP with Dominance Model 2 — RRBLUP_D2","title":"RR-BLUP with Dominance Model 2 — RRBLUP_D2","text":"Fits RR-BLUP model genomic predictions includes  dominance effects. implementation meant situations  RRBLUP_D slow. Note RRBLUP_D2  faster certain situations. users use  RRBLUP_D.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUP_D2.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"RR-BLUP with Dominance Model 2 — RRBLUP_D2","text":"","code":"RRBLUP_D2(   pop,   traits = 1,   use = \"pheno\",   snpChip = 1,   useQtl = FALSE,   maxIter = 10,   Va = NULL,   Vd = NULL,   Ve = NULL,   useEM = TRUE,   tol = 1e-06,   simParam = NULL,   ... )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUP_D2.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"RR-BLUP with Dominance Model 2 — RRBLUP_D2","text":"pop Pop-class serve training population traits integer indicating trait model, trait name, function traits returning single value. use train model using phenotypes \"pheno\", genetic values \"gv\",  estimated breeding values \"ebv\", breeding values \"bv\", randomly \"rand\" snpChip integer indicating SNP chip genotype  use useQtl QTL genotypes used instead SNP chip.  TRUE, snpChip specifies trait's QTL use, thus  QTL may match QTL underlying phenotype supplied traits. maxIter maximum number iterations. used  number traits greater 1. Va marker effect variance additive effects. value NULL,  reasonable starting point chosen automatically. Vd marker effect variance dominance effects. value NULL,  reasonable starting point chosen automatically. Ve error variance. value NULL,  reasonable starting point chosen automatically. useEM use EM solve variance components. false,  initial values considered true. tol tolerance EM algorithm convergence simParam object SimParam ... additional arguments using function  traits","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUP_D2.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"RR-BLUP with Dominance Model 2 — RRBLUP_D2","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=20)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitAD(10, meanDD=0.5) SP$setVarE(h2=0.5) SP$addSnpChip(10)  #Create population pop = newPop(founderPop, simParam=SP)  #Run GS model and set EBV ans = RRBLUP_D2(pop, simParam=SP) pop = setEBV(pop, ans, simParam=SP)  #Evaluate accuracy cor(gv(pop), ebv(pop)) #>        est_GV_Trait1 #> Trait1     0.5351522"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUP_GCA.html","id":null,"dir":"Reference","previous_headings":"","what":"RR-BLUP GCA Model — RRBLUP_GCA","title":"RR-BLUP GCA Model — RRBLUP_GCA","text":"Fits RR-BLUP model estimates seperate marker effects females males. Useful predicting GCA parents single cross hybrids. Can also predict performance specific  single cross hybrids.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUP_GCA.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"RR-BLUP GCA Model — RRBLUP_GCA","text":"","code":"RRBLUP_GCA(   pop,   traits = 1,   use = \"pheno\",   snpChip = 1,   useQtl = FALSE,   maxIter = 40L,   simParam = NULL,   ... )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUP_GCA.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"RR-BLUP GCA Model — RRBLUP_GCA","text":"pop Pop-class serve training population traits integer indicating trait model, trait name, function traits returning single value. use train model using phenotypes \"pheno\", genetic values \"gv\",  estimated breeding values \"ebv\", breeding values \"bv\", randomly \"rand\" snpChip integer indicating SNP chip genotype  use useQtl QTL genotypes used instead SNP chip.  TRUE, snpChip specifies trait's QTL use, thus  QTL may match QTL underlying phenotype supplied traits. maxIter maximum number iterations convergence. simParam object SimParam ... additional arguments using function  traits","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUP_GCA.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"RR-BLUP GCA Model — RRBLUP_GCA","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=20)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitA(10) SP$setVarE(h2=0.5) SP$addSnpChip(10)  #Create population pop = newPop(founderPop, simParam=SP)  #Run GS model and set EBV ans = RRBLUP_GCA(pop, simParam=SP) pop = setEBV(pop, ans, simParam=SP)  #Evaluate accuracy cor(gv(pop), ebv(pop)) #>        est_GV_Trait1 #> Trait1     0.8030224"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUP_GCA2.html","id":null,"dir":"Reference","previous_headings":"","what":"RR-BLUP GCA Model 2 — RRBLUP_GCA2","title":"RR-BLUP GCA Model 2 — RRBLUP_GCA2","text":"Fits RR-BLUP model estimates seperate marker effects females males. implementation meant situations  RRBLUP_GCA slow. Note RRBLUP_GCA2  faster certain situations. users use  RRBLUP_GCA.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUP_GCA2.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"RR-BLUP GCA Model 2 — RRBLUP_GCA2","text":"","code":"RRBLUP_GCA2(   pop,   traits = 1,   use = \"pheno\",   snpChip = 1,   useQtl = FALSE,   maxIter = 10,   VuF = NULL,   VuM = NULL,   Ve = NULL,   useEM = TRUE,   tol = 1e-06,   simParam = NULL,   ... )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUP_GCA2.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"RR-BLUP GCA Model 2 — RRBLUP_GCA2","text":"pop Pop-class serve training population traits integer indicating trait model, trait name, function traits returning single value. use train model using phenotypes \"pheno\", genetic values \"gv\",  estimated breeding values \"ebv\", breeding values \"bv\", randomly \"rand\" snpChip integer indicating SNP chip genotype  use useQtl QTL genotypes used instead SNP chip.  TRUE, snpChip specifies trait's QTL use, thus  QTL may match QTL underlying phenotype supplied traits. maxIter maximum number iterations convergence. VuF marker effect variance females. value NULL,  reasonable starting point chosen automatically. VuM marker effect variance males. value NULL,  reasonable starting point chosen automatically. Ve error variance. value NULL,  reasonable starting point chosen automatically. useEM use EM solve variance components. false,  initial values considered true. tol tolerance EM algorithm convergence simParam object SimParam ... additional arguments using function  traits","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUP_GCA2.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"RR-BLUP GCA Model 2 — RRBLUP_GCA2","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=20)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitA(10) SP$setVarE(h2=0.5) SP$addSnpChip(10)  #Create population pop = newPop(founderPop, simParam=SP)  #Run GS model and set EBV ans = RRBLUP_GCA2(pop, simParam=SP) pop = setEBV(pop, ans, simParam=SP)  #Evaluate accuracy cor(gv(pop), ebv(pop)) #>        est_GV_Trait1 #> Trait1     0.6225819"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUP_SCA.html","id":null,"dir":"Reference","previous_headings":"","what":"RR-BLUP SCA Model — RRBLUP_SCA","title":"RR-BLUP SCA Model — RRBLUP_SCA","text":"extention RRBLUP_GCA adds dominance effects.  Note seen consistent benefit model  RRBLUP_GCA.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUP_SCA.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"RR-BLUP SCA Model — RRBLUP_SCA","text":"","code":"RRBLUP_SCA(   pop,   traits = 1,   use = \"pheno\",   snpChip = 1,   useQtl = FALSE,   maxIter = 40L,   simParam = NULL,   ... )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUP_SCA.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"RR-BLUP SCA Model — RRBLUP_SCA","text":"pop Pop-class serve training population traits integer indicating trait model, trait name, function traits returning single value. use train model using phenotypes \"pheno\", genetic values \"gv\",  estimated breeding values \"ebv\", breeding values \"bv\", randomly \"rand\" snpChip integer indicating SNP chip genotype  use useQtl QTL genotypes used instead SNP chip.  TRUE, snpChip specifies trait's QTL use, thus  QTL may match QTL underlying phenotype supplied traits. maxIter maximum number iterations convergence. simParam object SimParam ... additional arguments using function  traits","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUP_SCA.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"RR-BLUP SCA Model — RRBLUP_SCA","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=2, nChr=1, segSites=20)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitA(10) SP$setVarE(h2=0.5) SP$addSnpChip(10)  #Create population pop = newPop(founderPop, simParam=SP)  #Run GS model and set EBV ans = RRBLUP_SCA(pop, simParam=SP) pop = setEBV(pop, ans, simParam=SP)  #Evaluate accuracy cor(gv(pop), ebv(pop)) #>        est_GV_Trait1 #> Trait1            NA"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUP_SCA2.html","id":null,"dir":"Reference","previous_headings":"","what":"RR-BLUP SCA Model 2 — RRBLUP_SCA2","title":"RR-BLUP SCA Model 2 — RRBLUP_SCA2","text":"Fits RR-BLUP model estimates seperate additive effects females males dominance effect. implementation meant  situations RRBLUP_SCA slow. Note  RRBLUP_SCA2 faster certain situations. users use  RRBLUP_SCA.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUP_SCA2.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"RR-BLUP SCA Model 2 — RRBLUP_SCA2","text":"","code":"RRBLUP_SCA2(   pop,   traits = 1,   use = \"pheno\",   snpChip = 1,   useQtl = FALSE,   maxIter = 10,   VuF = NULL,   VuM = NULL,   VuD = NULL,   Ve = NULL,   useEM = TRUE,   tol = 1e-06,   simParam = NULL,   ... )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUP_SCA2.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"RR-BLUP SCA Model 2 — RRBLUP_SCA2","text":"pop Pop-class serve training population traits integer indicating trait model, trait name, function traits returning single value. use train model using phenotypes \"pheno\", genetic values \"gv\",  estimated breeding values \"ebv\", breeding values \"bv\", randomly \"rand\" snpChip integer indicating SNP chip genotype  use useQtl QTL genotypes used instead SNP chip.  TRUE, snpChip specifies trait's QTL use, thus  QTL may match QTL underlying phenotype supplied traits. maxIter maximum number iterations convergence. VuF marker effect variance females. value NULL,  reasonable starting point chosen automatically. VuM marker effect variance males. value NULL,  reasonable starting point chosen automatically. VuD marker effect variance dominance. value NULL,  reasonable starting point chosen automatically. Ve error variance. value NULL,  reasonable starting point chosen automatically. useEM use EM solve variance components. false,  initial values considered true. tol tolerance EM algorithm convergence simParam object SimParam ... additional arguments using function  traits","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUP_SCA2.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"RR-BLUP SCA Model 2 — RRBLUP_SCA2","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=20)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitA(10) SP$setVarE(h2=0.5) SP$addSnpChip(10)  #Create population pop = newPop(founderPop, simParam=SP)  #Run GS model and set EBV ans = RRBLUP_SCA2(pop, simParam=SP) pop = setEBV(pop, ans, simParam=SP)  #Evaluate accuracy cor(gv(pop), ebv(pop)) #>        est_GV_Trait1 #> Trait1     0.5958648"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRsol-class.html","id":null,"dir":"Reference","previous_headings":"","what":"RR-BLUP Solution — RRsol-class","title":"RR-BLUP Solution — RRsol-class","text":"Contains output AlphaSimR's genomic  selection functions.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRsol-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"RR-BLUP Solution — RRsol-class","text":"gv Trait(s) estimating genetic values bv Trait(s) estimating breeding values female Trait(s) estimating GCA female pool male Trait(s) estimating GCA male pool Vu Estimated marker variance(s) Ve Estimated error variance","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RawPop-class.html","id":null,"dir":"Reference","previous_headings":"","what":"Raw Population — RawPop-class","title":"Raw Population — RawPop-class","text":"raw population class contains genotype data.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RawPop-class.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Raw Population — RawPop-class","text":"","code":"# S4 method for RawPop [(x, i)  # S4 method for RawPop c(x, ...)  # S4 method for RawPop show(object)  isRawPop(x)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RawPop-class.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Raw Population — RawPop-class","text":"x 'RawPop' object index individuals ... additional 'RawPop' objects object 'RawPop' object","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RawPop-class.html","id":"methods-by-generic-","dir":"Reference","previous_headings":"","what":"Methods (by generic)","title":"Raw Population — RawPop-class","text":"[: Extract RawPop index c(RawPop): Combine multiple RawPops show(RawPop): Show population summary","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RawPop-class.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Raw Population — RawPop-class","text":"isRawPop(): Test object RawPop class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RawPop-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"Raw Population — RawPop-class","text":"nInd number individuals nChr number chromosomes ploidy level ploidy nLoci number loci per chromosome geno list nChr length containing chromosome genotypes. element three dimensional array raw values. array dimensions nLoci ploidy nInd.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":null,"dir":"Reference","previous_headings":"","what":"Simulation parameters — SimParam","title":"Simulation parameters — SimParam","text":"Container global simulation parameters. Saving object SP allow accessed function defaults.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Simulation parameters — SimParam","text":"default founder population population used initalize SimParam object. population can changed replacing population founderPop slot. must run resetPop existing populations obtain new trait values.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"Simulation parameters — SimParam","text":"nThreads number threads used platforms OpenMP support snpChips list SNP chips invalidQtl list segregating sites valid QTL invalidSnp list segregating sites valid SNP founderPop founder population used variance scaling finalizePop function applied newly created populations. Currently nothing changed expert users. allowEmptyPop true, population arguments nInd=0 return empty population warning instead error. v crossover interference parameter gamma model recombination. value 1 indicates crossover interference (e.g. Haldane mapping function). value 2.6 approximates degree crossover interference implied Kosambi mapping function. (default 2.6) p proportion crossovers coming non-interfering pathway. (default 0) quadProb probability quadrivalent pairing autopolyploid. (default 0)","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"active-bindings","dir":"Reference","previous_headings":"","what":"Active bindings","title":"Simulation parameters — SimParam","text":"traitNames vector trait names snpChipNames vector chip names traits list traits nChr number chromosomes nTraits number traits nSnpChips number SNP chips segSites segregating sites per chromosome sexes sexes used mating sepMap seperate genetic maps males females genMap \"matrix\" chromosome genetic maps femaleMap \"matrix\" chromosome genetic maps females maleMap \"matrix\" chromosome genetic maps males centromere position centromeres genetic map femaleCentromere position centromeres female genetic map maleCentromere position centromeres male genetic map lastId last ID number assigned isTrackPed pedigree tracked pedigree pedigree matrix individuals isTrackRec recombination tracked recHist list historic recombination events haplotypes list computed IBD haplotypes varA additive genetic variance founderPop varG total genetic variance founderPop varE default error variance version version AlphaSimR used generate object","code":""},{"path":[]},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"Simulation parameters — SimParam","text":"SimParam$new() SimParam$setTrackPed() SimParam$setTrackRec() SimParam$resetPed() SimParam$restrSegSites() SimParam$setSexes() SimParam$setFounderHap() SimParam$addSnpChip() SimParam$addSnpChipByName() SimParam$addStructuredSnpChip() SimParam$addTraitA() SimParam$addTraitAD() SimParam$altAddTraitAD() SimParam$addTraitAG() SimParam$addTraitADG() SimParam$addTraitAE() SimParam$addTraitADE() SimParam$addTraitAEG() SimParam$addTraitADEG() SimParam$manAddTrait() SimParam$importTrait() SimParam$switchTrait() SimParam$removeTrait() SimParam$setVarE() SimParam$setCorE() SimParam$rescaleTraits() SimParam$setRecombRatio() SimParam$switchGenMap() SimParam$switchFemaleMap() SimParam$switchMaleMap() SimParam$addToRec() SimParam$ibdHaplo() SimParam$updateLastId() SimParam$addToPed() SimParam$clone()","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"Simulation parameters — SimParam","text":"Starts process building new simulation creating new SimParam object assigning founder population class. recommended save object name \"SP\", subsequent functions check global environment object name simParam arguments NULL. allows call functions without explicitly supplying simParam argument every call.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulation parameters — SimParam","text":"","code":"SimParam$new(founderPop)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulation parameters — SimParam","text":"founderPop object MapPop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Simulation parameters — SimParam","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"method-settrackped-","dir":"Reference","previous_headings":"","what":"Method setTrackPed()","title":"Simulation parameters — SimParam","text":"Sets pedigree tracking simulation. default pedigree tracking turned . turned , pedigree individuals created tracked, except created hybridCross. Turning pedigree tracking turn recombination tracking turned .","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulation parameters — SimParam","text":"","code":"SimParam$setTrackPed(isTrackPed, force = FALSE)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulation parameters — SimParam","text":"isTrackPed pedigree tracking . force check running simulation ignored. set TRUE know .","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"examples-1","dir":"Reference","previous_headings":"","what":"Examples","title":"Simulation parameters — SimParam","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) \\dontshow{SP$nThreads = 1L} SP$setTrackPed(TRUE)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"method-settrackrec-","dir":"Reference","previous_headings":"","what":"Method setTrackRec()","title":"Simulation parameters — SimParam","text":"Sets recombination tracking simulation. default recombination tracking turned . turned recombination tracking also turn pedigree tracking. Recombination tracking keeps records individuals created, except created hybridCross, pedigree tracked.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulation parameters — SimParam","text":"","code":"SimParam$setTrackRec(isTrackRec, force = FALSE)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulation parameters — SimParam","text":"isTrackRec recombination tracking . force check running simulation ignored. set TRUE know .","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"examples-2","dir":"Reference","previous_headings":"","what":"Examples","title":"Simulation parameters — SimParam","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) \\dontshow{SP$nThreads = 1L} SP$setTrackRec(TRUE)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"method-resetped-","dir":"Reference","previous_headings":"","what":"Method resetPed()","title":"Simulation parameters — SimParam","text":"Resets internal lastId, pedigree recombination tracking (use) supplied lastId. careful using function may introduce bug use individuals deleted portion pedigree.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulation parameters — SimParam","text":"","code":"SimParam$resetPed(lastId = 0L)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"arguments-3","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulation parameters — SimParam","text":"lastId last ID include pedigree","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"examples-3","dir":"Reference","previous_headings":"","what":"Examples","title":"Simulation parameters — SimParam","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) \\dontshow{SP$nThreads = 1L}  #Create population pop = newPop(founderPop, simParam=SP) pop@id # 1:10  #Create another population after reseting pedigree SP$resetPed() pop2 = newPop(founderPop, simParam=SP) pop2@id # 1:10"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"method-restrsegsites-","dir":"Reference","previous_headings":"","what":"Method restrSegSites()","title":"Simulation parameters — SimParam","text":"Sets restrictions segregating sites can serve SNP /QTL.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"usage-4","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulation parameters — SimParam","text":"","code":"SimParam$restrSegSites(   minQtlPerChr = NULL,   minSnpPerChr = NULL,   excludeQtl = NULL,   excludeSnp = NULL,   overlap = FALSE,   minSnpFreq = NULL )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"arguments-4","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulation parameters — SimParam","text":"minQtlPerChr minimum number segregating sites  QTLs. Can single value vector values chromosome. minSnpPerChr minimum number segregating sites SNPs. Can single value vector values chromosome. excludeQtl optional vector segregating site names  exclude consideration viable QTL. excludeSnp optional vector segregating site names  exclude consideration viable SNP. overlap SNP QTL sites allowed overlap. minSnpFreq minimum allowable frequency SNP loci. minimum SNP frequency used value NULL.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"examples-4","dir":"Reference","previous_headings":"","what":"Examples","title":"Simulation parameters — SimParam","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) \\dontshow{SP$nThreads = 1L} SP$restrSegSites(minQtlPerChr=5, minSnpPerChr=5)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"method-setsexes-","dir":"Reference","previous_headings":"","what":"Method setSexes()","title":"Simulation parameters — SimParam","text":"Changes sexes determined simulation. default sexes \"\", indicating individuals hermaphrodites. add sexes simulation, run function \"yes_sys\" \"yes_rand\". value \"yes_sys\" systematically assign sexes newly created individuals first male female. Populations odd number individuals one male female. value \"yes_rand\" randomly assign sex individual.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"usage-5","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulation parameters — SimParam","text":"","code":"SimParam$setSexes(sexes, force = FALSE)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"arguments-5","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulation parameters — SimParam","text":"sexes acceptable value \"\", \"yes_sys\", \"yes_rand\" force check running simulation ignored. set TRUE know .","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"examples-5","dir":"Reference","previous_headings":"","what":"Examples","title":"Simulation parameters — SimParam","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) \\dontshow{SP$nThreads = 1L} SP$setSexes(\"yes_sys\")"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"method-setfounderhap-","dir":"Reference","previous_headings":"","what":"Method setFounderHap()","title":"Simulation parameters — SimParam","text":"Allows manual setting founder haplotypes. functionality  fully documented, still experimental.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"usage-6","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulation parameters — SimParam","text":"","code":"SimParam$setFounderHap(hapMap)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"arguments-6","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulation parameters — SimParam","text":"hapMap list founder haplotypes","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"method-addsnpchip-","dir":"Reference","previous_headings":"","what":"Method addSnpChip()","title":"Simulation parameters — SimParam","text":"Randomly assigns eligible SNPs SNP chip","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"usage-7","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulation parameters — SimParam","text":"","code":"SimParam$addSnpChip(nSnpPerChr, minSnpFreq = NULL, refPop = NULL, name = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"arguments-7","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulation parameters — SimParam","text":"nSnpPerChr number SNPs per chromosome. Can single value nChr values. minSnpFreq minimum allowable frequency SNP loci. NULL, minimum frequency used. refPop reference population calculating SNP frequency. NULL, founder population used. name optional name chip","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"examples-6","dir":"Reference","previous_headings":"","what":"Examples","title":"Simulation parameters — SimParam","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) \\dontshow{SP$nThreads = 1L} SP$addSnpChip(10)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"method-addsnpchipbyname-","dir":"Reference","previous_headings":"","what":"Method addSnpChipByName()","title":"Simulation parameters — SimParam","text":"Assigns SNPs SNP chip supplying marker names. function  check excluded SNPs add SNPs list  excluded QTL purpose avoiding overlap SNPs QTL.  Excluding SNPs used QTL can accomplished using  excludeQtl argument SimParam's restrSegSites function.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"usage-8","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulation parameters — SimParam","text":"","code":"SimParam$addSnpChipByName(markers, name = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"arguments-8","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulation parameters — SimParam","text":"markers vector names markers name optional name chip","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"examples-7","dir":"Reference","previous_headings":"","what":"Examples","title":"Simulation parameters — SimParam","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$addSnpChipByName(c(\"1_1\",\"1_3\"))"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"method-addstructuredsnpchip-","dir":"Reference","previous_headings":"","what":"Method addStructuredSnpChip()","title":"Simulation parameters — SimParam","text":"Randomly selects number snps structure assigns chips based structure","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"usage-9","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulation parameters — SimParam","text":"","code":"SimParam$addStructuredSnpChip(nSnpPerChr, structure, force = FALSE)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"arguments-9","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulation parameters — SimParam","text":"nSnpPerChr number SNPs per chromosome. Can single value nChr values. structure matrix.  Rows snp chips, columns chips. value true snp chip. force check running simulation ignored. set TRUE know .","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"method-addtraita-","dir":"Reference","previous_headings":"","what":"Method addTraitA()","title":"Simulation parameters — SimParam","text":"Randomly assigns eligible QTLs one additive traits. simulating one trait, traits pleiotropic correlated additive effects.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"usage-10","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulation parameters — SimParam","text":"","code":"SimParam$addTraitA(   nQtlPerChr,   mean = 0,   var = 1,   corA = NULL,   gamma = FALSE,   shape = 1,   force = FALSE,   name = NULL )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"arguments-10","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulation parameters — SimParam","text":"nQtlPerChr number QTLs per chromosome. Can single value nChr values. mean vector desired mean genetic values one traits var vector desired genetic variances one traits corA matrix correlations additive effects gamma gamma distribution used instead normal shape shape parameter gamma distribution (rate/scale parameter gamma distribution accounted via desired level genetic variance, var argument) force check running simulation ignored. set TRUE know . name optional name trait(s)","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"examples-8","dir":"Reference","previous_headings":"","what":"Examples","title":"Simulation parameters — SimParam","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) \\dontshow{SP$nThreads = 1L} SP$addTraitA(10)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"method-addtraitad-","dir":"Reference","previous_headings":"","what":"Method addTraitAD()","title":"Simulation parameters — SimParam","text":"Randomly assigns eligible QTLs one traits dominance. simulating one trait, traits pleiotropic correlated effects.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"usage-11","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulation parameters — SimParam","text":"","code":"SimParam$addTraitAD(   nQtlPerChr,   mean = 0,   var = 1,   meanDD = 0,   varDD = 0,   corA = NULL,   corDD = NULL,   useVarA = TRUE,   gamma = FALSE,   shape = 1,   force = FALSE,   name = NULL )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"arguments-11","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulation parameters — SimParam","text":"nQtlPerChr number QTLs per chromosome. Can single value nChr values. mean vector desired mean genetic values one traits var vector desired genetic variances one traits meanDD mean dominance degree varDD variance dominance degree corA matrix correlations additive effects corDD matrix correlations dominance degrees useVarA tune according additive genetic variance true. FALSE, tuning performed according total genetic variance. gamma gamma distribution used instead normal shape shape parameter gamma distribution (rate/scale parameter gamma distribution accounted via desired level genetic variance, var argument) force check running simulation ignored. set TRUE know . name optional name trait(s)","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"examples-9","dir":"Reference","previous_headings":"","what":"Examples","title":"Simulation parameters — SimParam","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) \\dontshow{SP$nThreads = 1L} SP$addTraitAD(10, meanDD=0.5)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"method-altaddtraitad-","dir":"Reference","previous_headings":"","what":"Method altAddTraitAD()","title":"Simulation parameters — SimParam","text":"alternative method adding trait additive  dominance effects  AlphaSimR simulation. function attempts create trait matching  user defined values number QTL, inbreeding depression, additive genetic  variance dominance genetic variance.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"usage-12","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulation parameters — SimParam","text":"","code":"SimParam$altAddTraitAD(   nQtlPerChr,   mean = 0,   varA = 1,   varD = 0,   inbrDepr = 0,   limMeanDD = c(0, 1.5),   limVarDD = c(0, 0.5),   silent = FALSE,   force = FALSE,   name = NULL )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"arguments-12","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulation parameters — SimParam","text":"nQtlPerChr number QTLs per chromosome.  Can single value nChr values. mean desired mean trait varA desired additive variance varD desired dominance variance inbrDepr desired inbreeding depression, see details limMeanDD limits meanDD, see details limVarDD limits varDD, see details silent summary details printed console force check running simulation ignored. set TRUE know . name optional name trait","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Simulation parameters — SimParam","text":"function always add trait 'SimParam', unless error occurs  picking QTLs. resulting trait always desired mean  additive genetic variance. However, may desired values  inbreeding depression dominance variance. Thus, strongly recommended  check output printed console determine close trait's  parameters came desired values. mean additive genetic variance always achieved exactly.  function attempts achieve desired dominance variance inbreeding  depression staying within user supplied constraints  acceptable range dominance degree mean variance. desired values achieved, acceptable range need increased / number QTL may need increased. limits setting  range dominance degree mean variance, care taken  regards biological feasibility limits supplied.  default limits somewhat arbitrarily set, make claim  reasonable limits routine use. Inbreeding depression function defined difference mean  genetic value population allele frequency  reference population (population used initialize SimParam)  Hardy-Weinberg equilibrium compared population allele  frequency fully inbred. equivalent amount mean  population increases going inbreeding coefficient 1 (fully  inbred) population inbreeding coefficient 0 (Hardy-Weinberg  equilibrium). Note sign value (usually) positive.  corresponds detrimental effect inbreeding higher values  trait considered biologically beneficial. Summary information trait printed console silent=FALSE.  summary information reports inbreeding depression dominance  variance population well dominance degree mean variance  applied trait.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"examples-10","dir":"Reference","previous_headings":"","what":"Examples","title":"Simulation parameters — SimParam","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) \\dontshow{SP$nThreads = 1L} SP$altAddTraitAD(nQtlPerChr=10, mean=0, varA=1, varD=0.05, inbrDepr=0.2)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"method-addtraitag-","dir":"Reference","previous_headings":"","what":"Method addTraitAG()","title":"Simulation parameters — SimParam","text":"Randomly assigns eligible QTLs one additive GxE traits. simulating one trait, traits pleiotropic correlated effects.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"usage-13","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulation parameters — SimParam","text":"","code":"SimParam$addTraitAG(   nQtlPerChr,   mean = 0,   var = 1,   varGxE = 1e-06,   varEnv = 0,   corA = NULL,   corGxE = NULL,   gamma = FALSE,   shape = 1,   force = FALSE,   name = NULL )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"arguments-13","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulation parameters — SimParam","text":"nQtlPerChr number QTLs per chromosome. Can single value nChr values. mean vector desired mean genetic values one traits var vector desired genetic variances one traits varGxE vector total genotype--environment variances traits varEnv vector environmental variances one traits corA matrix correlations additive effects corGxE matrix correlations GxE effects gamma gamma distribution used instead normal shape shape parameter gamma distribution (rate/scale parameter gamma distribution accounted via desired level genetic variance, var argument) force check running simulation ignored. set TRUE know . name optional name trait(s)","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"examples-11","dir":"Reference","previous_headings":"","what":"Examples","title":"Simulation parameters — SimParam","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) \\dontshow{SP$nThreads = 1L} SP$addTraitAG(10, varGxE=2)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"method-addtraitadg-","dir":"Reference","previous_headings":"","what":"Method addTraitADG()","title":"Simulation parameters — SimParam","text":"Randomly assigns eligible QTLs trait dominance GxE.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"usage-14","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulation parameters — SimParam","text":"","code":"SimParam$addTraitADG(   nQtlPerChr,   mean = 0,   var = 1,   varEnv = 0,   varGxE = 1e-06,   meanDD = 0,   varDD = 0,   corA = NULL,   corDD = NULL,   corGxE = NULL,   useVarA = TRUE,   gamma = FALSE,   shape = 1,   force = FALSE,   name = NULL )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"arguments-14","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulation parameters — SimParam","text":"nQtlPerChr number QTLs per chromosome. Can single value nChr values. mean vector desired mean genetic values one traits var vector desired genetic variances one traits varEnv vector environmental variances one traits varGxE vector total genotype--environment variances traits meanDD mean dominance degree varDD variance dominance degree corA matrix correlations additive effects corDD matrix correlations dominance degrees corGxE matrix correlations GxE effects useVarA tune according additive genetic variance true gamma gamma distribution used instead normal shape shape parameter gamma distribution (rate/scale parameter gamma distribution accounted via desired level genetic variance, var argument) force check running simulation ignored. set TRUE know . name optional name trait(s)","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"examples-12","dir":"Reference","previous_headings":"","what":"Examples","title":"Simulation parameters — SimParam","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) \\dontshow{SP$nThreads = 1L} SP$addTraitADG(10, meanDD=0.5, varGxE=2)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"method-addtraitae-","dir":"Reference","previous_headings":"","what":"Method addTraitAE()","title":"Simulation parameters — SimParam","text":"Randomly assigns eligible QTLs one additive epistasis traits. simulating one trait, traits pleiotropic correlated additive effects.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"usage-15","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulation parameters — SimParam","text":"","code":"SimParam$addTraitAE(   nQtlPerChr,   mean = 0,   var = 1,   relAA = 0,   corA = NULL,   corAA = NULL,   useVarA = TRUE,   gamma = FALSE,   shape = 1,   force = FALSE,   name = NULL )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"arguments-15","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulation parameters — SimParam","text":"nQtlPerChr number QTLs per chromosome. Can single value nChr values. mean vector desired mean genetic values one traits var vector desired genetic variances one traits relAA relative value additive--additive variance compared additive variance diploid organism allele frequency 0.5 corA matrix correlations additive effects corAA matrix correlations additive--additive effects useVarA tune according additive genetic variance true. FALSE, tuning performed according total genetic variance. gamma gamma distribution used instead normal shape shape parameter gamma distribution (rate/scale parameter gamma distribution accounted via desired level genetic variance, var argument) force check running simulation ignored. set TRUE know . name optional name trait(s)","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"examples-13","dir":"Reference","previous_headings":"","what":"Examples","title":"Simulation parameters — SimParam","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) \\dontshow{SP$nThreads = 1L} SP$addTraitAE(10, relAA=0.1)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"method-addtraitade-","dir":"Reference","previous_headings":"","what":"Method addTraitADE()","title":"Simulation parameters — SimParam","text":"Randomly assigns eligible QTLs one traits dominance epistasis. simulating one trait, traits pleiotropic correlated effects.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"usage-16","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulation parameters — SimParam","text":"","code":"SimParam$addTraitADE(   nQtlPerChr,   mean = 0,   var = 1,   meanDD = 0,   varDD = 0,   relAA = 0,   corA = NULL,   corDD = NULL,   corAA = NULL,   useVarA = TRUE,   gamma = FALSE,   shape = 1,   force = FALSE,   name = NULL )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"arguments-16","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulation parameters — SimParam","text":"nQtlPerChr number QTLs per chromosome. Can single value nChr values. mean vector desired mean genetic values one traits var vector desired genetic variances one traits meanDD mean dominance degree varDD variance dominance degree relAA relative value additive--additive variance compared additive variance diploid organism allele frequency 0.5 corA matrix correlations additive effects corDD matrix correlations dominance degrees corAA matrix correlations additive--additive effects useVarA tune according additive genetic variance true. FALSE, tuning performed according total genetic variance. gamma gamma distribution used instead normal shape shape parameter gamma distribution (rate/scale parameter gamma distribution accounted via desired level genetic variance, var argument) force check running simulation ignored. set TRUE know . name optional name trait(s)","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"examples-14","dir":"Reference","previous_headings":"","what":"Examples","title":"Simulation parameters — SimParam","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) \\dontshow{SP$nThreads = 1L} SP$addTraitADE(10)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"method-addtraitaeg-","dir":"Reference","previous_headings":"","what":"Method addTraitAEG()","title":"Simulation parameters — SimParam","text":"Randomly assigns eligible QTLs one additive epistasis GxE traits. simulating one trait, traits pleiotropic correlated effects.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"usage-17","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulation parameters — SimParam","text":"","code":"SimParam$addTraitAEG(   nQtlPerChr,   mean = 0,   var = 1,   relAA = 0,   varGxE = 1e-06,   varEnv = 0,   corA = NULL,   corAA = NULL,   corGxE = NULL,   useVarA = TRUE,   gamma = FALSE,   shape = 1,   force = FALSE,   name = NULL )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"arguments-17","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulation parameters — SimParam","text":"nQtlPerChr number QTLs per chromosome. Can single value nChr values. mean vector desired mean genetic values one traits var vector desired genetic variances one traits relAA relative value additive--additive variance compared additive variance diploid organism allele frequency 0.5 varGxE vector total genotype--environment variances traits varEnv vector environmental variances one traits corA matrix correlations additive effects corAA matrix correlations additive--additive effects corGxE matrix correlations GxE effects useVarA tune according additive genetic variance true. FALSE, tuning performed according total genetic variance. gamma gamma distribution used instead normal shape shape parameter gamma distribution (rate/scale parameter gamma distribution accounted via desired level genetic variance, var argument) force check running simulation ignored. set TRUE know . name optional name trait(s)","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"examples-15","dir":"Reference","previous_headings":"","what":"Examples","title":"Simulation parameters — SimParam","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) \\dontshow{SP$nThreads = 1L} SP$addTraitAEG(10, varGxE=2)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"method-addtraitadeg-","dir":"Reference","previous_headings":"","what":"Method addTraitADEG()","title":"Simulation parameters — SimParam","text":"Randomly assigns eligible QTLs trait dominance, epistasis GxE.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"usage-18","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulation parameters — SimParam","text":"","code":"SimParam$addTraitADEG(   nQtlPerChr,   mean = 0,   var = 1,   varEnv = 0,   varGxE = 1e-06,   meanDD = 0,   varDD = 0,   relAA = 0,   corA = NULL,   corDD = NULL,   corAA = NULL,   corGxE = NULL,   useVarA = TRUE,   gamma = FALSE,   shape = 1,   force = FALSE,   name = NULL )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"arguments-18","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulation parameters — SimParam","text":"nQtlPerChr number QTLs per chromosome. Can single value nChr values. mean vector desired mean genetic values one traits var vector desired genetic variances one traits varEnv vector environmental variances one traits varGxE vector total genotype--environment variances traits meanDD mean dominance degree varDD variance dominance degree relAA relative value additive--additive variance compared additive variance diploid organism allele frequency 0.5 corA matrix correlations additive effects corDD matrix correlations dominance degrees corAA matrix correlations additive--additive effects corGxE matrix correlations GxE effects useVarA tune according additive genetic variance true gamma gamma distribution used instead normal shape shape parameter gamma distribution (rate/scale parameter gamma distribution accounted via desired level genetic variance, var argument) force check running simulation ignored. set TRUE know . name optional name trait(s)","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"examples-16","dir":"Reference","previous_headings":"","what":"Examples","title":"Simulation parameters — SimParam","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) \\dontshow{SP$nThreads = 1L} SP$addTraitADEG(10, meanDD=0.5, varGxE=2)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"method-manaddtrait-","dir":"Reference","previous_headings":"","what":"Method manAddTrait()","title":"Simulation parameters — SimParam","text":"Manually add new trait simulation. Trait must formatted LociMap-class. trait already formatted, consider using importTrait.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"usage-19","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulation parameters — SimParam","text":"","code":"SimParam$manAddTrait(lociMap, varE = NA_real_, force = FALSE)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"arguments-19","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulation parameters — SimParam","text":"lociMap new object descended LociMap-class varE default error variance phenotype, optional force check running simulation ignored. set TRUE know ","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"method-importtrait-","dir":"Reference","previous_headings":"","what":"Method importTrait()","title":"Simulation parameters — SimParam","text":"Manually add new trait(s) simulation. Unlike manAddTrait function, function require formatting trait LociMap-class. formatting performed automatically user, user friendly data.frames matrices taken inputs. function works AD trait types.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"usage-20","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulation parameters — SimParam","text":"","code":"SimParam$importTrait(   markerNames,   addEff,   domEff = NULL,   intercept = NULL,   name = NULL,   varE = NULL,   force = FALSE )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"arguments-20","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulation parameters — SimParam","text":"markerNames vector names QTL addEff matrix additive effects (nLoci x nTraits). Alternatively, vector length nLoci can supplied single trait. domEff optional dominance effects locus intercept optional intercepts trait name optional name(s) trait(s) varE default error variance phenotype, optional force check running simulation ignored. set TRUE know ","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"method-switchtrait-","dir":"Reference","previous_headings":"","what":"Method switchTrait()","title":"Simulation parameters — SimParam","text":"Switch trait simulation.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"usage-21","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulation parameters — SimParam","text":"","code":"SimParam$switchTrait(traitPos, lociMap, varE = NA_real_, force = FALSE)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"arguments-21","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulation parameters — SimParam","text":"traitPos integer indicate trait switch lociMap new object descended LociMap-class varE default error variance phenotype, optional force check running simulation ignored. set TRUE know ","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"method-removetrait-","dir":"Reference","previous_headings":"","what":"Method removeTrait()","title":"Simulation parameters — SimParam","text":"Remove trait simulation","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"usage-22","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulation parameters — SimParam","text":"","code":"SimParam$removeTrait(traits, force = FALSE)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"arguments-22","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulation parameters — SimParam","text":"traits integer vector indicating traits remove force check running simulation ignored. set TRUE know ","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"method-setvare-","dir":"Reference","previous_headings":"","what":"Method setVarE()","title":"Simulation parameters — SimParam","text":"Defines default values error variances used setPheno. defaults  used automatically generate phenotypes new  populations created. See details section setPheno information arguments  used.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"usage-23","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulation parameters — SimParam","text":"","code":"SimParam$setVarE(h2 = NULL, H2 = NULL, varE = NULL, corE = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"arguments-23","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulation parameters — SimParam","text":"h2 vector desired narrow-sense heritabilities H2 vector desired broad-sense heritabilities varE vector matrix error variances corE optional matrix error correlations","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"examples-17","dir":"Reference","previous_headings":"","what":"Examples","title":"Simulation parameters — SimParam","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) \\dontshow{SP$nThreads = 1L} SP$addTraitA(10) SP$setVarE(h2=0.5)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"method-setcore-","dir":"Reference","previous_headings":"","what":"Method setCorE()","title":"Simulation parameters — SimParam","text":"Defines correlation structure default error variances. must call setVarE first define default error variances.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"usage-24","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulation parameters — SimParam","text":"","code":"SimParam$setCorE(corE)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"arguments-24","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulation parameters — SimParam","text":"corE correlation matrix error variances","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"examples-18","dir":"Reference","previous_headings":"","what":"Examples","title":"Simulation parameters — SimParam","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) \\dontshow{SP$nThreads = 1L} SP$addTraitA(10, mean=c(0,0), var=c(1,1), corA=diag(2)) SP$setVarE(varE=c(1,1)) E = 0.5*diag(2)+0.5 #Positively correlated error SP$setCorE(E)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"method-rescaletraits-","dir":"Reference","previous_headings":"","what":"Method rescaleTraits()","title":"Simulation parameters — SimParam","text":"Linearly scales traits achieve desired values means variances founder population.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"usage-25","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulation parameters — SimParam","text":"","code":"SimParam$rescaleTraits(   mean = 0,   var = 1,   varEnv = 0,   varGxE = 1e-06,   useVarA = TRUE )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"arguments-25","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulation parameters — SimParam","text":"mean vector new trait means var vector new trait variances varEnv vector new environmental variances varGxE vector new GxE variances useVarA tune according additive genetic variance true","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"examples-19","dir":"Reference","previous_headings":"","what":"Examples","title":"Simulation parameters — SimParam","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$addTraitA(10)  #Create population pop = newPop(founderPop, simParam=SP) meanG(pop)  #Change mean to 1 SP$rescaleTraits(mean=1) \\dontshow{SP$nThreads = 1L} #Run resetPop for change to take effect pop = resetPop(pop, simParam=SP) meanG(pop)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"method-setrecombratio-","dir":"Reference","previous_headings":"","what":"Method setRecombRatio()","title":"Simulation parameters — SimParam","text":"Set relative recombination rates males females. allows sex-specific recombination rates, assumption equivalent recombination landscapes.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"usage-26","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulation parameters — SimParam","text":"","code":"SimParam$setRecombRatio(femaleRatio)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"arguments-26","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulation parameters — SimParam","text":"femaleRatio relative ratio recombination females compared males. value 2 indicate twice much recombination females. value must greater 0. (default 1)","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"examples-20","dir":"Reference","previous_headings":"","what":"Examples","title":"Simulation parameters — SimParam","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) \\dontshow{SP$nThreads = 1L} SP$setRecombRatio(2) #Twice as much recombination in females"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"method-switchgenmap-","dir":"Reference","previous_headings":"","what":"Method switchGenMap()","title":"Simulation parameters — SimParam","text":"Replaces existing genetic map.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"usage-27","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulation parameters — SimParam","text":"","code":"SimParam$switchGenMap(genMap, centromere = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"arguments-27","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulation parameters — SimParam","text":"genMap list length nChr containing numeric vectors position segregating site chromosome. centromere numeric vector centromere positions. NULL, centromere assumed metacentric.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"method-switchfemalemap-","dir":"Reference","previous_headings":"","what":"Method switchFemaleMap()","title":"Simulation parameters — SimParam","text":"Replaces existing female genetic map.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"usage-28","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulation parameters — SimParam","text":"","code":"SimParam$switchFemaleMap(genMap, centromere = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"arguments-28","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulation parameters — SimParam","text":"genMap list length nChr containing numeric vectors position segregating site chromosome. centromere numeric vector centromere positions. NULL, centromere assumed metacentric.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"method-switchmalemap-","dir":"Reference","previous_headings":"","what":"Method switchMaleMap()","title":"Simulation parameters — SimParam","text":"Replaces existing male genetic map.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"usage-29","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulation parameters — SimParam","text":"","code":"SimParam$switchMaleMap(genMap, centromere = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"arguments-29","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulation parameters — SimParam","text":"genMap list length nChr containing numeric vectors position segregating site chromosome. centromere numeric vector centromere positions. NULL, centromere assumed metacentric.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"method-addtorec-","dir":"Reference","previous_headings":"","what":"Method addToRec()","title":"Simulation parameters — SimParam","text":"internal use .","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"usage-30","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulation parameters — SimParam","text":"","code":"SimParam$addToRec(lastId, id, mother, father, isDH, hist, ploidy)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"arguments-30","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulation parameters — SimParam","text":"lastId ID last individual id name individual mother vector mother iids father vector father iids isDH indicator DH lines hist new recombination history ploidy ploidy level","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"method-ibdhaplo-","dir":"Reference","previous_headings":"","what":"Method ibdHaplo()","title":"Simulation parameters — SimParam","text":"internal use .","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"usage-31","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulation parameters — SimParam","text":"","code":"SimParam$ibdHaplo(iid)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"arguments-31","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulation parameters — SimParam","text":"iid internal ID","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"method-updatelastid-","dir":"Reference","previous_headings":"","what":"Method updateLastId()","title":"Simulation parameters — SimParam","text":"internal use .","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"usage-32","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulation parameters — SimParam","text":"","code":"SimParam$updateLastId(lastId)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"arguments-32","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulation parameters — SimParam","text":"lastId last ID assigned","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"method-addtoped-","dir":"Reference","previous_headings":"","what":"Method addToPed()","title":"Simulation parameters — SimParam","text":"internal use .","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"usage-33","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulation parameters — SimParam","text":"","code":"SimParam$addToPed(lastId, id, mother, father, isDH)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"arguments-33","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulation parameters — SimParam","text":"lastId ID last individual id name individual mother vector mother iids father vector father iids isDH indicator DH lines","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"Simulation parameters — SimParam","text":"objects class cloneable method.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"usage-34","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulation parameters — SimParam","text":"","code":"SimParam$clone(deep = FALSE)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"arguments-34","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulation parameters — SimParam","text":"deep Whether make deep clone.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Simulation parameters — SimParam","text":"","code":"## ------------------------------------------------ ## Method `SimParam$new` ## ------------------------------------------------  #Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop)  ## ------------------------------------------------ ## Method `SimParam$setTrackPed` ## ------------------------------------------------  #Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$setTrackPed(TRUE)  ## ------------------------------------------------ ## Method `SimParam$setTrackRec` ## ------------------------------------------------  #Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$setTrackRec(TRUE)  ## ------------------------------------------------ ## Method `SimParam$resetPed` ## ------------------------------------------------  #Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L  #Create population pop = newPop(founderPop, simParam=SP) pop@id # 1:10 #>  [1] \"1\"  \"2\"  \"3\"  \"4\"  \"5\"  \"6\"  \"7\"  \"8\"  \"9\"  \"10\"  #Create another population after reseting pedigree SP$resetPed() pop2 = newPop(founderPop, simParam=SP) pop2@id # 1:10 #>  [1] \"1\"  \"2\"  \"3\"  \"4\"  \"5\"  \"6\"  \"7\"  \"8\"  \"9\"  \"10\"  ## ------------------------------------------------ ## Method `SimParam$restrSegSites` ## ------------------------------------------------  #Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$restrSegSites(minQtlPerChr=5, minSnpPerChr=5)  ## ------------------------------------------------ ## Method `SimParam$setSexes` ## ------------------------------------------------  #Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$setSexes(\"yes_sys\")  ## ------------------------------------------------ ## Method `SimParam$addSnpChip` ## ------------------------------------------------  #Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addSnpChip(10)  ## ------------------------------------------------ ## Method `SimParam$addSnpChipByName` ## ------------------------------------------------  #Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$addSnpChipByName(c(\"1_1\",\"1_3\"))  ## ------------------------------------------------ ## Method `SimParam$addTraitA` ## ------------------------------------------------  #Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitA(10)  ## ------------------------------------------------ ## Method `SimParam$addTraitAD` ## ------------------------------------------------  #Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitAD(10, meanDD=0.5)  ## ------------------------------------------------ ## Method `SimParam$altAddTraitAD` ## ------------------------------------------------  #Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$altAddTraitAD(nQtlPerChr=10, mean=0, varA=1, varD=0.05, inbrDepr=0.2) #> A new trait called Trait1 was added.  #>    varD = 0.0500001  #>    inbrDepr = 0.2000003  #>    meanDD = 0.01138151  #>    varDD = 0.03436831   ## ------------------------------------------------ ## Method `SimParam$addTraitAG` ## ------------------------------------------------  #Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitAG(10, varGxE=2)  ## ------------------------------------------------ ## Method `SimParam$addTraitADG` ## ------------------------------------------------  #Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitADG(10, meanDD=0.5, varGxE=2)  ## ------------------------------------------------ ## Method `SimParam$addTraitAE` ## ------------------------------------------------  #Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitAE(10, relAA=0.1)  ## ------------------------------------------------ ## Method `SimParam$addTraitADE` ## ------------------------------------------------  #Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitADE(10)  ## ------------------------------------------------ ## Method `SimParam$addTraitAEG` ## ------------------------------------------------  #Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitAEG(10, varGxE=2)  ## ------------------------------------------------ ## Method `SimParam$addTraitADEG` ## ------------------------------------------------  #Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitADEG(10, meanDD=0.5, varGxE=2)  ## ------------------------------------------------ ## Method `SimParam$setVarE` ## ------------------------------------------------  #Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitA(10) SP$setVarE(h2=0.5)  ## ------------------------------------------------ ## Method `SimParam$setCorE` ## ------------------------------------------------  #Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitA(10, mean=c(0,0), var=c(1,1), corA=diag(2)) SP$setVarE(varE=c(1,1)) E = 0.5*diag(2)+0.5 #Positively correlated error SP$setCorE(E) #> Warning: This function has been deprecated. Use simParam$setVarE instead.  ## ------------------------------------------------ ## Method `SimParam$rescaleTraits` ## ------------------------------------------------  #Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$addTraitA(10)  #Create population pop = newPop(founderPop, simParam=SP) meanG(pop) #>       Trait1  #> 6.661338e-17   #Change mean to 1 SP$rescaleTraits(mean=1) SP$nThreads = 1L #Run resetPop for change to take effect pop = resetPop(pop, simParam=SP) meanG(pop) #> Trait1  #>      1   ## ------------------------------------------------ ## Method `SimParam$setRecombRatio` ## ------------------------------------------------  #Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$setRecombRatio(2) #Twice as much recombination in females"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/TraitA-class.html","id":null,"dir":"Reference","previous_headings":"","what":"Additive trait — TraitA-class","title":"Additive trait — TraitA-class","text":"Extends LociMap-class model additive traits","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/TraitA-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"Additive trait — TraitA-class","text":"addEff additive effects intercept adjustment factor gv","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/TraitA2-class.html","id":null,"dir":"Reference","previous_headings":"","what":"Sex specific additive trait — TraitA2-class","title":"Sex specific additive trait — TraitA2-class","text":"Extends TraitA-class model seperate additive effects parent origin. Used exclusively genomic selection.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/TraitA2-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"Sex specific additive trait — TraitA2-class","text":"addEffMale additive effects","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/TraitA2D-class.html","id":null,"dir":"Reference","previous_headings":"","what":"Sex specific additive and dominance trait — TraitA2D-class","title":"Sex specific additive and dominance trait — TraitA2D-class","text":"Extends TraitA2-class add dominance","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/TraitA2D-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"Sex specific additive and dominance trait — TraitA2D-class","text":"domEff dominance effects","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/TraitAD-class.html","id":null,"dir":"Reference","previous_headings":"","what":"Additive and dominance trait — TraitAD-class","title":"Additive and dominance trait — TraitAD-class","text":"Extends TraitA-class add dominance","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/TraitAD-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"Additive and dominance trait — TraitAD-class","text":"domEff dominance effects","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/TraitADE-class.html","id":null,"dir":"Reference","previous_headings":"","what":"Additive, dominance, and epistatic trait — TraitADE-class","title":"Additive, dominance, and epistatic trait — TraitADE-class","text":"Extends TraitAD-class add epistasis","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/TraitADE-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"Additive, dominance, and epistatic trait — TraitADE-class","text":"epiEff epistatic effects","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/TraitADEG-class.html","id":null,"dir":"Reference","previous_headings":"","what":"Additive, dominance, epistasis, and GxE trait — TraitADEG-class","title":"Additive, dominance, epistasis, and GxE trait — TraitADEG-class","text":"Extends TraitADE-class add GxE effects","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/TraitADEG-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"Additive, dominance, epistasis, and GxE trait — TraitADEG-class","text":"gxeEff GxE effects gxeInt GxE intercept envVar Environmental variance","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/TraitADG-class.html","id":null,"dir":"Reference","previous_headings":"","what":"Additive, dominance and GxE trait — TraitADG-class","title":"Additive, dominance and GxE trait — TraitADG-class","text":"Extends TraitAD-class add GxE effects","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/TraitADG-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"Additive, dominance and GxE trait — TraitADG-class","text":"gxeEff GxE effects gxeInt GxE intercept envVar Environmental variance","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/TraitAE-class.html","id":null,"dir":"Reference","previous_headings":"","what":"Additive and epistatic trait — TraitAE-class","title":"Additive and epistatic trait — TraitAE-class","text":"Extends TraitA-class add epistasis","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/TraitAE-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"Additive and epistatic trait — TraitAE-class","text":"epiEff epistatic effects","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/TraitAEG-class.html","id":null,"dir":"Reference","previous_headings":"","what":"Additive, epistasis and GxE trait — TraitAEG-class","title":"Additive, epistasis and GxE trait — TraitAEG-class","text":"Extends TraitAE-class add GxE effects","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/TraitAEG-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"Additive, epistasis and GxE trait — TraitAEG-class","text":"gxeEff GxE effects gxeInt GxE intercept envVar Environmental variance","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/TraitAG-class.html","id":null,"dir":"Reference","previous_headings":"","what":"Additive and GxE trait — TraitAG-class","title":"Additive and GxE trait — TraitAG-class","text":"Extends TraitA-class add GxE effects","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/TraitAG-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"Additive and GxE trait — TraitAG-class","text":"gxeEff GxE effects gxeInt GxE intercept envVar Environmental variance","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/aa.html","id":null,"dir":"Reference","previous_headings":"","what":"Additive-by-additive epistatic deviations — aa","title":"Additive-by-additive epistatic deviations — aa","text":"Returns additive--additive epistatic deviations traits","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/aa.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Additive-by-additive epistatic deviations — aa","text":"","code":"aa(pop, simParam = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/aa.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Additive-by-additive epistatic deviations — aa","text":"pop object Pop-class simParam object SimParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/aa.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Additive-by-additive epistatic deviations — aa","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$addTraitAD(10, meanDD=0.5) SP$setVarE(h2=0.5) SP$nThreads = 1L  #Create population pop = newPop(founderPop, simParam=SP) aa(pop, simParam=SP) #>       Trait1 #>  [1,]      0 #>  [2,]      0 #>  [3,]      0 #>  [4,]      0 #>  [5,]      0 #>  [6,]      0 #>  [7,]      0 #>  [8,]      0 #>  [9,]      0 #> [10,]      0"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/addSegSite.html","id":null,"dir":"Reference","previous_headings":"","what":"Add segregating site to MapPop — addSegSite","title":"Add segregating site to MapPop — addSegSite","text":"function allows adding new  segregating site user supplied genotypes MapPop.  position site set using genetic map position.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/addSegSite.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add segregating site to MapPop — addSegSite","text":"","code":"addSegSite(mapPop, siteName, chr, mapPos, haplo)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/addSegSite.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add segregating site to MapPop — addSegSite","text":"mapPop object MapPop-class siteName name give segregating site chr chromosome add site mapPos genetic map position site Morgans haplo haplotypes site","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/addSegSite.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add segregating site to MapPop — addSegSite","text":"object MapPop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/addSegSite.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add segregating site to MapPop — addSegSite","text":"","code":"# Creates a populations of 10 outbred individuals # Their genome consists of 1 chromosome and 2 segregating sites founderPop = quickHaplo(nInd=10,nChr=1,segSites=2)  # Add a locus a the 0.5 Morgan map position haplo = matrix(sample(x=0:1, size=20, replace=TRUE), ncol=1)  founderPop2 = addSegSite(founderPop, siteName=\"x\", chr=1, mapPos=0.5, haplo=haplo)  pullSegSiteHaplo(founderPop2) #>      1_1 x 1_2 #> 1_1    0 1   0 #> 1_2    0 0   1 #> 2_1    1 0   0 #> 2_2    0 1   0 #> 3_1    0 1   0 #> 3_2    0 0   1 #> 4_1    1 1   1 #> 4_2    0 1   0 #> 5_1    1 0   0 #> 5_2    1 0   1 #> 6_1    0 0   1 #> 6_2    0 1   1 #> 7_1    1 0   1 #> 7_2    1 1   1 #> 8_1    0 1   0 #> 8_2    0 0   1 #> 9_1    1 1   0 #> 9_2    0 1   0 #> 10_1   0 1   1 #> 10_2   0 0   1"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/attrition.html","id":null,"dir":"Reference","previous_headings":"","what":"Lose individuals at random — attrition","title":"Lose individuals at random — attrition","text":"Samples individuals random remove population.  user supplies probability individuals  removed population.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/attrition.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Lose individuals at random — attrition","text":"","code":"attrition(pop, p)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/attrition.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Lose individuals at random — attrition","text":"pop object Pop-class p expected proportion individuals lost attrition.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/attrition.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Lose individuals at random — attrition","text":"object Pop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/attrition.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Lose individuals at random — attrition","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=100, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L  #Create population pop = newPop(founderPop, simParam=SP)  #Lose an expected 5% of individuals pop = attrition(pop, p=0.05)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/bv.html","id":null,"dir":"Reference","previous_headings":"","what":"Breeding value — bv","title":"Breeding value — bv","text":"Returns breeding values traits","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/bv.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Breeding value — bv","text":"","code":"bv(pop, simParam = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/bv.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Breeding value — bv","text":"pop object Pop-class simParam object SimParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/bv.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Breeding value — bv","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$addTraitAD(10, meanDD=0.5) SP$setVarE(h2=0.5) SP$nThreads = 1L  #Create population pop = newPop(founderPop, simParam=SP) bv(pop, simParam=SP) #>            Trait1 #>  [1,] -1.52021353 #>  [2,]  0.04919273 #>  [3,]  0.36564386 #>  [4,] -1.29908982 #>  [5,]  0.67839291 #>  [6,] -0.54851557 #>  [7,]  2.01490898 #>  [8,] -0.36768982 #>  [9,] -0.28308287 #> [10,]  0.91045313"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/cChr.html","id":null,"dir":"Reference","previous_headings":"","what":"Combine MapPop chromosomes — cChr","title":"Combine MapPop chromosomes — cChr","text":"Merges chromosomes multiple MapPop-class NamedMapPop-class objects. MapPop must number chromosomes","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/cChr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Combine MapPop chromosomes — cChr","text":"","code":"cChr(...)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/cChr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Combine MapPop chromosomes — cChr","text":"... MapPop-class NamedMapPop-class objects combined","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/cChr.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Combine MapPop chromosomes — cChr","text":"Returns object MapPop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/cChr.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Combine MapPop chromosomes — cChr","text":"","code":"pop1 = quickHaplo(nInd=10, nChr=1, segSites=10) pop2 = quickHaplo(nInd=10, nChr=1, segSites=10)  combinedPop = cChr(pop1, pop2)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/calcGCA.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate GCA — calcGCA","title":"Calculate GCA — calcGCA","text":"Calculate general combining ability test crosses. Intended output hybridCross using \"testcross\" option, work population.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/calcGCA.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate GCA — calcGCA","text":"","code":"calcGCA(pop, use = \"pheno\")"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/calcGCA.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate GCA — calcGCA","text":"pop object Pop-class HybridPop-class use tabulate either genetic values \"gv\", estimated breeding values \"ebv\", phenotypes \"pheno\"","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/calcGCA.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate GCA — calcGCA","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10, inbred=TRUE)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitA(10)  #Create population pop = newPop(founderPop, simParam=SP)  #Make crosses for full diallele pop2 = hybridCross(pop, pop, simParam=SP) GCA = calcGCA(pop2, use=\"gv\")"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/dd.html","id":null,"dir":"Reference","previous_headings":"","what":"Dominance deviations — dd","title":"Dominance deviations — dd","text":"Returns dominance deviations traits","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/dd.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Dominance deviations — dd","text":"","code":"dd(pop, simParam = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/dd.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Dominance deviations — dd","text":"pop object Pop-class simParam object SimParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/dd.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Dominance deviations — dd","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$addTraitAD(10, meanDD=0.5) SP$setVarE(h2=0.5) SP$nThreads = 1L  #Create population pop = newPop(founderPop, simParam=SP) dd(pop, simParam=SP) #>             Trait1 #>  [1,] -0.248419109 #>  [2,]  0.179293756 #>  [3,] -0.007379679 #>  [4,] -0.434840829 #>  [5,]  0.250492859 #>  [6,]  0.097297389 #>  [7,]  0.152831587 #>  [8,]  0.254442736 #>  [9,]  0.507650125 #> [10,] -0.751368836"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/dot-newPop.html","id":null,"dir":"Reference","previous_headings":"","what":"Create new population (internal) — .newPop","title":"Create new population (internal) — .newPop","text":"Creates new Pop-class object Pop superclass.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/dot-newPop.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create new population (internal) — .newPop","text":"","code":".newPop(   rawPop,   id = NULL,   mother = NULL,   father = NULL,   iMother = NULL,   iFather = NULL,   isDH = NULL,   femaleParentPop = NULL,   maleParentPop = NULL,   hist = NULL,   simParam = NULL,   ... )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/dot-newPop.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create new population (internal) — .newPop","text":"rawPop object pop superclass id optional id new individuals mother optional id mothers father optional id fathers iMother optional internal id mothers iFather optional internal id fathers isDH optional indicator DH/inbred individuals femaleParentPop optional population female parents maleParentPop optional population male parents hist optional recombination history simParam object SimParam ... additional arguments passed finalizePop function simParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/dot-newPop.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create new population (internal) — .newPop","text":"Returns object Pop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/doubleGenome.html","id":null,"dir":"Reference","previous_headings":"","what":"Double the ploidy of individuals — doubleGenome","title":"Double the ploidy of individuals — doubleGenome","text":"Creates new individuals twice ploidy.  function created model formation tetraploid  potatoes diploid potatoes. function work  population.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/doubleGenome.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Double the ploidy of individuals — doubleGenome","text":"","code":"doubleGenome(pop, keepParents = TRUE, simParam = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/doubleGenome.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Double the ploidy of individuals — doubleGenome","text":"pop object 'Pop' superclass keepParents previous parents used mother  father. simParam object 'SimParam' class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/doubleGenome.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Double the ploidy of individuals — doubleGenome","text":"Returns object Pop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/doubleGenome.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Double the ploidy of individuals — doubleGenome","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=2, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L  #Create population pop = newPop(founderPop, simParam=SP)  #Create individuals with doubled ploidy pop2 = doubleGenome(pop, simParam=SP)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/ebv.html","id":null,"dir":"Reference","previous_headings":"","what":"Estimated breeding value — ebv","title":"Estimated breeding value — ebv","text":"wrapper accessing ebv slot","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/ebv.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Estimated breeding value — ebv","text":"","code":"ebv(pop)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/ebv.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Estimated breeding value — ebv","text":"pop Pop-class similar object","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/ebv.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Estimated breeding value — ebv","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitAD(10, meanDD=0.5) SP$setVarE(h2=0.5)  #Create population pop = newPop(founderPop, simParam=SP) pop@ebv = matrix(rnorm(pop@nInd), nrow=pop@nInd, ncol=1) ebv(pop) #>             [,1] #>  [1,] -0.8976515 #>  [2,]  0.2214317 #>  [3,] -1.6471820 #>  [4,] -0.3329894 #>  [5,] -0.1626929 #>  [6,] -1.0593087 #>  [7,] -0.1943854 #>  [8,] -0.1747776 #>  [9,] -0.1671519 #> [10,]  0.4216361"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/editGenome.html","id":null,"dir":"Reference","previous_headings":"","what":"Edit genome — editGenome","title":"Edit genome — editGenome","text":"Edits selected loci selected individuals homozygous  state either 1 0 allele. gv slot recalculated  reflect changes due editing, slots remain .","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/editGenome.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Edit genome — editGenome","text":"","code":"editGenome(pop, ind, chr, segSites, allele, simParam = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/editGenome.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Edit genome — editGenome","text":"pop object Pop-class ind vector individuals edit chr vector chromosomes edit.  Length must match length segSites. segSites vector segregating sites edit. Length must  match length chr. allele either 0 1 desired allele simParam object SimParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/editGenome.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Edit genome — editGenome","text":"Returns object Pop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/editGenome.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Edit genome — editGenome","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=2, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitA(10)  #Create population pop = newPop(founderPop, simParam=SP)  #Change individual 1 to homozygous for the 1 allele  #at locus 1, chromosome 1 pop2 = editGenome(pop, ind=1, chr=1, segSites=1,                    allele=1, simParam=SP)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/editGenomeTopQtl.html","id":null,"dir":"Reference","previous_headings":"","what":"Edit genome - the top QTL — editGenomeTopQtl","title":"Edit genome - the top QTL — editGenomeTopQtl","text":"Edits top QTL (largest additive effect) homozygous  state allele increasing. nonfixed QTL edited gv slot recalculated reflect changes due editing, slots remain .","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/editGenomeTopQtl.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Edit genome - the top QTL — editGenomeTopQtl","text":"","code":"editGenomeTopQtl(pop, ind, nQtl, trait = 1, increase = TRUE, simParam = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/editGenomeTopQtl.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Edit genome - the top QTL — editGenomeTopQtl","text":"pop object Pop-class ind vector individuals edit nQtl number QTL edit trait trait effects guide selection top QTL increase trait value increased decreased simParam object SimParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/editGenomeTopQtl.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Edit genome - the top QTL — editGenomeTopQtl","text":"Returns object Pop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/editGenomeTopQtl.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Edit genome - the top QTL — editGenomeTopQtl","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=2, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitA(10)  #Create population pop = newPop(founderPop, simParam=SP)  #Change up to 10 loci for individual 1  pop2 = editGenomeTopQtl(pop, ind=1, nQtl=10, simParam=SP)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/fastRRBLUP.html","id":null,"dir":"Reference","previous_headings":"","what":"Fast RR-BLUP — fastRRBLUP","title":"Fast RR-BLUP — fastRRBLUP","text":"Solves RR-BLUP model genomic predictions given known variance  components. implementation meant fast low memory  alternative RRBLUP RRBLUP2. Unlike  functions, fastRRBLUP fit fixed effects ( intercept) account unequal replication.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/fastRRBLUP.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fast RR-BLUP — fastRRBLUP","text":"","code":"fastRRBLUP(   pop,   traits = 1,   use = \"pheno\",   snpChip = 1,   useQtl = FALSE,   maxIter = 1000,   Vu = NULL,   Ve = NULL,   simParam = NULL,   ... )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/fastRRBLUP.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fast RR-BLUP — fastRRBLUP","text":"pop Pop-class serve training population traits integer indicating trait model, trait name,  function traits returning single value. univariate models  supported. use train model using phenotypes \"pheno\", genetic values \"gv\",  estimated breeding values \"ebv\", breeding values \"bv\", randomly \"rand\" snpChip integer indicating SNP chip genotype  use useQtl QTL genotypes used instead SNP chip.  TRUE, snpChip specifies trait's QTL use, thus  QTL may match QTL underlying phenotype supplied traits. maxIter maximum number iterations. Vu marker effect variance. value NULL,  reasonable value chosen automatically. Ve error variance. value NULL,  reasonable value chosen automatically. simParam object SimParam ... additional arguments using function  traits","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/fastRRBLUP.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Fast RR-BLUP — fastRRBLUP","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=20)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitA(10) SP$setVarE(h2=0.5) SP$addSnpChip(10)  #Create population pop = newPop(founderPop, simParam=SP)  #Run GS model and set EBV ans = fastRRBLUP(pop, simParam=SP) pop = setEBV(pop, ans, simParam=SP)  #Evaluate accuracy cor(gv(pop), ebv(pop)) #>        est_GV_Trait1 #> Trait1     0.8010933"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/genParam.html","id":null,"dir":"Reference","previous_headings":"","what":"Sumarize genetic parameters — genParam","title":"Sumarize genetic parameters — genParam","text":"Calculates genetic genic additive dominance variances object Pop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/genParam.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sumarize genetic parameters — genParam","text":"","code":"genParam(pop, simParam = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/genParam.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sumarize genetic parameters — genParam","text":"pop object Pop-class simParam object SimParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/genParam.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Sumarize genetic parameters — genParam","text":"varA nTrait nTrait matrix additive genetic variances varD nTrait nTrait matrix dominance genetic variances varAA nTrait nTrait matrix additive--additive genetic variances varG nTrait nTrait matrix total genetic variances genicVarA nTrait vector additive genic variances genicVarD nTrait vector dominance genic variances genicVarAA nTrait vector additive--additive genic variances genicVarG nTrait vector total genic variances covA_HW nTrait vector additive covariances due non-random mating covD_HW nTrait vector dominance covariances due non-random mating covAA_HW nTrait vector additive--additive covariances due non-random mating covG_HW nTrait vector total genic covariances due non-random mating covA_L nTrait vector additive covariances due linkage disequilibrium covD_L nTrait vector dominance covariances due linkage disequilibrium covAA_L nTrait vector additive--additive covariances due linkage disequilibrium covAD_L nTrait vector additive dominance covariances due linkage disequilibrium covAAA_L nTrait vector additive additive--additive covariances due linkage disequilibrium covDAA_L nTrait vector dominance additive--additive covariances due linkage disequilibrium covG_L nTrait vector total genic covariances due linkage disequilibrium mu nTrait vector trait means mu_HW nTrait vector expected trait means random mating gv matrix genetic values dimensions nInd nTraits bv matrix breeding values dimensions nInd nTraits dd matrix dominance deviations dimensions nInd nTraits aa matrix additive--additive epistatic deviations dimensions nInd nTraits gv_mu nTrait vector intercepts dimensions nInd nTraits gv_a matrix additive genetic values dimensions nInd nTraits gv_d matrix dominance genetic values dimensions nInd nTraits gv_aa matrix additive--additive genetic values dimensions nInd nTraits","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/genParam.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Sumarize genetic parameters — genParam","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$addTraitAD(10, meanDD=0.5) SP$setVarE(h2=0.5) SP$nThreads = 1L  #Create population pop = newPop(founderPop, simParam=SP) ans = genParam(pop, simParam=SP)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/genicVarA.html","id":null,"dir":"Reference","previous_headings":"","what":"Additive genic variance — genicVarA","title":"Additive genic variance — genicVarA","text":"Returns additive genic variance traits","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/genicVarA.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Additive genic variance — genicVarA","text":"","code":"genicVarA(pop, simParam = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/genicVarA.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Additive genic variance — genicVarA","text":"pop object Pop-class simParam object SimParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/genicVarA.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Additive genic variance — genicVarA","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$addTraitAD(10, meanDD=0.5) SP$setVarE(h2=0.5) SP$nThreads = 1L  #Create population pop = newPop(founderPop, simParam=SP) genicVarA(pop, simParam=SP) #>    Trait1  #> 0.8569866"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/genicVarAA.html","id":null,"dir":"Reference","previous_headings":"","what":"Additive-by-additive genic variance — genicVarAA","title":"Additive-by-additive genic variance — genicVarAA","text":"Returns additive--additive epistatic genic variance traits","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/genicVarAA.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Additive-by-additive genic variance — genicVarAA","text":"","code":"genicVarAA(pop, simParam = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/genicVarAA.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Additive-by-additive genic variance — genicVarAA","text":"pop object Pop-class simParam object SimParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/genicVarAA.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Additive-by-additive genic variance — genicVarAA","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$addTraitAD(10, meanDD=0.5) SP$setVarE(h2=0.5) SP$nThreads = 1L  #Create population pop = newPop(founderPop, simParam=SP) genicVarAA(pop, simParam=SP) #> Trait1  #>      0"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/genicVarD.html","id":null,"dir":"Reference","previous_headings":"","what":"Dominance genic variance — genicVarD","title":"Dominance genic variance — genicVarD","text":"Returns dominance genic variance traits","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/genicVarD.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Dominance genic variance — genicVarD","text":"","code":"genicVarD(pop, simParam = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/genicVarD.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Dominance genic variance — genicVarD","text":"pop object Pop-class simParam object SimParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/genicVarD.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Dominance genic variance — genicVarD","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$addTraitAD(10, meanDD=0.5) SP$setVarE(h2=0.5) SP$nThreads = 1L  #Create population pop = newPop(founderPop, simParam=SP) genicVarD(pop, simParam=SP) #>    Trait1  #> 0.1472531"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/genicVarG.html","id":null,"dir":"Reference","previous_headings":"","what":"Total genic variance — genicVarG","title":"Total genic variance — genicVarG","text":"Returns total genic variance traits","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/genicVarG.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Total genic variance — genicVarG","text":"","code":"genicVarG(pop, simParam = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/genicVarG.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Total genic variance — genicVarG","text":"pop object Pop-class simParam object SimParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/genicVarG.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Total genic variance — genicVarG","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$addTraitAD(10, meanDD=0.5) SP$setVarE(h2=0.5) SP$nThreads = 1L  #Create population pop = newPop(founderPop, simParam=SP) genicVarG(pop, simParam=SP) #>    Trait1  #> 0.5949148"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/getGenMap.html","id":null,"dir":"Reference","previous_headings":"","what":"Get genetic map — getGenMap","title":"Get genetic map — getGenMap","text":"Retrieves genetic map loci.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/getGenMap.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get genetic map — getGenMap","text":"","code":"getGenMap(object = NULL, sex = \"A\")"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/getGenMap.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get genetic map — getGenMap","text":"object retrieve genetic map.  Can object SimParam  MapPop-class. NULL, function  look SimParam object called \"SP\"  global environment. sex determines sex specific map  returned. Options \"\" average map, \"F\"  female map, \"M\" male map. options  equivalent using sex specific maps using  pulling MapPop.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/getGenMap.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get genetic map — getGenMap","text":"Returns data.frame : id Unique identifier locus chr Chromosome containing locus pos Genetic map position","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/getGenMap.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get genetic map — getGenMap","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters getGenMap(founderPop) #>      id chr       pos #> 1   1_1   1 0.0000000 #> 2   1_2   1 0.1111111 #> 3   1_3   1 0.2222222 #> 4   1_4   1 0.3333333 #> 5   1_5   1 0.4444444 #> 6   1_6   1 0.5555556 #> 7   1_7   1 0.6666667 #> 8   1_8   1 0.7777778 #> 9   1_9   1 0.8888889 #> 10 1_10   1 1.0000000"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/getMisc.html","id":null,"dir":"Reference","previous_headings":"","what":"Get miscelaneous information in a population — getMisc","title":"Get miscelaneous information in a population — getMisc","text":"Get miscelaneous information population","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/getMisc.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get miscelaneous information in a population — getMisc","text":"","code":"getMisc(x, node = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/getMisc.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get miscelaneous information in a population — getMisc","text":"x Pop-class node character, name node get x@misc slot; NULL whole x@misc slot returned","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/getMisc.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get miscelaneous information in a population — getMisc","text":"x@misc slot nodes x@misc[[*]][[node]]","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/getMisc.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get miscelaneous information in a population — getMisc","text":"","code":"founderGenomes <- quickHaplo(nInd = 3, nChr = 1, segSites = 100) SP <- SimParam$new(founderGenomes) SP$nThreads = 1L basePop <- newPop(founderGenomes) #> Error in get(\"SP\", envir = .GlobalEnv): object 'SP' not found  basePop <- setMisc(basePop, node = \"info\", value = 1) #> Error in eval(expr, envir, enclos): object 'basePop' not found basePop@misc #> Error in eval(expr, envir, enclos): object 'basePop' not found getMisc(x = basePop, node = \"info\") #> Error in eval(expr, envir, enclos): object 'basePop' not found  basePop <- setMisc(basePop, node = \"info2\", value = c(\"A\", \"B\", \"C\")) #> Error in eval(expr, envir, enclos): object 'basePop' not found basePop@misc #> Error in eval(expr, envir, enclos): object 'basePop' not found getMisc(x = basePop, node = \"info2\") #> Error in eval(expr, envir, enclos): object 'basePop' not found  n <- nInd(basePop) #> Error in eval(expr, envir, enclos): object 'basePop' not found location <- vector(mode = \"list\", length = n) #> Error in eval(expr, envir, enclos): object 'n' not found for (ind in seq_len(n)) {   location[[ind]] <- runif(n = 2, min = 0, max = 100) } #> Error in eval(expr, envir, enclos): object 'n' not found location #> Error in eval(expr, envir, enclos): object 'location' not found basePop <- setMisc(basePop, node = \"location\", value = location) #> Error in eval(expr, envir, enclos): object 'basePop' not found basePop@misc #> Error in eval(expr, envir, enclos): object 'basePop' not found getMisc(x = basePop, node = \"location\") #> Error in eval(expr, envir, enclos): object 'basePop' not found  n <- nInd(basePop) #> Error in eval(expr, envir, enclos): object 'basePop' not found location <- vector(mode = \"list\", length = n) #> Error in eval(expr, envir, enclos): object 'n' not found for (ind in c(1, 3)) {   location[[ind]] <- runif(n = 2, min = 0, max = 100) } #> Error: object 'location' not found location #> Error in eval(expr, envir, enclos): object 'location' not found basePop <- setMisc(basePop, node = \"location\", value = location) #> Error in eval(expr, envir, enclos): object 'basePop' not found basePop@misc #> Error in eval(expr, envir, enclos): object 'basePop' not found getMisc(x = basePop, node = \"location\") #> Error in eval(expr, envir, enclos): object 'basePop' not found  getMisc(x = basePop) #> Error in eval(expr, envir, enclos): object 'basePop' not found"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/getNumThreads.html","id":null,"dir":"Reference","previous_headings":"","what":"Number of available threads — getNumThreads","title":"Number of available threads — getNumThreads","text":"Gets number available threads calling OpenMP function omp_get_max_threads()","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/getNumThreads.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Number of available threads — getNumThreads","text":"","code":"getNumThreads()"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/getNumThreads.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Number of available threads — getNumThreads","text":"integer","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/getNumThreads.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Number of available threads — getNumThreads","text":"","code":"getNumThreads() #> [1] 2"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/getPed.html","id":null,"dir":"Reference","previous_headings":"","what":"Get pedigree — getPed","title":"Get pedigree — getPed","text":"Returns population's pedigree stored  id, mother father slots. NULL returned  input population lacks required.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/getPed.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get pedigree — getPed","text":"","code":"getPed(pop)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/getPed.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get pedigree — getPed","text":"pop population","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/getPed.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get pedigree — getPed","text":"","code":"# Create a founder population founderPop = quickHaplo(2,1,2)  # Set simulation parameters SP = SimParam$new(founderPop)  # Create a population pop = newPop(founderPop, simParam=SP)  # Get the pedigree getPed(pop) #>   id mother father #> 1  1      0      0 #> 2  2      0      0  # Returns NULL when a population lacks a pedigree getPed(founderPop) #> NULL"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/getQtlMap.html","id":null,"dir":"Reference","previous_headings":"","what":"Get QTL genetic map — getQtlMap","title":"Get QTL genetic map — getQtlMap","text":"Retrieves genetic map  QTL given trait.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/getQtlMap.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get QTL genetic map — getQtlMap","text":"","code":"getQtlMap(trait = 1, sex = \"A\", simParam = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/getQtlMap.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get QTL genetic map — getQtlMap","text":"trait integer sex determines sex specific map  returned. Options \"\" average map, \"F\"  female map, \"M\" male map. options  equivalent using sex specific maps. simParam object SimParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/getQtlMap.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get QTL genetic map — getQtlMap","text":"Returns data.frame : id Unique identifier QTL chr Chromosome containing QTL site Segregating site chromosome pos Genetic map position","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/getQtlMap.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get QTL genetic map — getQtlMap","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitA(5)  #Pull SNP map getQtlMap(trait=1, simParam=SP) #>        id chr site       pos #> 1_2   1_2   1    2 0.1111111 #> 1_3   1_3   1    3 0.2222222 #> 1_6   1_6   1    6 0.5555556 #> 1_7   1_7   1    7 0.6666667 #> 1_10 1_10   1   10 1.0000000"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/getSnpMap.html","id":null,"dir":"Reference","previous_headings":"","what":"Get SNP genetic map — getSnpMap","title":"Get SNP genetic map — getSnpMap","text":"Retrieves genetic map  given SNP chip.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/getSnpMap.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get SNP genetic map — getSnpMap","text":"","code":"getSnpMap(snpChip = 1, sex = \"A\", simParam = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/getSnpMap.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get SNP genetic map — getSnpMap","text":"snpChip integer. Indicates SNP chip's map retrieve. sex determines sex specific map  returned. Options \"\" average map, \"F\"  female map, \"M\" male map. options  equivalent using sex specific maps. simParam object SimParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/getSnpMap.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get SNP genetic map — getSnpMap","text":"Returns data.frame : id Unique identifier SNP chr Chromosome containing SNP site Segregating site chromosome pos Genetic map position","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/getSnpMap.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get SNP genetic map — getSnpMap","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addSnpChip(5)  #Pull SNP map getSnpMap(snpChip=1, simParam=SP) #>        id chr site       pos #> 1_1   1_1   1    1 0.0000000 #> 1_4   1_4   1    4 0.3333333 #> 1_5   1_5   1    5 0.4444444 #> 1_8   1_8   1    8 0.7777778 #> 1_10 1_10   1   10 1.0000000"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/gv.html","id":null,"dir":"Reference","previous_headings":"","what":"Genetic value — gv","title":"Genetic value — gv","text":"wrapper accessing gv slot","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/gv.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Genetic value — gv","text":"","code":"gv(pop)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/gv.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Genetic value — gv","text":"pop Pop-class similar object","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/gv.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Genetic value — gv","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$addTraitAD(10, meanDD=0.5) SP$setVarE(h2=0.5) SP$nThreads = 1L  #Create population pop = newPop(founderPop, simParam=SP) gv(pop) #>            Trait1 #>  [1,] -2.41548806 #>  [2,]  0.90689241 #>  [3,] -1.80278854 #>  [4,] -0.01096506 #>  [5,]  0.66019369 #>  [6,]  1.05091577 #>  [7,]  0.48108102 #>  [8,]  0.69332057 #>  [9,] -0.39240571 #> [10,]  0.82924390"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/hybridCross.html","id":null,"dir":"Reference","previous_headings":"","what":"Hybrid crossing — hybridCross","title":"Hybrid crossing — hybridCross","text":"convience function hybrid plant breeding simulations. Allows easy specification test cross scheme /creation object HybridPop-class. Note HybridPop-class used parents created using makeDH function newPop using inbred founders. id new individuals [mother_id]_[father_id]","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/hybridCross.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Hybrid crossing — hybridCross","text":"","code":"hybridCross(   females,   males,   crossPlan = \"testcross\",   returnHybridPop = FALSE,   simParam = NULL )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/hybridCross.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Hybrid crossing — hybridCross","text":"females female population, object Pop-class males male population, object Pop-class crossPlan either \"testcross\" possible combinantions matrix two columns designed crosses returnHybridPop results returned HybridPop-class. false returns results Pop-class. Population must fully inbred TRUE. simParam object SimParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/hybridCross.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Hybrid crossing — hybridCross","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=2, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L  #Create population pop = newPop(founderPop, simParam=SP)  #Make crosses for full diallele pop2 = hybridCross(pop, pop, simParam=SP)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/importGenMap.html","id":null,"dir":"Reference","previous_headings":"","what":"Import genetic map — importGenMap","title":"Import genetic map — importGenMap","text":"Formats genetic map stored data.frame AlphaSimR's internal format. Map positions must  Morgans.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/importGenMap.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Import genetic map — importGenMap","text":"","code":"importGenMap(genMap)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/importGenMap.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Import genetic map — importGenMap","text":"genMap genetic map data.frame. first three columns must : marker name, chromosome,  map position (Morgans). Marker name chromosome  coerced using .character.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/importGenMap.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Import genetic map — importGenMap","text":"list named vectors","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/importGenMap.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Import genetic map — importGenMap","text":"","code":"genMap = data.frame(markerName=letters[1:5],                     chromosome=c(1,1,1,2,2),                     position=c(0,0.5,1,0.15,0.4))  asrMap = importGenMap(genMap=genMap)  str(asrMap) #> List of 2 #>  $ 1: Named num [1:3] 0 0.5 1 #>   ..- attr(*, \"names\")= chr [1:3] \"a\" \"b\" \"c\" #>  $ 2: Named num [1:2] 0 0.25 #>   ..- attr(*, \"names\")= chr [1:2] \"d\" \"e\""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/importHaplo.html","id":null,"dir":"Reference","previous_headings":"","what":"Import haplotypes — importHaplo","title":"Import haplotypes — importHaplo","text":"Formats haplotype matrix format  AlphaSimR population can used  initialize simulation. function serves  wrapper newMapPop  utilizes user friendly input format.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/importHaplo.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Import haplotypes — importHaplo","text":"","code":"importHaplo(haplo, genMap, ploidy = 2L, ped = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/importHaplo.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Import haplotypes — importHaplo","text":"haplo matrix haplotypes genMap genetic map data.frame. first three columns must : marker name, chromosome,  map position (Morgans). Marker name chromosome  coerced using .character. See importGenMap ploidy ploidy level organism ped optional pedigree supplied  genotypes. See details.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/importHaplo.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Import haplotypes — importHaplo","text":"MapPop-class ped NULL, otherwise NamedMapPop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/importHaplo.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Import haplotypes — importHaplo","text":"optional pedigree can data.frame, matrix vector.  object data.frame matrix, first three  columns must include information following order: id,  mother, father. values coerced using  .character. object vector, assumed  include id. case, mother father set  \"0\" individuals.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/importHaplo.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Import haplotypes — importHaplo","text":"","code":"haplo = rbind(c(1,1,0,1,0),               c(1,1,0,1,0),               c(0,1,1,0,0),               c(0,1,1,0,0)) colnames(haplo) = letters[1:5]  genMap = data.frame(markerName=letters[1:5],                     chromosome=c(1,1,1,2,2),                     position=c(0,0.5,1,0.15,0.4))  ped = data.frame(id=c(\"a\",\"b\"),                  mother=c(0,0),                  father=c(0,0))  founderPop = importHaplo(haplo=haplo,                           genMap=genMap,                          ploidy=2L,                          ped=ped)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/importInbredGeno.html","id":null,"dir":"Reference","previous_headings":"","what":"Import inbred, diploid genotypes — importInbredGeno","title":"Import inbred, diploid genotypes — importInbredGeno","text":"Formats genotypes inbred, diploid lines  AlphaSimR population can used  initialize simulation. attempt made  automatically detect 0,1,2 -1,0,1 genotype coding.  Heterozygotes probabilistic genotypes allowed,  coerced nearest homozygote. Pedigree  information optional provided  passed population easier identification  simulation.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/importInbredGeno.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Import inbred, diploid genotypes — importInbredGeno","text":"","code":"importInbredGeno(geno, genMap, ped = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/importInbredGeno.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Import inbred, diploid genotypes — importInbredGeno","text":"geno matrix genotypes genMap genetic map data.frame. first three columns must : marker name, chromosome,  map position (Morgans). Marker name chromosome  coerced using .character. See importGenMap ped optional pedigree supplied  genotypes. See details.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/importInbredGeno.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Import inbred, diploid genotypes — importInbredGeno","text":"MapPop-class ped NULL, otherwise NamedMapPop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/importInbredGeno.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Import inbred, diploid genotypes — importInbredGeno","text":"optional pedigree can data.frame, matrix vector.  object data.frame matrix, first three  columns must include information following order: id,  mother, father. values coerced using  .character. object vector, assumed  include id. case, mother father set  \"0\" individuals.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/importInbredGeno.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Import inbred, diploid genotypes — importInbredGeno","text":"","code":"geno = rbind(c(2,2,0,2,0),              c(0,2,2,0,0)) colnames(geno) = letters[1:5]  genMap = data.frame(markerName=letters[1:5],                     chromosome=c(1,1,1,2,2),                     position=c(0,0.5,1,0.15,0.4))  ped = data.frame(id=c(\"a\",\"b\"),                  mother=c(0,0),                  father=c(0,0))  founderPop = importInbredGeno(geno=geno,                               genMap=genMap,                               ped=ped)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/isFemale.html","id":null,"dir":"Reference","previous_headings":"","what":"Test if individuals of a population are female or male — isFemale","title":"Test if individuals of a population are female or male — isFemale","text":"Test individuals population female male","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/isFemale.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Test if individuals of a population are female or male — isFemale","text":"","code":"isFemale(x)  isMale(x)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/isFemale.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Test if individuals of a population are female or male — isFemale","text":"x Pop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/isFemale.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Test if individuals of a population are female or male — isFemale","text":"logical","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/isFemale.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Test if individuals of a population are female or male — isFemale","text":"isMale(): Test individuals population female male","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/isFemale.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Test if individuals of a population are female or male — isFemale","text":"","code":"founderGenomes <- quickHaplo(nInd = 3, nChr = 1, segSites = 100) SP <- SimParam$new(founderGenomes) SP$setSexes(sexes = \"yes_sys\") pop <- newPop(founderGenomes) #> Error in get(\"SP\", envir = .GlobalEnv): object 'SP' not found  isFemale(pop) #> Error in eval(expr, envir, enclos): object 'pop' not found isMale(pop) #> Error in eval(expr, envir, enclos): object 'pop' not found  pop[isFemale(pop)] #> Error in eval(expr, envir, enclos): object 'pop' not found pop[isFemale(pop)]@sex #> Error in eval(expr, envir, enclos): object 'pop' not found"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/isPop.html","id":null,"dir":"Reference","previous_headings":"","what":"Test if object is of a Population class — isPop","title":"Test if object is of a Population class — isPop","text":"Utilify function test object Population class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/isPop.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Test if object is of a Population class — isPop","text":"","code":"isPop(x)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/isPop.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Test if object is of a Population class — isPop","text":"x Pop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/isPop.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Test if object is of a Population class — isPop","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=2, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$addTraitA(10)  #Create population pop = newPop(founderPop, simParam=SP) isPop(pop) #> [1] TRUE isPop(SP) #> [1] FALSE"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/makeCross.html","id":null,"dir":"Reference","previous_headings":"","what":"Make designed crosses — makeCross","title":"Make designed crosses — makeCross","text":"Makes crosses within population using user supplied crossing plan.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/makeCross.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make designed crosses — makeCross","text":"","code":"makeCross(pop, crossPlan, nProgeny = 1, simParam = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/makeCross.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make designed crosses — makeCross","text":"pop object Pop-class crossPlan matrix two column representing female male parents. Either integers position population character strings IDs. nProgeny number progeny per cross simParam object SimParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/makeCross.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make designed crosses — makeCross","text":"Returns object Pop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/makeCross.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Make designed crosses — makeCross","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L  #Create population pop = newPop(founderPop, simParam=SP)  #Cross individual 1 with individual 10 crossPlan = matrix(c(1,10), nrow=1, ncol=2) pop2 = makeCross(pop, crossPlan, simParam=SP)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/makeCross2.html","id":null,"dir":"Reference","previous_headings":"","what":"Make designed crosses — makeCross2","title":"Make designed crosses — makeCross2","text":"Makes crosses two populations using user supplied crossing plan.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/makeCross2.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make designed crosses — makeCross2","text":"","code":"makeCross2(females, males, crossPlan, nProgeny = 1, simParam = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/makeCross2.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make designed crosses — makeCross2","text":"females object Pop-class female parents. males object Pop-class male parents. crossPlan matrix two column representing female male parents. Either integers position population character strings IDs. nProgeny number progeny per cross simParam object SimParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/makeCross2.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make designed crosses — makeCross2","text":"Returns object Pop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/makeCross2.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Make designed crosses — makeCross2","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L  #Create population pop = newPop(founderPop, simParam=SP)  #Cross individual 1 with individual 10 crossPlan = matrix(c(1,10), nrow=1, ncol=2) pop2 = makeCross2(pop, pop, crossPlan, simParam=SP)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/makeDH.html","id":null,"dir":"Reference","previous_headings":"","what":"Generates DH lines — makeDH","title":"Generates DH lines — makeDH","text":"Creates DH lines individual population. works diploid individuals. polyploids, use reduceGenome doubleGenome.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/makeDH.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generates DH lines — makeDH","text":"","code":"makeDH(pop, nDH = 1, useFemale = TRUE, keepParents = TRUE, simParam = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/makeDH.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generates DH lines — makeDH","text":"pop object 'Pop' superclass nDH total number DH lines per individual useFemale female recombination rates used. keepParents previous parents used mother father. simParam object 'SimParam' class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/makeDH.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generates DH lines — makeDH","text":"Returns object Pop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/makeDH.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Generates DH lines — makeDH","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=2, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L  #Create population pop = newPop(founderPop, simParam=SP)  #Create 1 DH for each individual pop2 = makeDH(pop, simParam=SP)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/meanG.html","id":null,"dir":"Reference","previous_headings":"","what":"Mean genetic values — meanG","title":"Mean genetic values — meanG","text":"Returns mean genetic values traits","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/meanG.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Mean genetic values — meanG","text":"","code":"meanG(pop)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/meanG.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Mean genetic values — meanG","text":"pop object Pop-class HybridPop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/meanG.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Mean genetic values — meanG","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$addTraitA(10) SP$setVarE(h2=0.5) SP$nThreads = 1L  #Create population pop = newPop(founderPop, simParam=SP) meanG(pop) #>        Trait1  #> -1.110223e-17"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/meanP.html","id":null,"dir":"Reference","previous_headings":"","what":"Mean phenotypic values — meanP","title":"Mean phenotypic values — meanP","text":"Returns mean phenotypic values traits","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/meanP.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Mean phenotypic values — meanP","text":"","code":"meanP(pop)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/meanP.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Mean phenotypic values — meanP","text":"pop object Pop-class HybridPop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/meanP.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Mean phenotypic values — meanP","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$addTraitA(10) SP$setVarE(h2=0.5) SP$nThreads = 1L  #Create population pop = newPop(founderPop, simParam=SP) meanP(pop) #>      Trait1  #> -0.06565018"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/mergeGenome.html","id":null,"dir":"Reference","previous_headings":"","what":"Combine genomes of individuals — mergeGenome","title":"Combine genomes of individuals — mergeGenome","text":"function designed model pairing gametes. male female individuals treated gametes, ploidy newly  created individuals sum parents.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/mergeGenome.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Combine genomes of individuals — mergeGenome","text":"","code":"mergeGenome(females, males, crossPlan, simParam = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/mergeGenome.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Combine genomes of individuals — mergeGenome","text":"females object Pop-class female parents. males object Pop-class male parents. crossPlan matrix two column representing female male parents. Either integers position population character strings IDs. simParam object SimParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/mergeGenome.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Combine genomes of individuals — mergeGenome","text":"Returns object Pop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/mergeGenome.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Combine genomes of individuals — mergeGenome","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L  #Create population pop = newPop(founderPop, simParam=SP)  #Cross individual 1 with individual 10 crossPlan = matrix(c(1,10), nrow=1, ncol=2) pop2 = mergeGenome(pop, pop, crossPlan, simParam=SP)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/mergePops.html","id":null,"dir":"Reference","previous_headings":"","what":"Merge list of populations — mergePops","title":"Merge list of populations — mergePops","text":"Rapidly merges list populations single population","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/mergePops.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Merge list of populations — mergePops","text":"","code":"mergePops(popList)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/mergePops.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Merge list of populations — mergePops","text":"popList list containing Pop-class elements MultiPop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/mergePops.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Merge list of populations — mergePops","text":"Returns Pop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/mergePops.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Merge list of populations — mergePops","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L  #Create a list of populations and merge list pop = newPop(founderPop, simParam=SP) popList = list(pop, pop) pop2 = mergePops(popList)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/mutate.html","id":null,"dir":"Reference","previous_headings":"","what":"Add Random Mutations — mutate","title":"Add Random Mutations — mutate","text":"Adds random mutations individuals  population. Note existing phenotypes  EBVs kept. Thus, user need run  setPheno /setEBV  generate new phenotypes EBVs reflect  changes introduced new mutations.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/mutate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add Random Mutations — mutate","text":"","code":"mutate(pop, mutRate = 2.5e-08, returnPos = FALSE, simParam = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/mutate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add Random Mutations — mutate","text":"pop object Pop-class mutRate rate new mutations returnPos positions mutations returned simParam object SimParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/mutate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add Random Mutations — mutate","text":"object Pop-class  returnPos=FALSE list containing  Pop-class data.frame containing  postions mutations returnPos=TRUE","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/mutate.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add Random Mutations — mutate","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=2, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitA(10)  #Create population pop = newPop(founderPop, simParam=SP)  #Introduce mutations pop = mutate(pop, simParam=SP)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/nInd.html","id":null,"dir":"Reference","previous_headings":"","what":"Number of individuals — nInd","title":"Number of individuals — nInd","text":"wrapper accessing nInd slot","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/nInd.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Number of individuals — nInd","text":"","code":"nInd(pop)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/nInd.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Number of individuals — nInd","text":"pop Pop-class similar object","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/nInd.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Number of individuals — nInd","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitAD(10, meanDD=0.5) SP$setVarE(h2=0.5)  #Create population pop = newPop(founderPop, simParam=SP) nInd(pop) #> [1] 10"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/newEmptyPop.html","id":null,"dir":"Reference","previous_headings":"","what":"Creates an empty population — newEmptyPop","title":"Creates an empty population — newEmptyPop","text":"Creates empty Pop-class object user defined ploidy parameters taken simParam.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/newEmptyPop.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Creates an empty population — newEmptyPop","text":"","code":"newEmptyPop(ploidy = 2L, simParam = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/newEmptyPop.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Creates an empty population — newEmptyPop","text":"ploidy ploidy population simParam object SimParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/newEmptyPop.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Creates an empty population — newEmptyPop","text":"Returns object Pop-class zero individuals","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/newEmptyPop.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Creates an empty population — newEmptyPop","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=2, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$addTraitA(10)  #Create empty population pop = newEmptyPop(simParam=SP) isPop(pop) #> [1] TRUE"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/newMapPop.html","id":null,"dir":"Reference","previous_headings":"","what":"New MapPop — newMapPop","title":"New MapPop — newMapPop","text":"Creates new MapPop-class user supplied  genetic maps haplotypes.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/newMapPop.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"New MapPop — newMapPop","text":"","code":"newMapPop(genMap, haplotypes, inbred = FALSE, ploidy = 2L)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/newMapPop.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"New MapPop — newMapPop","text":"genMap list genetic maps haplotypes list matrices data.frames  can coerced matrices. See details. inbred individuals fully inbred ploidy ploidy level organism","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/newMapPop.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"New MapPop — newMapPop","text":"object MapPop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/newMapPop.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"New MapPop — newMapPop","text":"item genMap must vector ordered genetic lengths  Morgans. first value must zero. length vector  determines number segregating sites chromosome. item haplotypes must coercible matrix. columns  matrix correspond segregating sites. number rows  must match number individuals times ploidy using  inbred=FALSE. using inbred=TRUE, number rows must equal  number individuals. haplotypes can stored numeric,  integer raw. underlying C++ function use raw.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/newMapPop.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"New MapPop — newMapPop","text":"","code":"# Create genetic map for two chromosomes, each 1 Morgan long # Each chromosome contains 11 equally spaced segregating sites genMap = list(seq(0,1,length.out=11),                seq(0,1,length.out=11))                 # Create haplotypes for 10 outbred individuals chr1 = sample(x=0:1,size=20*11,replace=TRUE) chr1 = matrix(chr1,nrow=20,ncol=11) chr2 = sample(x=0:1,size=20*11,replace=TRUE) chr2 = matrix(chr2,nrow=20,ncol=11) haplotypes = list(chr1,chr2)  founderPop = newMapPop(genMap=genMap, haplotypes=haplotypes)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/newMultiPop.html","id":null,"dir":"Reference","previous_headings":"","what":"Create new Multi Population — newMultiPop","title":"Create new Multi Population — newMultiPop","text":"Creates new MultiPop-class one Pop-class /MultiPop-class objects.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/newMultiPop.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create new Multi Population — newMultiPop","text":"","code":"newMultiPop(...)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/newMultiPop.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create new Multi Population — newMultiPop","text":"... one Pop-class /MultiPop-class objects.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/newMultiPop.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create new Multi Population — newMultiPop","text":"Returns object MultiPop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/newMultiPop.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create new Multi Population — newMultiPop","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=2, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$addTraitA(10)  #Create population pop = newPop(founderPop, simParam=SP) megaPop = newMultiPop(pop=pop) isMultiPop(megaPop) #> [1] TRUE"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/newPop.html","id":null,"dir":"Reference","previous_headings":"","what":"Create new population — newPop","title":"Create new population — newPop","text":"Creates initial Pop-class object MapPop-class NamedMapPop-class. function intended us output functions runMacs, newMapPop, quickHaplo.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/newPop.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create new population — newPop","text":"","code":"newPop(rawPop, simParam = NULL, ...)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/newPop.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create new population — newPop","text":"rawPop object MapPop-class NamedMapPop-class simParam object SimParam ... additional arguments used internally","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/newPop.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create new population — newPop","text":"Returns object Pop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/newPop.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create new population — newPop","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=2, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$addTraitA(10)  #Create population pop = newPop(founderPop, simParam=SP) isPop(pop) #> [1] TRUE"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pedigreeCross.html","id":null,"dir":"Reference","previous_headings":"","what":"Pedigree cross — pedigreeCross","title":"Pedigree cross — pedigreeCross","text":"Creates Pop-class generic pedigree set founder individuals. way user supplied pedigree used depends value matchID. matchID TRUE, IDs user supplied pedigree matched founderNames. matchID FALSE, founder individuals user supplied pedigree randomly sampled founderPop.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pedigreeCross.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pedigree cross — pedigreeCross","text":"","code":"pedigreeCross(   founderPop,   id,   mother,   father,   matchID = FALSE,   maxCycle = 100,   DH = NULL,   nSelf = NULL,   useFemale = TRUE,   simParam = NULL )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pedigreeCross.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pedigree cross — pedigreeCross","text":"founderPop Pop-class id vector unique identifiers individuals pedigree. values IDs seperate IDs founderPop matchID=FALSE. mother vector identifiers mothers individuals pedigree. Must match one elements id vector treated unknown. father vector identifiers fathers individuals pedigree. Must match one elements id vector treated unknown. matchID indicates IDs founderPop matched id argument. See details. maxCycle maximum number loops make pedigree sort . DH optional vector indicating individual made doubled haploid. nSelf optional vector indicating many generations individual selfed. useFemale creating DH lines, female recombination rates used. parameter effect , recombRatio=1. simParam object 'SimParam' class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pedigreeCross.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Pedigree cross — pedigreeCross","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=2, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L  #Create population pop = newPop(founderPop, simParam=SP)  #Pedigree for a biparental cross with 7 generations of selfing id = 1:10 mother = c(0,0,1,3:9) father = c(0,0,2,3:9) pop2 = pedigreeCross(pop, id, mother, father, simParam=SP)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pheno.html","id":null,"dir":"Reference","previous_headings":"","what":"Phenotype — pheno","title":"Phenotype — pheno","text":"wrapper accessing pheno slot","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pheno.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Phenotype — pheno","text":"","code":"pheno(pop)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pheno.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Phenotype — pheno","text":"pop Pop-class similar object","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pheno.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Phenotype — pheno","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$addTraitAD(10, meanDD=0.5) SP$setVarE(h2=0.5) SP$nThreads = 1L  #Create population pop = newPop(founderPop, simParam=SP) pheno(pop) #>            Trait1 #>  [1,]  1.75233273 #>  [2,]  0.04779009 #>  [3,] -0.47833216 #>  [4,]  0.91171314 #>  [5,] -0.31582165 #>  [6,] -2.15293640 #>  [7,] -0.21603999 #>  [8,] -0.24092177 #>  [9,] -1.76981196 #> [10,] -0.83956663"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/popVar.html","id":null,"dir":"Reference","previous_headings":"","what":"Population variance — popVar","title":"Population variance — popVar","text":"Calculates population variance matrix  opposed sample variance matrix calculated  var. .e. divides n instead  n-1","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/popVar.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Population variance — popVar","text":"","code":"popVar(X)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/popVar.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Population variance — popVar","text":"X n m matrix","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/popVar.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Population variance — popVar","text":"m m variance-covariance matrix","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullIbdHaplo.html","id":null,"dir":"Reference","previous_headings":"","what":"Pull IBD haplotypes — pullIbdHaplo","title":"Pull IBD haplotypes — pullIbdHaplo","text":"Retrieves IBD haplotype data","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullIbdHaplo.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pull IBD haplotypes — pullIbdHaplo","text":"","code":"pullIbdHaplo(pop, chr = NULL, snpChip = NULL, simParam = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullIbdHaplo.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pull IBD haplotypes — pullIbdHaplo","text":"pop object Pop-class chr vector chromosomes retrieve. NULL, chromosomes retrieved. snpChip integer indicating SNP array loci  retrieved. NULL, sites retrieved. simParam object SimParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullIbdHaplo.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pull IBD haplotypes — pullIbdHaplo","text":"Returns matrix IBD haplotypes.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullIbdHaplo.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Pull IBD haplotypes — pullIbdHaplo","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=15)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitA(10) SP$addSnpChip(5) SP$setTrackRec(TRUE)  #Create population pop = newPop(founderPop, simParam=SP) pullIbdHaplo(pop, simParam=SP) #>      1_1 1_2 1_3 1_4 1_5 1_6 1_7 1_8 1_9 1_10 1_11 1_12 1_13 1_14 1_15 #> 1_1    1   1   1   1   1   1   1   1   1    1    1    1    1    1    1 #> 1_2    2   2   2   2   2   2   2   2   2    2    2    2    2    2    2 #> 2_1    3   3   3   3   3   3   3   3   3    3    3    3    3    3    3 #> 2_2    4   4   4   4   4   4   4   4   4    4    4    4    4    4    4 #> 3_1    5   5   5   5   5   5   5   5   5    5    5    5    5    5    5 #> 3_2    6   6   6   6   6   6   6   6   6    6    6    6    6    6    6 #> 4_1    7   7   7   7   7   7   7   7   7    7    7    7    7    7    7 #> 4_2    8   8   8   8   8   8   8   8   8    8    8    8    8    8    8 #> 5_1    9   9   9   9   9   9   9   9   9    9    9    9    9    9    9 #> 5_2   10  10  10  10  10  10  10  10  10   10   10   10   10   10   10 #> 6_1   11  11  11  11  11  11  11  11  11   11   11   11   11   11   11 #> 6_2   12  12  12  12  12  12  12  12  12   12   12   12   12   12   12 #> 7_1   13  13  13  13  13  13  13  13  13   13   13   13   13   13   13 #> 7_2   14  14  14  14  14  14  14  14  14   14   14   14   14   14   14 #> 8_1   15  15  15  15  15  15  15  15  15   15   15   15   15   15   15 #> 8_2   16  16  16  16  16  16  16  16  16   16   16   16   16   16   16 #> 9_1   17  17  17  17  17  17  17  17  17   17   17   17   17   17   17 #> 9_2   18  18  18  18  18  18  18  18  18   18   18   18   18   18   18 #> 10_1  19  19  19  19  19  19  19  19  19   19   19   19   19   19   19 #> 10_2  20  20  20  20  20  20  20  20  20   20   20   20   20   20   20"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullMarkerGeno.html","id":null,"dir":"Reference","previous_headings":"","what":"Pull marker genotypes — pullMarkerGeno","title":"Pull marker genotypes — pullMarkerGeno","text":"Retrieves genotype data user specified loci","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullMarkerGeno.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pull marker genotypes — pullMarkerGeno","text":"","code":"pullMarkerGeno(pop, markers, asRaw = FALSE, simParam = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullMarkerGeno.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pull marker genotypes — pullMarkerGeno","text":"pop object RawPop-class MapPop-class markers character vector. Indicates names loci retrieved. asRaw return raw (byte) format simParam object SimParam,  used pop MapPop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullMarkerGeno.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pull marker genotypes — pullMarkerGeno","text":"Returns matrix genotypes.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullMarkerGeno.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Pull marker genotypes — pullMarkerGeno","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=15)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitA(10) SP$addSnpChip(5)  #Create population pop = newPop(founderPop, simParam=SP)  #Pull genotype data for first two markers on chromosome one. #Marker name is consistent with default naming in AlphaSimR. pullMarkerGeno(pop, markers=c(\"1_1\",\"1_2\"), simParam=SP) #>    1_1 1_2 #> 1    2   0 #> 2    0   1 #> 3    1   1 #> 4    1   0 #> 5    1   1 #> 6    1   1 #> 7    1   1 #> 8    2   0 #> 9    2   2 #> 10   1   1"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullMarkerHaplo.html","id":null,"dir":"Reference","previous_headings":"","what":"Pull marker haplotypes — pullMarkerHaplo","title":"Pull marker haplotypes — pullMarkerHaplo","text":"Retrieves haplotype data user specified loci","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullMarkerHaplo.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pull marker haplotypes — pullMarkerHaplo","text":"","code":"pullMarkerHaplo(pop, markers, haplo = \"all\", asRaw = FALSE, simParam = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullMarkerHaplo.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pull marker haplotypes — pullMarkerHaplo","text":"pop object RawPop-class MapPop-class markers character vector. Indicates names loci retrieved haplo either \"\" haplotypes integer single set haplotypes. Use value 1 female haplotypes value 2 male haplotypes diploids. asRaw return raw (byte) format simParam object SimParam,  used pop MapPop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullMarkerHaplo.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pull marker haplotypes — pullMarkerHaplo","text":"Returns matrix genotypes.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullMarkerHaplo.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Pull marker haplotypes — pullMarkerHaplo","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=15)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitA(10) SP$addSnpChip(5) SP$setTrackRec(TRUE)  #Create population pop = newPop(founderPop, simParam=SP)  #Pull haplotype data for first two markers on chromosome one. #Marker name is consistent with default naming in AlphaSimR. pullMarkerHaplo(pop, markers=c(\"1_1\",\"1_2\"), simParam=SP) #>      1_1 1_2 #> 1_1    1   0 #> 1_2    0   0 #> 2_1    0   1 #> 2_2    1   0 #> 3_1    0   0 #> 3_2    0   0 #> 4_1    0   0 #> 4_2    1   1 #> 5_1    1   1 #> 5_2    0   0 #> 6_1    0   1 #> 6_2    0   1 #> 7_1    0   0 #> 7_2    0   1 #> 8_1    1   1 #> 8_2    1   1 #> 9_1    0   0 #> 9_2    0   1 #> 10_1   1   0 #> 10_2   0   0"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullQtlGeno.html","id":null,"dir":"Reference","previous_headings":"","what":"Pull QTL genotypes — pullQtlGeno","title":"Pull QTL genotypes — pullQtlGeno","text":"Retrieves QTL genotype data","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullQtlGeno.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pull QTL genotypes — pullQtlGeno","text":"","code":"pullQtlGeno(pop, trait = 1, chr = NULL, asRaw = FALSE, simParam = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullQtlGeno.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pull QTL genotypes — pullQtlGeno","text":"pop object Pop-class trait integer. Indicates trait's QTL genotypes retrieve. chr vector chromosomes retrieve. NULL, chromosome retrieved. asRaw return raw (byte) format simParam object SimParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullQtlGeno.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pull QTL genotypes — pullQtlGeno","text":"Returns matrix QTL genotypes.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullQtlGeno.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Pull QTL genotypes — pullQtlGeno","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=15)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitA(10) SP$addSnpChip(5)  #Create population pop = newPop(founderPop, simParam=SP) pullQtlGeno(pop, simParam=SP) #>    1_1 1_2 1_3 1_4 1_5 1_7 1_8 1_10 1_11 1_15 #> 1    1   1   0   1   1   0   2    1    1    2 #> 2    0   1   2   1   0   1   1    0    0    2 #> 3    2   1   2   2   2   1   1    0    0    0 #> 4    0   1   0   1   1   1   1    0    2    1 #> 5    1   2   2   1   2   1   2    1    1    0 #> 6    1   1   2   2   0   2   0    1    1    0 #> 7    1   0   1   2   1   1   1    1    0    1 #> 8    0   1   1   1   1   0   1    2    2    1 #> 9    2   1   1   1   0   0   1    2    0    0 #> 10   2   1   0   1   0   1   1    1    1    0"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullQtlHaplo.html","id":null,"dir":"Reference","previous_headings":"","what":"Pull QTL haplotypes — pullQtlHaplo","title":"Pull QTL haplotypes — pullQtlHaplo","text":"Retrieves QTL haplotype data","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullQtlHaplo.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pull QTL haplotypes — pullQtlHaplo","text":"","code":"pullQtlHaplo(   pop,   trait = 1,   haplo = \"all\",   chr = NULL,   asRaw = FALSE,   simParam = NULL )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullQtlHaplo.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pull QTL haplotypes — pullQtlHaplo","text":"pop object Pop-class trait integer. Indicates trait's QTL haplotypes retrieve. haplo either \"\" haplotypes integer single set haplotypes. Use value 1 female haplotypes value 2 male haplotypes diploids. chr vector chromosomes retrieve. NULL, chromosome retrieved. asRaw return raw (byte) format simParam object SimParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullQtlHaplo.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pull QTL haplotypes — pullQtlHaplo","text":"Returns matrix QTL haplotypes.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullQtlHaplo.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Pull QTL haplotypes — pullQtlHaplo","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=15)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitA(10) SP$addSnpChip(5)  #Create population pop = newPop(founderPop, simParam=SP) pullQtlHaplo(pop, simParam=SP) #>      1_2 1_3 1_4 1_8 1_9 1_11 1_12 1_13 1_14 1_15 #> 1_1    0   0   0   1   1    0    1    1    0    1 #> 1_2    0   1   1   0   1    1    1    1    0    1 #> 2_1    1   1   1   1   1    0    0    1    1    1 #> 2_2    0   0   1   0   1    1    1    1    0    1 #> 3_1    0   0   0   1   1    1    0    0    1    1 #> 3_2    1   0   0   1   1    0    0    1    0    0 #> 4_1    1   1   0   1   0    0    1    0    0    0 #> 4_2    0   0   0   1   0    1    1    0    1    1 #> 5_1    0   0   0   0   0    0    0    0    0    0 #> 5_2    1   1   1   0   1    0    0    0    0    0 #> 6_1    0   1   0   1   0    0    0    0    1    0 #> 6_2    0   1   1   1   1    0    0    1    1    0 #> 7_1    0   0   1   1   0    0    1    0    1    0 #> 7_2    0   0   1   0   1    1    1    1    1    1 #> 8_1    1   1   1   1   1    0    1    0    1    0 #> 8_2    0   1   1   0   0    0    1    1    1    1 #> 9_1    1   0   0   1   1    1    0    0    1    0 #> 9_2    1   0   0   1   0    0    1    0    0    0 #> 10_1   0   1   1   0   1    0    1    0    1    1 #> 10_2   1   1   0   1   1    0    1    0    0    1"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullSegSiteGeno.html","id":null,"dir":"Reference","previous_headings":"","what":"Pull segregating site genotypes — pullSegSiteGeno","title":"Pull segregating site genotypes — pullSegSiteGeno","text":"Retrieves genotype data segregating sites","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullSegSiteGeno.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pull segregating site genotypes — pullSegSiteGeno","text":"","code":"pullSegSiteGeno(pop, chr = NULL, asRaw = FALSE, simParam = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullSegSiteGeno.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pull segregating site genotypes — pullSegSiteGeno","text":"pop object RawPop-class MapPop-class chr vector chromosomes retrieve. NULL, chromosome retrieved. asRaw return raw (byte) format simParam object SimParam,  used pop MapPop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullSegSiteGeno.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pull segregating site genotypes — pullSegSiteGeno","text":"Returns matrix genotypes","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullSegSiteGeno.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Pull segregating site genotypes — pullSegSiteGeno","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=15)  #Set simulation parameters SP = SimParam$new(founderPop) SP$addTraitA(10) SP$addSnpChip(5)  #Create population pop = newPop(founderPop, simParam=SP) pullSegSiteGeno(pop, simParam=SP) #>    1_1 1_2 1_3 1_4 1_5 1_6 1_7 1_8 1_9 1_10 1_11 1_12 1_13 1_14 1_15 #> 1    1   1   2   1   2   0   2   1   1    2    1    2    0    0    2 #> 2    1   1   0   1   1   1   2   2   0    2    2    0    0    2    0 #> 3    2   0   2   2   1   1   2   0   0    0    1    0    0    1    1 #> 4    0   1   1   2   0   0   1   1   0    2    0    0    1    0    1 #> 5    2   1   0   1   1   1   0   2   2    1    0    2    1    1    1 #> 6    1   2   1   1   1   1   2   0   1    1    1    1    0    2    1 #> 7    1   1   1   1   2   1   0   1   0    0    2    1    2    0    0 #> 8    1   1   0   1   1   1   1   0   2    2    2    2    2    2    1 #> 9    0   0   0   0   0   1   2   0   1    1    0    0    2    1    1 #> 10   0   1   1   0   2   1   2   2   1    1    0    0    1    2    1"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullSegSiteHaplo.html","id":null,"dir":"Reference","previous_headings":"","what":"Pull seg site haplotypes — pullSegSiteHaplo","title":"Pull seg site haplotypes — pullSegSiteHaplo","text":"Retrieves haplotype data segregating sites","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullSegSiteHaplo.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pull seg site haplotypes — pullSegSiteHaplo","text":"","code":"pullSegSiteHaplo(   pop,   haplo = \"all\",   chr = NULL,   asRaw = FALSE,   simParam = NULL )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullSegSiteHaplo.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pull seg site haplotypes — pullSegSiteHaplo","text":"pop object RawPop-class MapPop-class haplo either \"\" haplotypes integer single set haplotypes. Use value 1 female haplotypes value 2 male haplotypes diploids. chr vector chromosomes retrieve. NULL, chromosome retrieved. asRaw return raw (byte) format simParam object SimParam,  used pop MapPop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullSegSiteHaplo.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pull seg site haplotypes — pullSegSiteHaplo","text":"Returns matrix haplotypes","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullSegSiteHaplo.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Pull seg site haplotypes — pullSegSiteHaplo","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=15)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitA(10) SP$addSnpChip(5)  #Create population pop = newPop(founderPop, simParam=SP) pullSegSiteHaplo(pop, simParam=SP) #>      1_1 1_2 1_3 1_4 1_5 1_6 1_7 1_8 1_9 1_10 1_11 1_12 1_13 1_14 1_15 #> 1_1    1   0   0   0   0   0   0   0   0    0    0    1    1    0    1 #> 1_2    0   1   1   1   1   0   1   1   1    1    0    0    1    0    0 #> 2_1    1   1   1   1   0   0   0   1   1    0    0    1    0    0    1 #> 2_2    1   1   0   1   0   1   0   0   0    1    0    0    0    1    0 #> 3_1    1   1   1   0   0   0   0   0   0    1    0    0    0    0    1 #> 3_2    0   1   0   1   0   1   0   1   0    1    0    1    0    0    0 #> 4_1    0   0   0   0   0   1   1   1   0    0    0    1    0    1    1 #> 4_2    0   0   1   0   0   0   1   0   0    1    0    0    1    1    0 #> 5_1    1   1   1   1   0   0   1   0   0    1    0    1    0    1    0 #> 5_2    1   1   0   0   1   0   1   1   0    0    0    0    0    1    1 #> 6_1    0   1   0   1   0   0   0   0   0    1    0    1    1    0    0 #> 6_2    0   1   0   0   0   0   0   0   1    0    1    1    1    0    0 #> 7_1    1   1   1   0   1   1   0   1   1    0    0    1    1    1    1 #> 7_2    1   0   0   1   1   0   1   1   1    1    0    0    0    0    1 #> 8_1    0   1   0   1   1   1   1   0   0    1    1    1    0    1    1 #> 8_2    1   1   1   1   1   1   1   1   0    0    1    0    1    0    0 #> 9_1    0   0   1   1   1   0   1   1   1    1    0    1    0    1    0 #> 9_2    1   0   0   1   0   1   0   0   0    0    1    0    1    1    0 #> 10_1   0   1   1   0   1   0   1   0   0    1    0    0    1    0    0 #> 10_2   0   0   0   1   0   1   0   1   1    0    1    1    1    0    1"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullSnpGeno.html","id":null,"dir":"Reference","previous_headings":"","what":"Pull SNP genotypes — pullSnpGeno","title":"Pull SNP genotypes — pullSnpGeno","text":"Retrieves SNP genotype data","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullSnpGeno.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pull SNP genotypes — pullSnpGeno","text":"","code":"pullSnpGeno(pop, snpChip = 1, chr = NULL, asRaw = FALSE, simParam = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullSnpGeno.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pull SNP genotypes — pullSnpGeno","text":"pop object Pop-class snpChip integer. Indicates SNP chip's genotypes retrieve. chr vector chromosomes retrieve. NULL, chromosome retrieved. asRaw return raw (byte) format simParam object SimParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullSnpGeno.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pull SNP genotypes — pullSnpGeno","text":"Returns matrix SNP genotypes.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullSnpGeno.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Pull SNP genotypes — pullSnpGeno","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=15)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitA(10) SP$addSnpChip(5)  #Create population pop = newPop(founderPop, simParam=SP) pullSnpGeno(pop, simParam=SP) #>    1_1 1_3 1_7 1_9 1_14 #> 1    2   1   1   2    1 #> 2    1   0   1   2    1 #> 3    1   1   0   0    0 #> 4    0   2   1   2    1 #> 5    1   2   0   1    2 #> 6    0   1   1   0    0 #> 7    0   0   1   1    2 #> 8    0   2   2   1    1 #> 9    2   2   2   1    1 #> 10   1   1   1   2    1"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullSnpHaplo.html","id":null,"dir":"Reference","previous_headings":"","what":"Pull SNP haplotypes — pullSnpHaplo","title":"Pull SNP haplotypes — pullSnpHaplo","text":"Retrieves SNP haplotype data","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullSnpHaplo.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pull SNP haplotypes — pullSnpHaplo","text":"","code":"pullSnpHaplo(   pop,   snpChip = 1,   haplo = \"all\",   chr = NULL,   asRaw = FALSE,   simParam = NULL )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullSnpHaplo.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pull SNP haplotypes — pullSnpHaplo","text":"pop object Pop-class snpChip integer. Indicates SNP chip's haplotypes retrieve. haplo either \"\" haplotypes integer single set haplotypes. Use value 1 female haplotypes value 2 male haplotypes diploids. chr vector chromosomes retrieve. NULL, chromosome retrieved. asRaw return raw (byte) format simParam object SimParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullSnpHaplo.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pull SNP haplotypes — pullSnpHaplo","text":"Returns matrix SNP haplotypes.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullSnpHaplo.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Pull SNP haplotypes — pullSnpHaplo","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=15)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitA(10) SP$addSnpChip(5)  #Create population pop = newPop(founderPop, simParam=SP) pullSnpHaplo(pop, simParam=SP) #>      1_3 1_4 1_8 1_11 1_14 #> 1_1    0   0   0    1    0 #> 1_2    1   1   0    1    1 #> 2_1    1   0   0    0    1 #> 2_2    0   1   1    0    1 #> 3_1    1   0   1    1    0 #> 3_2    1   0   0    1    0 #> 4_1    1   1   0    0    0 #> 4_2    1   0   0    0    1 #> 5_1    1   1   1    0    1 #> 5_2    1   0   0    0    1 #> 6_1    0   1   0    1    0 #> 6_2    0   1   0    0    1 #> 7_1    1   1   1    0    0 #> 7_2    0   1   0    0    1 #> 8_1    1   0   1    1    1 #> 8_2    0   0   0    1    1 #> 9_1    1   0   0    0    1 #> 9_2    1   0   1    1    1 #> 10_1   0   0   0    1    0 #> 10_2   0   1   1    0    1"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/quickHaplo.html","id":null,"dir":"Reference","previous_headings":"","what":"Quick founder haplotype simulation — quickHaplo","title":"Quick founder haplotype simulation — quickHaplo","text":"Rapidly simulates founder haplotypes randomly  sampling 0s 1s. equivalent loci  allele frequency 0.5 linkage equilibrium.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/quickHaplo.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Quick founder haplotype simulation — quickHaplo","text":"","code":"quickHaplo(nInd, nChr, segSites, genLen = 1, ploidy = 2L, inbred = FALSE)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/quickHaplo.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Quick founder haplotype simulation — quickHaplo","text":"nInd number individuals simulate nChr number chromosomes simulate segSites number segregating sites per chromosome genLen genetic length chromosomes ploidy ploidy level organism inbred founder individuals inbred","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/quickHaplo.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Quick founder haplotype simulation — quickHaplo","text":"object MapPop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/quickHaplo.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Quick founder haplotype simulation — quickHaplo","text":"","code":"# Creates a populations of 10 outbred individuals # Their genome consists of 1 chromosome and 100 segregating sites founderPop = quickHaplo(nInd=10,nChr=1,segSites=100)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/randCross.html","id":null,"dir":"Reference","previous_headings":"","what":"Make random crosses — randCross","title":"Make random crosses — randCross","text":"wrapper makeCross randomly selects parental combinations possible combinantions.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/randCross.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make random crosses — randCross","text":"","code":"randCross(   pop,   nCrosses,   nProgeny = 1,   balance = TRUE,   parents = NULL,   ignoreSexes = FALSE,   simParam = NULL )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/randCross.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make random crosses — randCross","text":"pop object Pop-class nCrosses total number crosses make nProgeny number progeny per cross balance using sexes, option balance number progeny per parent parents optional vector indices allowable parents ignoreSexes sexes ignored simParam object SimParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/randCross.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make random crosses — randCross","text":"Returns object Pop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/randCross.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Make random crosses — randCross","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L  #Create population pop = newPop(founderPop, simParam=SP)  #Make 10 crosses pop2 = randCross(pop, 10, simParam=SP)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/randCross2.html","id":null,"dir":"Reference","previous_headings":"","what":"Make random crosses — randCross2","title":"Make random crosses — randCross2","text":"wrapper makeCross2 randomly selects parental combinations possible combinantions two populations.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/randCross2.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make random crosses — randCross2","text":"","code":"randCross2(   females,   males,   nCrosses,   nProgeny = 1,   balance = TRUE,   femaleParents = NULL,   maleParents = NULL,   ignoreSexes = FALSE,   simParam = NULL )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/randCross2.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make random crosses — randCross2","text":"females object Pop-class female parents. males object Pop-class male parents. nCrosses total number crosses make nProgeny number progeny per cross balance option balance number progeny per parent femaleParents optional vector indices allowable female parents maleParents optional vector indices allowable male parents ignoreSexes sex ignored simParam object SimParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/randCross2.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make random crosses — randCross2","text":"Returns object Pop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/randCross2.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Make random crosses — randCross2","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L  #Create population pop = newPop(founderPop, simParam=SP)  #Make 10 crosses pop2 = randCross2(pop, pop, 10, simParam=SP)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/reduceGenome.html","id":null,"dir":"Reference","previous_headings":"","what":"Create individuals with reduced ploidy — reduceGenome","title":"Create individuals with reduced ploidy — reduceGenome","text":"Creates new individuals gametes. function  created model creation diploid potatoes  tetraploid potatoes. can used population  even ploidy level. newly created individuals half  ploidy level originals. reduction can occur  without genetic recombination.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/reduceGenome.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create individuals with reduced ploidy — reduceGenome","text":"","code":"reduceGenome(   pop,   nProgeny = 1,   useFemale = TRUE,   keepParents = TRUE,   simRecomb = TRUE,   simParam = NULL )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/reduceGenome.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create individuals with reduced ploidy — reduceGenome","text":"pop object 'Pop' superclass nProgeny total number progeny per individual useFemale female recombination rates used. keepParents previous parents used mother  father. simRecomb genetic recombination modeled. simParam object 'SimParam' class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/reduceGenome.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create individuals with reduced ploidy — reduceGenome","text":"Returns object Pop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/reduceGenome.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create individuals with reduced ploidy — reduceGenome","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=2, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L  #Create population pop = newPop(founderPop, simParam=SP)  #Create individuals with reduced ploidy pop2 = reduceGenome(pop, simParam=SP)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/resetPop.html","id":null,"dir":"Reference","previous_headings":"","what":"Reset population — resetPop","title":"Reset population — resetPop","text":"Recalculates population's genetic values resets phenotypes EBVs.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/resetPop.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Reset population — resetPop","text":"","code":"resetPop(pop, simParam = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/resetPop.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Reset population — resetPop","text":"pop object Pop-class simParam object SimParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/resetPop.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Reset population — resetPop","text":"object Pop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/resetPop.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Reset population — resetPop","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=2, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$addTraitA(10)  #Create population pop = newPop(founderPop, simParam=SP)  #Rescale to set mean to 1 SP$rescaleTraits(mean=1) pop = resetPop(pop, simParam=SP)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/runMacs.html","id":null,"dir":"Reference","previous_headings":"","what":"Create founder haplotypes using MaCS — runMacs","title":"Create founder haplotypes using MaCS — runMacs","text":"Uses MaCS software produce founder haplotypes  (Chen et al. 2009) .","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/runMacs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create founder haplotypes using MaCS — runMacs","text":"","code":"runMacs(   nInd,   nChr = 1,   segSites = NULL,   inbred = FALSE,   species = \"GENERIC\",   split = NULL,   ploidy = 2L,   manualCommand = NULL,   manualGenLen = NULL,   nThreads = NULL )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/runMacs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create founder haplotypes using MaCS — runMacs","text":"nInd number individuals simulate nChr number chromosomes simulate segSites number segregating sites keep per chromosome.  value NULL results sites retained. inbred founder individuals inbred species species history simulate. See details. split optional historic population split terms generations ago. ploidy ploidy level organism manualCommand user provided MaCS options. advanced users . manualGenLen user provided genetic length. must supplied using  manualCommand. using manualCommand, value replace predefined  genetic length species. However, genetic length used  AlphaSimR passed MaCS, MaCS still uses predefined genetic length.  advanced users . nThreads OpenMP available, allow simulating chromosomes parallel.  value NULL, number threads automatically detected.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/runMacs.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create founder haplotypes using MaCS — runMacs","text":"object MapPop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/runMacs.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Create founder haplotypes using MaCS — runMacs","text":"currently three species histories available: GENERIC, CATTLE, WHEAT, MAIZE. GENERIC history meant reasonable -purpose choice. runs quickly  models population effective populations size gone several historic  bottlenecks. species history used default arguments runMacs2  function, user examine function details species modeled. CATTLE history based real genome sequence data (MacLeod et al. 2013) . WHEAT (Gaynor et al. 2017)  MAIZE (Hickey et al. 2014)   histories included due use previous simulations. However,  noted neither faithfully simulates respective species. apparent  low number segregating sites simulated history relative real-world  analogs. Adjusting histories better represent real-world analogs result  drastic increase runtime.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/runMacs.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Create founder haplotypes using MaCS — runMacs","text":"Chen GK, Marjoram P, Wall JD (2009). “Fast Flexible Simulation DNA Sequence Data.” Genome Research, 19, 136-142. https://genome.cshlp.org/content/19/1/136. Gaynor RC, Gorjanc G, Bentley AR, Ober ES, Howell P, Jackson R, Mackay IJ, Hickey JM (2017). “Two-Part Strategy Using Genomic Selection Develop Inbred Lines.” Crop Science, 57(5), 2372--2386. ISSN 0011-183X, doi:10.2135/cropsci2016.09.0742 , https://acsess.onlinelibrary.wiley.com/doi/full/10.2135/cropsci2016.09.0742. Hickey JM, Dreisigacker S, Crossa J, Hearne S, Babu R, Prasanna BM, Grondona M, Zambelli , Windhausen VS, Mathews K, Gorjanc G (2014). “Evaluation Genomic Selection Training Population Designs Genotyping Strategies Plant Breeding Programs Using Simulation.” Crop Science, 54(4), 1476-1488. doi:10.2135/cropsci2013.03.0195 . MacLeod IM, Larkin DM, Lewin HA, Hayes BJ, Goddard (2013). “Inferring Demography Runs Homozygosity Whole-Genome Sequence, Correction Sequence Errors.” Molecular Biology Evolution, 30(9), 2209–2223. doi:10.1093/molbev/mst125 .","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/runMacs.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create founder haplotypes using MaCS — runMacs","text":"","code":"# Creates a populations of 10 outbred individuals # Their genome consists of 1 chromosome and 100 segregating sites if (FALSE) { founderPop = runMacs(nInd=10,nChr=1,segSites=100) }"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/runMacs2.html","id":null,"dir":"Reference","previous_headings":"","what":"Alternative wrapper for MaCS — runMacs2","title":"Alternative wrapper for MaCS — runMacs2","text":"wrapper function runMacs. wrapper designed  provide intuitive interface writing custom commands MaCS (Chen et al. 2009) . effectively automates creation  appropriate line manualCommand argument runMacs  using user supplied variables, allows subset functionality  offered argument. default arguments function chosen match  species=\"GENERIC\" runMacs.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/runMacs2.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Alternative wrapper for MaCS — runMacs2","text":"","code":"runMacs2(   nInd,   nChr = 1,   segSites = NULL,   Ne = 100,   bp = 1e+08,   genLen = 1,   mutRate = 2.5e-08,   histNe = c(500, 1500, 6000, 12000, 1e+05),   histGen = c(100, 1000, 10000, 1e+05, 1e+06),   inbred = FALSE,   split = NULL,   ploidy = 2L,   returnCommand = FALSE,   nThreads = NULL )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/runMacs2.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Alternative wrapper for MaCS — runMacs2","text":"nInd number individuals simulate nChr number chromosomes simulate segSites number segregating sites keep per chromosome Ne effective population size bp base pair length chromosome genLen genetic length chromosome Morgans mutRate per base pair mutation rate histNe effective population size previous  generations histGen number generations ago effective  population sizes given histNe inbred founder individuals inbred split optional historic population split terms generations ago ploidy ploidy level organism returnCommand command passed manualCommand  runMacs returned. TRUE, MaCS called  command returned instead. nThreads OpenMP available, allow simulating chromosomes parallel.  value NULL, number threads automatically detected.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/runMacs2.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Alternative wrapper for MaCS — runMacs2","text":"object MapPop-class  returnCommand true string giving MaCS command passed   manualCommand argument runMacs.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/runMacs2.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Alternative wrapper for MaCS — runMacs2","text":"Chen GK, Marjoram P, Wall JD (2009). “Fast Flexible Simulation DNA Sequence Data.” Genome Research, 19, 136-142. https://genome.cshlp.org/content/19/1/136.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/runMacs2.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Alternative wrapper for MaCS — runMacs2","text":"","code":"# Creates a populations of 10 outbred individuals # Their genome consists of 1 chromosome and 100 segregating sites # The command is equivalent to using species=\"GENERIC\" in runMacs if (FALSE) { founderPop = runMacs2(nInd=10,nChr=1,segSites=100) }"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/sampleHaplo.html","id":null,"dir":"Reference","previous_headings":"","what":"Sample haplotypes from a MapPop — sampleHaplo","title":"Sample haplotypes from a MapPop — sampleHaplo","text":"Creates new MapPop-class existing  MapPop-class randomly sampling haplotypes.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/sampleHaplo.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sample haplotypes from a MapPop — sampleHaplo","text":"","code":"sampleHaplo(mapPop, nInd, inbred = FALSE, ploidy = NULL, replace = TRUE)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/sampleHaplo.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sample haplotypes from a MapPop — sampleHaplo","text":"mapPop MapPop-class used  sample haplotypes nInd number individuals create inbred new individuals fully inbred ploidy new ploidy level organism. NULL,  ploidy level mapPop used. replace haplotypes sampled replacement","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/sampleHaplo.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Sample haplotypes from a MapPop — sampleHaplo","text":"object MapPop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/sampleHaplo.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Sample haplotypes from a MapPop — sampleHaplo","text":"","code":"founderPop = quickHaplo(nInd=2,nChr=1,segSites=11,inbred=TRUE) founderPop = sampleHaplo(mapPop=founderPop,nInd=20)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/selIndex.html","id":null,"dir":"Reference","previous_headings":"","what":"Selection index — selIndex","title":"Selection index — selIndex","text":"Calculates values selection index given trait values  weights. function intended used combination  selection functions working populations  selectInd.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/selIndex.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Selection index — selIndex","text":"","code":"selIndex(Y, b, scale = FALSE)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/selIndex.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Selection index — selIndex","text":"Y matrix trait values b vector weights scale Y scaled centered","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/selIndex.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Selection index — selIndex","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L #Model two genetically correlated traits G = 1.5*diag(2)-0.5 #Genetic correlation matrix SP$addTraitA(10, mean=c(0,0), var=c(1,1), corA=G) SP$setVarE(h2=c(0.5,0.5))  #Create population pop = newPop(founderPop, simParam=SP)  #Calculate Smith-Hazel weights econWt = c(1, 1) b = smithHazel(econWt, varG(pop), varP(pop))  #Selection 2 best individuals using Smith-Hazel index #selIndex is used as a trait pop2 = selectInd(pop, nInd=2, trait=selIndex,                   simParam=SP, b=b)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/selInt.html","id":null,"dir":"Reference","previous_headings":"","what":"Selection intensity — selInt","title":"Selection intensity — selInt","text":"Calculates standardized selection intensity","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/selInt.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Selection intensity — selInt","text":"","code":"selInt(p)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/selInt.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Selection intensity — selInt","text":"p proportion individuals selected","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/selInt.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Selection intensity — selInt","text":"","code":"selInt(0.1) #> [1] 1.754983"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/selectCross.html","id":null,"dir":"Reference","previous_headings":"","what":"Select and randomly cross — selectCross","title":"Select and randomly cross — selectCross","text":"wrapper combines functionalities randCross selectInd. purpose wrapper combine selection crossing one function call minimized amount intermediate populations created. reduces RAM usage simplifies code writing. Note wrapper provide full functionality either function.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/selectCross.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Select and randomly cross — selectCross","text":"","code":"selectCross(   pop,   nInd = NULL,   nFemale = NULL,   nMale = NULL,   nCrosses,   nProgeny = 1,   trait = 1,   use = \"pheno\",   selectTop = TRUE,   simParam = NULL,   ...,   balance = TRUE )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/selectCross.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Select and randomly cross — selectCross","text":"pop object Pop-class nInd number individuals select. individuals selected without regards sex supercedes values nFemale nMale. Thus simulation uses sexes, likely better leave value NULL use nFemale nMale instead. nFemale number females select. value ignored nInd set. nMale number males select. value ignored nInd set. nCrosses total number crosses make nProgeny number progeny per cross trait trait selection. Either number indicating single trait function returning vector length nInd. use select genetic values \"gv\", estimated breeding values \"ebv\", breeding values \"bv\", phenotypes \"pheno\", randomly \"rand\" selectTop selects highest values true. Selects lowest values false. simParam object SimParam ... additional arguments using function trait balance using sexes, option balance number progeny per parent. argument occurs ..., argument name must matched exactly.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/selectCross.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Select and randomly cross — selectCross","text":"Returns object Pop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/selectCross.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Select and randomly cross — selectCross","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitA(10) SP$setVarE(h2=0.5)  #Create population pop = newPop(founderPop, simParam=SP)  #Select 4 individuals and make 8 crosses pop2 = selectCross(pop, nInd=4, nCrosses=8, simParam=SP)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/selectFam.html","id":null,"dir":"Reference","previous_headings":"","what":"Select families — selectFam","title":"Select families — selectFam","text":"Selects subset full-sib families population.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/selectFam.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Select families — selectFam","text":"","code":"selectFam(   pop,   nFam,   trait = 1,   use = \"pheno\",   sex = \"B\",   famType = \"B\",   selectTop = TRUE,   returnPop = TRUE,   candidates = NULL,   simParam = NULL,   ... )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/selectFam.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Select families — selectFam","text":"pop object Pop-class, HybridPop-class MultiPop-class nFam number families select trait trait selection. Either number indicating single trait function returning vector length nInd. function must work vector matrix use values. See examples selectInd selIndex. use select genetic values \"gv\", estimated breeding values \"ebv\", breeding values \"bv\", phenotypes \"pheno\", randomly \"rand\" sex sex select. Use \"B\" , \"F\" females \"M\" males. simulation using sexes, argument ignored. famType type family select. Use \"B\" full-sib families, \"F\" half-sib families female side \"M\" half-sib families male side. selectTop selects highest values true. Selects lowest values false. returnPop results returned Pop-class. FALSE, index selected individuals returned. candidates optional vector eligible selection candidates. simParam object SimParam ... additional arguments using function trait","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/selectFam.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Select families — selectFam","text":"Returns object Pop-class, HybridPop-class MultiPop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/selectFam.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Select families — selectFam","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitA(10) SP$setVarE(h2=0.5)  #Create population pop = newPop(founderPop, simParam=SP)  #Create 3 biparental families with 10 progeny pop2 = randCross(pop, nCrosses=3, nProgeny=10, simParam=SP)  #Select best 2 families pop3 = selectFam(pop2, 2, simParam=SP)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/selectInd.html","id":null,"dir":"Reference","previous_headings":"","what":"Select individuals — selectInd","title":"Select individuals — selectInd","text":"Selects subset nInd individuals population.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/selectInd.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Select individuals — selectInd","text":"","code":"selectInd(   pop,   nInd,   trait = 1,   use = \"pheno\",   sex = \"B\",   selectTop = TRUE,   returnPop = TRUE,   candidates = NULL,   simParam = NULL,   ... )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/selectInd.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Select individuals — selectInd","text":"pop object Pop-class, HybridPop-class MultiPop-class nInd number individuals select trait trait selection. Either number indicating single trait function returning vector length nInd. function must work vector matrix use values. See examples selIndex. use select genetic values \"gv\", estimated breeding values \"ebv\", breeding values \"bv\", phenotypes \"pheno\", randomly \"rand\" sex sex select. Use \"B\" , \"F\" females \"M\" males. simulation using sexes, argument ignored. selectTop selects highest values true. Selects lowest values false. returnPop results returned Pop-class. FALSE, index selected individuals returned. candidates optional vector eligible selection candidates. simParam object SimParam ... additional arguments using function trait","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/selectInd.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Select individuals — selectInd","text":"Returns object Pop-class, HybridPop-class MultiPop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/selectInd.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Select individuals — selectInd","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitA(10) SP$setVarE(h2=0.5)  #Create population pop = newPop(founderPop, simParam=SP)  #Select top 5 (directional selection) pop2 = selectInd(pop, 5, simParam=SP) hist(pop@pheno); abline(v = pop@pheno, lwd = 2) abline(v = pop2@pheno, col = \"red\", lwd = 2)   #Select 5 most deviating from an optima (disruptive selection) squaredDeviation = function(x, optima = 0) (x - optima)^2 pop3 = selectInd(pop, 5, simParam=SP, trait = squaredDeviation, selectTop = TRUE) hist(pop@pheno); abline(v = pop@pheno, lwd = 2) abline(v = pop3@pheno, col = \"red\", lwd = 2)   #Select 5 least deviating from an optima (stabilising selection) pop4 = selectInd(pop, 5, simParam=SP, trait = squaredDeviation, selectTop = FALSE) hist(pop@pheno); abline(v = pop@pheno, lwd = 2) abline(v = pop4@pheno, col = \"red\", lwd = 2)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/selectOP.html","id":null,"dir":"Reference","previous_headings":"","what":"Select open pollinating plants — selectOP","title":"Select open pollinating plants — selectOP","text":"function models selection open pollinating plant population. allows varying percentage selfing. function also provides option modeling selection occuring pollination.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/selectOP.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Select open pollinating plants — selectOP","text":"","code":"selectOP(   pop,   nInd,   nSeeds,   probSelf = 0,   pollenControl = FALSE,   trait = 1,   use = \"pheno\",   selectTop = TRUE,   candidates = NULL,   simParam = NULL,   ... )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/selectOP.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Select open pollinating plants — selectOP","text":"pop object Pop-class MultiPop-class nInd number plants select nSeeds number seeds per plant probSelf percentage seeds expected selfing. Value ranges 0 1. pollenControl plants selected pollination trait trait selection. Either number indicating single trait function returning vector length nInd. function must work vector matrix use values. See examples selectInd selIndex. use select genetic values \"gv\", estimated breeding values \"ebv\", breeding values \"bv\", phenotypes \"pheno\", randomly \"rand\" selectTop selects highest values true. Selects lowest values false. candidates optional vector eligible selection candidates. simParam object SimParam ... additional arguments using function trait","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/selectOP.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Select open pollinating plants — selectOP","text":"Returns object Pop-class MultiPop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/selectOP.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Select open pollinating plants — selectOP","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitA(10) SP$setVarE(h2=0.5)  #Create population pop = newPop(founderPop, simParam=SP)  #Create new population by selecting the best 3 plant #Assuming 50% selfing in plants and 10 seeds per plant pop2 = selectOP(pop, nInd=3, nSeeds=10, probSelf=0.5, simParam=SP)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/selectWithinFam.html","id":null,"dir":"Reference","previous_headings":"","what":"Select individuals within families — selectWithinFam","title":"Select individuals within families — selectWithinFam","text":"Selects subset nInd individuals full-sib family within population. return individuals full-sib family less equal nInd individuals.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/selectWithinFam.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Select individuals within families — selectWithinFam","text":"","code":"selectWithinFam(   pop,   nInd,   trait = 1,   use = \"pheno\",   sex = \"B\",   famType = \"B\",   selectTop = TRUE,   returnPop = TRUE,   candidates = NULL,   simParam = NULL,   ... )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/selectWithinFam.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Select individuals within families — selectWithinFam","text":"pop object Pop-class, HybridPop-class MultiPop-class nInd number individuals select within family trait trait selection. Either number indicating single trait function returning vector length nInd. function must work vector matrix use values. See examples selectInd selIndex. use select genetic values \"gv\", estimated breeding values \"ebv\", breeding values \"bv\", phenotypes \"pheno\", randomly \"rand\" sex sex select. Use \"B\" , \"F\" females \"M\" males. simulation using sexes, argument ignored. famType type family select. Use \"B\" full-sib families, \"F\" half-sib families female side \"M\" half-sib families male side. selectTop selects highest values true. Selects lowest values false. returnPop results returned Pop-class. FALSE, index selected individuals returned. candidates optional vector eligible selection candidates. simParam object SimParam ... additional arguments using function trait","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/selectWithinFam.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Select individuals within families — selectWithinFam","text":"Returns object Pop-class, HybridPop-class MultiPop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/selectWithinFam.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Select individuals within families — selectWithinFam","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitA(10) SP$setVarE(h2=0.5)  #Create population pop = newPop(founderPop, simParam=SP)  #Create 3 biparental families with 10 progeny pop2 = randCross(pop, nCrosses=3, nProgeny=10, simParam=SP)  #Select best individual per family pop3 = selectWithinFam(pop2, 1, simParam=SP)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/self.html","id":null,"dir":"Reference","previous_headings":"","what":"Self individuals — self","title":"Self individuals — self","text":"Creates selfed progeny individual population. works sexes \"\".","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/self.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Self individuals — self","text":"","code":"self(pop, nProgeny = 1, parents = NULL, keepParents = TRUE, simParam = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/self.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Self individuals — self","text":"pop object Pop-class nProgeny total number selfed progeny per individual parents optional vector indices allowable parents keepParents previous parents used mother father. simParam object SimParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/self.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Self individuals — self","text":"Returns object Pop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/self.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Self individuals — self","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=2, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L  #Create population pop = newPop(founderPop, simParam=SP)  #Self pollinate each individual pop2 = self(pop, simParam=SP)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/setEBV.html","id":null,"dir":"Reference","previous_headings":"","what":"Set EBV — setEBV","title":"Set EBV — setEBV","text":"Adds genomic estimated values populations's EBV  slot using output genomic selection functions.  genomic estimated values can either estimated  breeding values, estimated genetic values,  estimated general combining values.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/setEBV.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set EBV — setEBV","text":"","code":"setEBV(   pop,   solution,   value = \"gv\",   targetPop = NULL,   append = FALSE,   simParam = NULL )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/setEBV.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set EBV — setEBV","text":"pop object Pop-class solution object RRsol-class value genomic value estimated. Can  either \"gv\", \"bv\", \"female\", \"male\". targetPop optional target population can  used value \"bv\", \"female\", \"male\".  supplied, allele frequency targetPop used  set values. append estimated values appended  existing data EBV slot. TRUE, new column  added. FALSE, existing data replaced  new estimates. simParam object SimParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/setEBV.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set EBV — setEBV","text":"Returns object Pop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/setEBV.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set EBV — setEBV","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=20)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitA(10) SP$setVarE(h2=0.5) SP$addSnpChip(10)  #Create population pop = newPop(founderPop, simParam=SP)  #Run GS model and set EBV ans = RRBLUP(pop, simParam=SP) pop = setEBV(pop, ans, simParam=SP)  #Evaluate accuracy cor(gv(pop), ebv(pop)) #>        est_GV_Trait1 #> Trait1     0.3229975"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/setMarkerHaplo.html","id":null,"dir":"Reference","previous_headings":"","what":"Set marker haplotypes — setMarkerHaplo","title":"Set marker haplotypes — setMarkerHaplo","text":"Manually sets haplotypes population  individuals one loci.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/setMarkerHaplo.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set marker haplotypes — setMarkerHaplo","text":"","code":"setMarkerHaplo(pop, haplo, simParam = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/setMarkerHaplo.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set marker haplotypes — setMarkerHaplo","text":"pop object RawPop-class MapPop-class haplo matrix haplotypes, see details simParam object SimParam,  used pop MapPop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/setMarkerHaplo.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set marker haplotypes — setMarkerHaplo","text":"object class \"pop\" input","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/setMarkerHaplo.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Set marker haplotypes — setMarkerHaplo","text":"format haplotype matrix match  format output pullMarkerHaplo option haplo=\"\". Thus, recommended  function first used extract haplotypes  desired changes made output pullMarkerHaplo  passing matrix setMarkerHaplo. changes made QTL  may potentially result changes individuals genetic  value. changes reflected gv /gxe slot.  slots remain unchanged, ebv pheno slots  reflect new genotypes.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/setMarkerHaplo.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set marker haplotypes — setMarkerHaplo","text":"","code":"# Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=15)  # Extract haplotypes for marker \"1_1\" H = pullMarkerHaplo(founderPop, markers=\"1_1\")  # Set the first haplotype to 1 H[1,1] = 1L  # Set marker haplotypes founderPop = setMarkerHaplo(founderPop, haplo=H)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/setMisc.html","id":null,"dir":"Reference","previous_headings":"","what":"Set miscelaneous information in a population — setMisc","title":"Set miscelaneous information in a population — setMisc","text":"Set miscelaneous information population","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/setMisc.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set miscelaneous information in a population — setMisc","text":"","code":"setMisc(x, node = NULL, value = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/setMisc.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set miscelaneous information in a population — setMisc","text":"x Pop-class node character, name node set within x@misc slot value, value saved x@misc[[*]][[node]]; length value equal nInd(x); length 1, repeated using rep (see examples)","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/setMisc.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set miscelaneous information in a population — setMisc","text":"Pop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/setMisc.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Set miscelaneous information in a population — setMisc","text":"NULL value ignored","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/setPheno.html","id":null,"dir":"Reference","previous_headings":"","what":"Set phenotypes — setPheno","title":"Set phenotypes — setPheno","text":"Sets phenotypes traits adding random error multivariate normal distribution.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/setPheno.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set phenotypes — setPheno","text":"","code":"setPheno(   pop,   h2 = NULL,   H2 = NULL,   varE = NULL,   corE = NULL,   reps = 1,   fixEff = 1L,   p = NULL,   onlyPheno = FALSE,   traits = NULL,   simParam = NULL )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/setPheno.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set phenotypes — setPheno","text":"pop object Pop-class HybridPop-class h2 vector desired narrow-sense heritabilities trait. See details. H2 vector desired broad-sense heritabilities trait. See details. varE error (co)variances traits. See details. corE optional matrix correlations errors. See details. reps number replications phenotype. See details. fixEff fixed effect assign population. Used genomic selection models . p p-value environmental covariate used GxE traits. NULL, value sampled random. onlyPheno phenotype returned, see return traits integer vector indicate traits set. NULL, traits set. simParam object SimParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/setPheno.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set phenotypes — setPheno","text":"Returns object Pop-class HybridPop-class onlyPheno=FALSE, onlyPheno=TRUE matrix returned","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/setPheno.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Set phenotypes — setPheno","text":"three arguments setting error variance phenotype: h2, H2, varE. user use one arguments. user supplies values one, one used according order listed . h2 argument allows user specify error variance according narrow-sense heritability. calculation uses additive genetic variance total genetic variance founder population. Thus, heritability relates founder population current population. H2 argument allows user specify error variance according broad-sense heritability. calculation uses total genetic variance founder population. Thus, heritability relates founder population current population. varE argument allows user specify error variance directly. user may supply vector describing error variance trait supply matrix specify covariance errors. corE argument allows user specify correlations error covariance matrix. correlations supplied addition h2, H2, varE arguments. correlations used construct covariance matrix vector variances. user supplied covariance matrix varE, correlations supercede values provided matrix. reps parameter convenient representation replicated data. intended represent replicated yield trials plant breeding programs. case, varE set plot error reps set number plots per entry. resulting phenotype represents entry-means.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/setPheno.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set phenotypes — setPheno","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitA(10)  #Create population pop = newPop(founderPop, simParam=SP)  #Add phenotype with error variance of 1 pop = setPheno(pop, varE=1) #> Error in get(\"SP\", envir = .GlobalEnv): object 'SP' not found"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/setPhenoGCA.html","id":null,"dir":"Reference","previous_headings":"","what":"Set GCA as phenotype — setPhenoGCA","title":"Set GCA as phenotype — setPhenoGCA","text":"Calculates general combining ability set testers returns values phenotypes population.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/setPhenoGCA.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set GCA as phenotype — setPhenoGCA","text":"","code":"setPhenoGCA(   pop,   testers,   use = \"pheno\",   h2 = NULL,   H2 = NULL,   varE = NULL,   corE = NULL,   reps = 1,   fixEff = 1L,   p = NULL,   inbred = FALSE,   onlyPheno = FALSE,   simParam = NULL )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/setPhenoGCA.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set GCA as phenotype — setPhenoGCA","text":"pop object Pop-class testers object Pop-class use true genetic value (gv) phenotypes (pheno, default) h2 vector desired narrow-sense heritabilities trait. See details setPheno. H2 vector desired broad-sense heritabilities trait. See details setPheno. varE error (co)variances traits. See details setPheno. corE optional matrix correlations errors. See details setPheno. reps number replications phenotype. See details setPheno. fixEff fixed effect assign population. Used genomic selection models . p p-value environmental covariate used GxE traits. NULL, value sampled random. inbred pop testers fully inbred. fully inbred created newPop using inbred founders makeDH function onlyPheno phenotype returned, see return simParam object SimParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/setPhenoGCA.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set GCA as phenotype — setPhenoGCA","text":"Returns object Pop-class matrix onlyPheno=TRUE","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/setPhenoGCA.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set GCA as phenotype — setPhenoGCA","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10, inbred=TRUE)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitA(10)  #Create population pop = newPop(founderPop, simParam=SP)  #Set phenotype to average per pop2 = setPhenoGCA(pop, pop, use=\"gv\", inbred=TRUE, simParam=SP)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/setPhenoProgTest.html","id":null,"dir":"Reference","previous_headings":"","what":"Set progeny test as phenotype — setPhenoProgTest","title":"Set progeny test as phenotype — setPhenoProgTest","text":"Models progeny test individuals 'pop'. Returns 'pop' phenotype representing average performance progeny. phenotype generated mating individuals 'pop' randomly chosen individuals testPop number times equal 'nMatePerInd'.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/setPhenoProgTest.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set progeny test as phenotype — setPhenoProgTest","text":"","code":"setPhenoProgTest(   pop,   testPop,   nMatePerInd = 1L,   use = \"pheno\",   h2 = NULL,   H2 = NULL,   varE = NULL,   corE = NULL,   reps = 1,   fixEff = 1L,   p = NULL,   onlyPheno = FALSE,   simParam = NULL )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/setPhenoProgTest.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set progeny test as phenotype — setPhenoProgTest","text":"pop object Pop-class testPop object Pop-class nMatePerInd number times individual 'pop' mated individual testPop use true genetic value (gv) phenotypes (pheno, default) h2 vector desired narrow-sense heritabilities trait. See details setPheno. H2 vector desired broad-sense heritabilities trait. See details setPheno. varE error (co)variances traits. See details setPheno. corE optional matrix correlations errors. See details setPheno. reps number replications phenotype. See details setPheno. fixEff fixed effect assign population. Used genomic selection models . p p-value environmental covariate used GxE traits. NULL, value sampled random. onlyPheno phenotype returned, see return simParam object SimParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/setPhenoProgTest.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set progeny test as phenotype — setPhenoProgTest","text":"Returns object Pop-class matrix onlyPheno=TRUE","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/setPhenoProgTest.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Set progeny test as phenotype — setPhenoProgTest","text":"reps parameter convenient representation replicated data. intended representation replicated yield trials plant breeding programs. case, varE set plot error reps set number plots per entry. resulting phenotype reflect mean replications.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/setPhenoProgTest.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set progeny test as phenotype — setPhenoProgTest","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10, inbred=TRUE)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitA(10)  #Create two populations of 5 individuals pop1 = newPop(founderPop[1:5], simParam=SP) pop2 = newPop(founderPop[6:10], simParam=SP)  #Set phenotype according to a progeny test pop3 = setPhenoProgTest(pop1, pop2, use=\"gv\", simParam=SP)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/smithHazel.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate Smith-Hazel weights — smithHazel","title":"Calculate Smith-Hazel weights — smithHazel","text":"Calculates weights Smith-Hazel index given economice weights  phenotypic genotypic variance-covariance matrices.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/smithHazel.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate Smith-Hazel weights — smithHazel","text":"","code":"smithHazel(econWt, varG, varP)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/smithHazel.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate Smith-Hazel weights — smithHazel","text":"econWt vector economic weights varG genetic variance-covariance matrix varP phenotypic variance-covariance matrix","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/smithHazel.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate Smith-Hazel weights — smithHazel","text":"vector weight calculating index values","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/smithHazel.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate Smith-Hazel weights — smithHazel","text":"","code":"G = 1.5*diag(2)-0.5 E = diag(2) P = G+E wt = c(1,1) smithHazel(wt, G, P) #>           [,1] #> [1,] 0.3333333 #> [2,] 0.3333333"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/solveMKM.html","id":null,"dir":"Reference","previous_headings":"","what":"Solve Multikernel Model — solveMKM","title":"Solve Multikernel Model — solveMKM","text":"Solves univariate mixed model multiple random effects.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/solveMKM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Solve Multikernel Model — solveMKM","text":"","code":"solveMKM(y, X, Zlist, Klist, maxIter = 40L, tol = 1e-04)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/solveMKM.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Solve Multikernel Model — solveMKM","text":"y matrix n rows 1 column X matrix n rows x columns Zlist list Z matrices Klist list K matrices maxIter maximum number iteration tol tolerance convergence","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/solveMVM.html","id":null,"dir":"Reference","previous_headings":"","what":"Solve Multivariate Model — solveMVM","title":"Solve Multivariate Model — solveMVM","text":"Solves multivariate mixed model form \\(Y=X\\beta+Zu+e\\)","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/solveMVM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Solve Multivariate Model — solveMVM","text":"","code":"solveMVM(Y, X, Z, K, tol = 1e-06, maxIter = 1000L)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/solveMVM.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Solve Multivariate Model — solveMVM","text":"Y matrix n rows q columns X matrix n rows x columns Z matrix n rows m columns K matrix m rows m columns tol tolerance convergence maxIter maximum number iteration","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/solveRRBLUP.html","id":null,"dir":"Reference","previous_headings":"","what":"Solve RR-BLUP — solveRRBLUP","title":"Solve RR-BLUP — solveRRBLUP","text":"Solves univariate mixed model form \\(y=X\\beta+Mu+e\\)","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/solveRRBLUP.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Solve RR-BLUP — solveRRBLUP","text":"","code":"solveRRBLUP(y, X, M)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/solveRRBLUP.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Solve RR-BLUP — solveRRBLUP","text":"y matrix n rows 1 column X matrix n rows x columns M matrix n rows m columns","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/solveRRBLUPMK.html","id":null,"dir":"Reference","previous_headings":"","what":"Solve Multikernel RR-BLUP — solveRRBLUPMK","title":"Solve Multikernel RR-BLUP — solveRRBLUPMK","text":"Solves univariate mixed model multiple random effects.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/solveRRBLUPMK.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Solve Multikernel RR-BLUP — solveRRBLUPMK","text":"","code":"solveRRBLUPMK(y, X, Mlist, maxIter = 40L)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/solveRRBLUPMK.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Solve Multikernel RR-BLUP — solveRRBLUPMK","text":"y matrix n rows 1 column X matrix n rows x columns Mlist list M matrices maxIter maximum number iteration","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/solveRRBLUPMV.html","id":null,"dir":"Reference","previous_headings":"","what":"Solve Multivariate RR-BLUP — solveRRBLUPMV","title":"Solve Multivariate RR-BLUP — solveRRBLUPMV","text":"Solves multivariate mixed model form \\(Y=X\\beta+Mu+e\\)","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/solveRRBLUPMV.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Solve Multivariate RR-BLUP — solveRRBLUPMV","text":"","code":"solveRRBLUPMV(Y, X, M, maxIter = 1000L, tol = 1e-06)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/solveRRBLUPMV.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Solve Multivariate RR-BLUP — solveRRBLUPMV","text":"Y matrix n rows q columns X matrix n rows x columns M matrix n rows m columns maxIter maximum number iteration tol tolerance convergence","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/solveRRBLUP_EM.html","id":null,"dir":"Reference","previous_headings":"","what":"Solve RR-BLUP with EM — solveRRBLUP_EM","title":"Solve RR-BLUP with EM — solveRRBLUP_EM","text":"Solves univariate mixed model form \\(y=X\\beta+Mu+e\\) using Expectation-Maximization algorithm.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/solveRRBLUP_EM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Solve RR-BLUP with EM — solveRRBLUP_EM","text":"","code":"solveRRBLUP_EM(Y, X, M, Vu, Ve, tol, maxIter, useEM)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/solveRRBLUP_EM.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Solve RR-BLUP with EM — solveRRBLUP_EM","text":"Y matrix n rows 1 column X matrix n rows x columns M matrix n rows m columns Vu initial guess variance marker effects Ve initial guess error variance tol tolerance declaring convergence maxIter maximum iteration attempting convergence useEM EM algorithm used. false, estimation variance components performed. initial values treated true.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/solveRRBLUP_EM2.html","id":null,"dir":"Reference","previous_headings":"","what":"Solve RR-BLUP with EM and 2 random effects — solveRRBLUP_EM2","title":"Solve RR-BLUP with EM and 2 random effects — solveRRBLUP_EM2","text":"Solves univariate mixed model form \\(y=X\\beta+M_1u_1+M_2u_2+e\\) using Expectation-Maximization algorithm.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/solveRRBLUP_EM2.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Solve RR-BLUP with EM and 2 random effects — solveRRBLUP_EM2","text":"","code":"solveRRBLUP_EM2(Y, X, M1, M2, Vu1, Vu2, Ve, tol, maxIter, useEM)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/solveRRBLUP_EM2.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Solve RR-BLUP with EM and 2 random effects — solveRRBLUP_EM2","text":"Y matrix n rows 1 column X matrix n rows x columns M1 matrix n rows m1 columns M2 matrix n rows m2 columns Vu1 initial guess variance first marker effects Vu2 initial guess variance second marker effects Ve initial guess error variance tol tolerance declaring convergence maxIter maximum iteration attempting convergence useEM EM algorithm used. false, estimation variance components performed. initial values treated true.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/solveRRBLUP_EM3.html","id":null,"dir":"Reference","previous_headings":"","what":"Solve RR-BLUP with EM and 3 random effects — solveRRBLUP_EM3","title":"Solve RR-BLUP with EM and 3 random effects — solveRRBLUP_EM3","text":"Solves univariate mixed model form \\(y=X\\beta+M_1u_1+M_2u_2+M_3u_3+e\\) using Expectation-Maximization algorithm.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/solveRRBLUP_EM3.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Solve RR-BLUP with EM and 3 random effects — solveRRBLUP_EM3","text":"","code":"solveRRBLUP_EM3(Y, X, M1, M2, M3, Vu1, Vu2, Vu3, Ve, tol, maxIter, useEM)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/solveRRBLUP_EM3.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Solve RR-BLUP with EM and 3 random effects — solveRRBLUP_EM3","text":"Y matrix n rows 1 column X matrix n rows x columns M1 matrix n rows m1 columns M2 matrix n rows m2 columns M3 matrix n rows m3 columns Vu1 initial guess variance first marker effects Vu2 initial guess variance second marker effects Vu3 initial guess variance second marker effects Ve initial guess error variance tol tolerance declaring convergence maxIter maximum iteration attempting convergence useEM EM algorithm used. false, estimation variance components performed. initial values treated true.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/solveUVM.html","id":null,"dir":"Reference","previous_headings":"","what":"Solve Univariate Model — solveUVM","title":"Solve Univariate Model — solveUVM","text":"Solves univariate mixed model form \\(y=X\\beta+Zu+e\\)","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/solveUVM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Solve Univariate Model — solveUVM","text":"","code":"solveUVM(y, X, Z, K)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/solveUVM.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Solve Univariate Model — solveUVM","text":"y matrix n rows 1 column X matrix n rows x columns Z matrix n rows m columns K matrix m rows m columns","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/transMat.html","id":null,"dir":"Reference","previous_headings":"","what":"Linear transformation matrix — transMat","title":"Linear transformation matrix — transMat","text":"Creates m m linear transformation matrix  can applied n m uncorrelated deviates  sampled standard normal distribution produce correlated deviates arbitrary correlation  R. R positive semi-definite, function  returns smoothing returns warning (see details).","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/transMat.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Linear transformation matrix — transMat","text":"","code":"transMat(R)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/transMat.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Linear transformation matrix — transMat","text":"R correlation matrix","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/transMat.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Linear transformation matrix — transMat","text":"eigendecomposition applied correlation  matrix used test positive semi-definite.  matrix positive semi-definite,  valid correlation matrix. case, smoothing  applied matrix (described 'cor.smooth'  'psych' library) obtain valid correlation matrix.  resulting deviates thus exactly match  desired correlation, hopefully close  input matrix far removed valid  correlation matrix.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/transMat.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Linear transformation matrix — transMat","text":"","code":"# Create an 2x2 correlation matrix R = 0.5*diag(2) + 0.5  # Sample 1000 uncorrelated deviates from a  # bivariate standard normal distribution X = matrix(rnorm(2*1000), ncol=2)  # Compute the transformation matrix T = transMat(R)  # Apply the transformation to the deviates Y = X%*%T  # Measure the sample correlation cor(Y) #>           [,1]      [,2] #> [1,] 1.0000000 0.4989095 #> [2,] 0.4989095 1.0000000"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/usefulness.html","id":null,"dir":"Reference","previous_headings":"","what":"Usefulness criterion — usefulness","title":"Usefulness criterion — usefulness","text":"Calculates usefulness criterion","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/usefulness.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Usefulness criterion — usefulness","text":"","code":"usefulness(   pop,   trait = 1,   use = \"gv\",   p = 0.1,   selectTop = TRUE,   simParam = NULL,   ... )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/usefulness.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Usefulness criterion — usefulness","text":"pop object Pop-class  HybridPop-class trait trait selection. Either number indicating  single trait function returning vector length nInd. use select genetic values (gv, default), estimated breeding values (ebv), breeding values (bv),  phenotypes (pheno) p proportion individuals selected selectTop selects highest values true.  Selects lowest values false. simParam object SimParam ... additional arguments using function  trait","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/usefulness.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Usefulness criterion — usefulness","text":"Returns numeric value","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/usefulness.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Usefulness criterion — usefulness","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=2, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitA(10)  #Create population pop = newPop(founderPop, simParam=SP)  #Determine usefulness of population  usefulness(pop, simParam=SP) #> [1] 1  #Should be equivalent to GV of best individual max(gv(pop)) #> [1] 1"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/varA.html","id":null,"dir":"Reference","previous_headings":"","what":"Additive variance — varA","title":"Additive variance — varA","text":"Returns additive variance traits","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/varA.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Additive variance — varA","text":"","code":"varA(pop, simParam = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/varA.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Additive variance — varA","text":"pop object Pop-class simParam object SimParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/varA.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Additive variance — varA","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$addTraitAD(10, meanDD=0.5) SP$setVarE(h2=0.5) SP$nThreads = 1L  #Create population pop = newPop(founderPop, simParam=SP) varA(pop, simParam=SP) #>        Trait1 #> Trait1      1"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/varAA.html","id":null,"dir":"Reference","previous_headings":"","what":"Additive-by-additive epistatic variance — varAA","title":"Additive-by-additive epistatic variance — varAA","text":"Returns additive--additive epistatic variance traits","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/varAA.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Additive-by-additive epistatic variance — varAA","text":"","code":"varAA(pop, simParam = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/varAA.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Additive-by-additive epistatic variance — varAA","text":"pop object Pop-class simParam object SimParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/varAA.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Additive-by-additive epistatic variance — varAA","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$addTraitAD(10, meanDD=0.5) SP$setVarE(h2=0.5) SP$nThreads = 1L  #Create population pop = newPop(founderPop, simParam=SP) varAA(pop, simParam=SP) #>        Trait1 #> Trait1      0"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/varD.html","id":null,"dir":"Reference","previous_headings":"","what":"Dominance variance — varD","title":"Dominance variance — varD","text":"Returns dominance variance traits","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/varD.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Dominance variance — varD","text":"","code":"varD(pop, simParam = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/varD.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Dominance variance — varD","text":"pop object Pop-class simParam object SimParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/varD.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Dominance variance — varD","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$addTraitAD(10, meanDD=0.5) SP$setVarE(h2=0.5) SP$nThreads = 1L  #Create population pop = newPop(founderPop, simParam=SP) varD(pop, simParam=SP) #>           Trait1 #> Trait1 0.2133749"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/varG.html","id":null,"dir":"Reference","previous_headings":"","what":"Total genetic variance — varG","title":"Total genetic variance — varG","text":"Returns total genetic variance traits","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/varG.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Total genetic variance — varG","text":"","code":"varG(pop)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/varG.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Total genetic variance — varG","text":"pop object Pop-class HybridPop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/varG.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Total genetic variance — varG","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$addTraitA(10) SP$setVarE(h2=0.5) SP$nThreads = 1L  #Create population pop = newPop(founderPop, simParam=SP) varG(pop) #>        Trait1 #> Trait1      1"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/varP.html","id":null,"dir":"Reference","previous_headings":"","what":"Phenotypic variance — varP","title":"Phenotypic variance — varP","text":"Returns phenotypic variance traits","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/varP.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Phenotypic variance — varP","text":"","code":"varP(pop)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/varP.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Phenotypic variance — varP","text":"pop object Pop-class HybridPop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/varP.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Phenotypic variance — varP","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$addTraitA(10) SP$setVarE(h2=0.5) SP$nThreads = 1L  #Create population pop = newPop(founderPop, simParam=SP) varP(pop) #>         Trait1 #> Trait1 1.86957"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/writePlink.html","id":null,"dir":"Reference","previous_headings":"","what":"Writes a Pop-class as PLINK files — writePlink","title":"Writes a Pop-class as PLINK files — writePlink","text":"Writes Pop-class PLINK PED MAP files. arguments  function chosen consistency  RRBLUP2. base pair coordinate locus position stored AlphaSimR actual base pair  position. AlphaSimR track base pair  positions, relative positions loci used  simulation.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/writePlink.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Writes a Pop-class as PLINK files — writePlink","text":"","code":"writePlink(   pop,   baseName,   traits = 1,   use = \"pheno\",   snpChip = 1,   useQtl = FALSE,   simParam = NULL,   ... )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/writePlink.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Writes a Pop-class as PLINK files — writePlink","text":"pop object Pop-class baseName basename PED MAP files. traits integer indicating trait write, trait name, function traits returning single value. use use PLINK's phenotype field. Either phenotypes \"pheno\",  genetic values \"gv\", estimated breeding values \"ebv\", breeding values \"bv\",  random values \"rand\". snpChip integer indicating SNP chip genotype  use useQtl QTL genotypes used instead SNP chip.  TRUE, snpChip specifies trait's QTL use, thus  QTL may match QTL underlying phenotype supplied traits. simParam object SimParam ... additional arguments using function  traits","code":""},{"path":[]},{"path":"https://gaynorr.github.io/AlphaSimR/reference/writeRecords.html","id":null,"dir":"Reference","previous_headings":"","what":"Write data records — writeRecords","title":"Write data records — writeRecords","text":"Saves population's phenotypic marker data directory.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/writeRecords.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Write data records — writeRecords","text":"","code":"writeRecords(   pop,   dir,   snpChip = 1,   useQtl = FALSE,   includeHaplo = FALSE,   append = TRUE,   simParam = NULL )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/writeRecords.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Write data records — writeRecords","text":"pop object Pop-class dir path directory saving output snpChip SNP chip genotype save. useQtl=TRUE, value indicate trait's QTL genotype save. value 0 skip writing snpChip. useQtl QTL genotype written instead SNP chip genotypes. includeHaplo markers separated female male haplotypes. append true, new records added existing records. false, existing records deleted writing new records. Note delete files 'dir' directory. simParam object SimParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-152","dir":"Changelog","previous_headings":"","what":"AlphaSimR 1.5.2","title":"AlphaSimR 1.5.2","text":"CRAN release: 2023-11-01 *fix SimParam examples CRAN","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-151","dir":"Changelog","previous_headings":"","what":"AlphaSimR 1.5.1","title":"AlphaSimR 1.5.1","text":"*deleted bad example code setMisc *changed examples use single thread CRAN testing change shown documentation","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-150","dir":"Changelog","previous_headings":"","what":"AlphaSimR 1.5.0","title":"AlphaSimR 1.5.0","text":"*renamed MegaPop MultiPop *fixed bug writePlink correctly export map positions cM *fixed bug writeRecords due removed reps slot pops *added altAddTraitAD specifying traits dominance effects using dominance variance inbreeding depression *add miscPop slot class Pop","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-142","dir":"Changelog","previous_headings":"","what":"AlphaSimR 1.4.2","title":"AlphaSimR 1.4.2","text":"CRAN release: 2023-03-27 *updated MaCS citation https site","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-141","dir":"Changelog","previous_headings":"","what":"AlphaSimR 1.4.1","title":"AlphaSimR 1.4.1","text":"*Changed citation use bibentry instead citEntry","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-140","dir":"Changelog","previous_headings":"","what":"AlphaSimR 1.4.0","title":"AlphaSimR 1.4.0","text":"*fixed bug IBD tracking *add setFounderHap SimParam applying custom haplotypes founders *added addSnpChipByName SimParam defining SNP chips marker names","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-134","dir":"Changelog","previous_headings":"","what":"AlphaSimR 1.3.4","title":"AlphaSimR 1.3.4","text":"CRAN release: 2022-12-09 *changed C++ using sprintf use snprintf","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-133","dir":"Changelog","previous_headings":"","what":"AlphaSimR 1.3.3","title":"AlphaSimR 1.3.3","text":"*fixed bug calculation genic variance *fixed importHaplo passing ploidy newMapPop *fixed bug correlated error variances","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-132","dir":"Changelog","previous_headings":"","what":"AlphaSimR 1.3.2","title":"AlphaSimR 1.3.2","text":"CRAN release: 2022-11-02 *fixed column name bug multiple traits setEBV *fixed CTD caused runMacs many segSites requested *fixed missing names GV using resetPop *fixed bug importTrait *popVar now deals matrices 1 row","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-131","dir":"Changelog","previous_headings":"","what":"AlphaSimR 1.3.1","title":"AlphaSimR 1.3.1","text":"CRAN release: 2022-08-25 *updated link Gaynor, 2017","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-130","dir":"Changelog","previous_headings":"","what":"AlphaSimR 1.3.0","title":"AlphaSimR 1.3.0","text":"*added ability exclude loci name SimParam$restrSegSites *pullMarkerGeno pullMarkerHaplo now work MapPop class *added setMarkerHaplo manually change genotypes Pop MapPop *added addSegSite manually adding segregating sites MapPop class *simParam$setCorE deprecated favor corE argument simParam$setVarE *setPheno now takes corE argument *setPheno now allows user set phenotypes subset traits *add newEmptyPop create populations zero individuals *removed reps slot populations heterogeneous residual variance GS models *added h2, H2, corE setPhenoGCA setPhenoProgTest *“EUROPEAN” species history removed runMacs due lengthy runtime","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-122","dir":"Changelog","previous_headings":"","what":"AlphaSimR 1.2.2","title":"AlphaSimR 1.2.2","text":"*added getPed quick extract population’s pedigree *added getGenMap pull genetic map data.frame format","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-121","dir":"Changelog","previous_headings":"","what":"AlphaSimR 1.2.1","title":"AlphaSimR 1.2.1","text":"CRAN release: 2022-07-05 *fixed bugs relating importData functions *fixed writePlink errors longer requires equal length chromosomes","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-120","dir":"Changelog","previous_headings":"","what":"AlphaSimR 1.2.0","title":"AlphaSimR 1.2.0","text":"*added importGenMap format genetic maps AlphaSimR *added importInbredGeno importHaplo make easier create simulation external data *added importSnpChip, importTrait SimParam make easier manually define traits *added pullMarkerGeno pullMarkerHaplo make easier extract genotypes haplotypes specific loci without defining trait SNP chip *reduceGenome, mergeGenome doubleGenome really now work pedigree recombination tracking","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-112","dir":"Changelog","previous_headings":"","what":"AlphaSimR 1.1.2","title":"AlphaSimR 1.1.2","text":"CRAN release: 2022-02-17 *added missing #ifdef _OPENMP OCS.cpp","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-111","dir":"Changelog","previous_headings":"","what":"AlphaSimR 1.1.1","title":"AlphaSimR 1.1.1","text":"*removed use PI variable C++ code due compiler specific","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-110","dir":"Changelog","previous_headings":"","what":"AlphaSimR 1.1.0","title":"AlphaSimR 1.1.0","text":"*added snpChip argument pullIbdHaplo backwards compatibility *exposed internal mixed model solvers *selection functions now return warning enough individuals *fixed error pullIbdHaplo chr isn’t NULL *fixed error assigning 1 QTL /SNP *changed geno slot matrix list support future RcppArmadillo changes *doubleGenome reduceGenome now work IBD tracking","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-104","dir":"Changelog","previous_headings":"","what":"AlphaSimR 1.0.4","title":"AlphaSimR 1.0.4","text":"CRAN release: 2021-09-08 *fixed errors implementation Gamma Sprinkling model","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-103","dir":"Changelog","previous_headings":"","what":"AlphaSimR 1.0.3","title":"AlphaSimR 1.0.3","text":"CRAN release: 2021-07-29 *fixed formatting error genetic maps created runMacs broke genotype extraction functions","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-102","dir":"Changelog","previous_headings":"","what":"AlphaSimR 1.0.2","title":"AlphaSimR 1.0.2","text":"CRAN release: 2021-07-28 *added h2 H2 setPhenoGCA *pullGeno pullHaplo functions now report marker names genetic map","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-101","dir":"Changelog","previous_headings":"","what":"AlphaSimR 1.0.1","title":"AlphaSimR 1.0.1","text":"CRAN release: 2021-05-14 *removed lazyData field DESCRIPTION","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-100","dir":"Changelog","previous_headings":"","what":"AlphaSimR 1.0.0","title":"AlphaSimR 1.0.0","text":"*AlphaSimR manuscript published G3 (citation added) *changed Gamma Sprinkling model crossovers, default still Gamma model *change default interference parameter (v) 2.6 consistent Kosambi mapping function (1, consistent Haldane mapping function) *new internal id (iid) allows user freely change id slot populations *runMacs2 now adjusts Ne autopolyploids *parent populations now passed finalizePop *check added throws error use discontinued “gender” argument detected *added experimental MegaPop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-0130","dir":"Changelog","previous_headings":"","what":"AlphaSimR 0.13.0","title":"AlphaSimR 0.13.0","text":"CRAN release: 2020-10-11 *references gender changed appropriate terms sex sexes *added misc slot populations *added finalizePop SimParam *added physical positions getSnpMap getQtlMap *can now use h2 H2 specify error variance setPheno *SimParam$setVarE now accepts matrix varE *fixed bug editGenome making multiple edits *adding merging centromere vector cChr","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-0122","dir":"Changelog","previous_headings":"","what":"AlphaSimR 0.12.2","title":"AlphaSimR 0.12.2","text":"CRAN release: 2020-05-19 *GxE traits now default random sampling p-values *fixed bug restrSegSites","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-0121","dir":"Changelog","previous_headings":"","what":"AlphaSimR 0.12.1","title":"AlphaSimR 0.12.1","text":"CRAN release: 2020-03-30 *fixed bug selection segSites","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-0120","dir":"Changelog","previous_headings":"","what":"AlphaSimR 0.12.0","title":"AlphaSimR 0.12.0","text":"*changed output genParam match Bulmer, 1976 *nProgeny added makeCross makeCross2 *SimParam documentation now ?SimParam *non-overlapping QTL SNP now default *new interface restrSegSites SimParam *fixed subset id populations *fixed major bug newMapPop","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-0111","dir":"Changelog","previous_headings":"","what":"AlphaSimR 0.11.1","title":"AlphaSimR 0.11.1","text":"CRAN release: 2020-01-13 *switched circular design balance option randCross randCross2 *added reduceGenome doubleGenome changing ploidy levels *added minSnpFreq SimParam_addSnpChip reference population *c function now merges individuals MapPop objects (chromosomes ) *cChr function new merges chromosomes MapPop objects *fixed broken SimParam_addStructuredSnpChip *removed broken pullMultipleSnpGeno pullMultipleSnpHaplo *fixed broken writePlink","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-0110","dir":"Changelog","previous_headings":"","what":"AlphaSimR 0.11.0","title":"AlphaSimR 0.11.0","text":"CRAN release: 2019-10-11 *rework setEBV (breaks scripts) *genotype data now stored bits (bytes) *implemented gamma model crossover interference *added mutate function model random mutations *added vignette explaining biological model traits *GS models now handle polyploids *heterogenous error variance now optional GS models (default homogeneous error) *improved gene drop functionality pedigreeCross *added keepParents option makeDH self (indirectly extends selectFam selectWithinFam) *added RRBLUP_SCA2 *set methods “show” function applied populations *fixed bug returning first individual selecting 0 *fixed error recombination track using makeDH *fixed error causing epistatic effects mask GxE effects *fixed error pullSegSiteGeno pullSegSiteHaplo variable number sites per chromosome","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-0100","dir":"Changelog","previous_headings":"","what":"AlphaSimR 0.10.0","title":"AlphaSimR 0.10.0","text":"CRAN release: 2019-03-15 *added traits epistasis *Max number threads automatically detected *added RRBLUP_D2 *added version tracking SimParam *removed trackHaploPop (super-ceded pullIbdHaplo) *added fastRRBLUP *fixed faulty double crossover logic *fixed broken writePlink *fixed broken pullIbdHaplo *mergePops longer assumes diploidy","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-090","dir":"Changelog","previous_headings":"","what":"AlphaSimR 0.9.0","title":"AlphaSimR 0.9.0","text":"CRAN release: 2019-02-07 *added support autopolyploids *added RRBLUP_GCA2 *randCross2 can now “balance” crossing using gender *fixed recombination tracking bug createDH2 *removed bug setEBV append=TRUE","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-082","dir":"Changelog","previous_headings":"","what":"AlphaSimR 0.8.2","title":"AlphaSimR 0.8.2","text":"CRAN release: 2018-10-15 *fixed ambiguous overloading optimize.cpp","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-081","dir":"Changelog","previous_headings":"","what":"AlphaSimR 0.8.1","title":"AlphaSimR 0.8.1","text":"CRAN release: 2018-10-12 *setPheno (setPhenoGCA) passes number reps populations *fixed bug editGenomeTopQtl *fixed bug RRBLUP_D *fixed bug resetPop *fixed bug SimParam_rescaleTraits *removed unimplemented SimParam_restrSnpSites SimParam_restrQtlSites *add error message traits calcGCA","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-080","dir":"Changelog","previous_headings":"","what":"AlphaSimR 0.8.0","title":"AlphaSimR 0.8.0","text":"*added GxE traits zero environmental variance *faster trait scaling *faster calculation genetic values *dsyevr now called via arma_fortran *added OpenMP support *parallelized cross2 *parallelized runMacs *parallelized calculation genetic values *variance calculations now account inbreeding *fixes male selection selectOP","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-071","dir":"Changelog","previous_headings":"","what":"AlphaSimR 0.7.1","title":"AlphaSimR 0.7.1","text":"*add fixEff setPhenoGCA","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-070","dir":"Changelog","previous_headings":"","what":"AlphaSimR 0.7.0","title":"AlphaSimR 0.7.0","text":"*added default runMacs option return segSites *added ability specify separate male female genetic maps *pullGeno pullHaplo functions can now specify chromosomes *added RRBLUP2 special GS cases *improved speed replacing Rcpp random number generators *changed available MaCS species *GS functions now use populations directly *added pullIbdHaplo *added writePlink *fixed population sub-setting checks prevent invalid selections *fixed slow calcGCA *fixed error addTraitAG preventing multiple traits *fixed bug mergePops merging ebv *fixed bug setVarE using H2 multiple traits","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-061","dir":"Changelog","previous_headings":"","what":"AlphaSimR 0.6.1","title":"AlphaSimR 0.6.1","text":"*selectFam now handles half-sib families *selectWithinFam now handles half-sib families *Removed restriction varE=NULL setPhenoGCA","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-060","dir":"Changelog","previous_headings":"","what":"AlphaSimR 0.6.0","title":"AlphaSimR 0.6.0","text":"*Added NEWS file *Added selectOP model selection open pollinating plants *Added runMacs2 wrapper runMacs *Fixed error using H2 SimParam_setVarE","code":""}]
+[{"path":"https://gaynorr.github.io/AlphaSimR/articles/intro.html","id":"example-breeding-program","dir":"Articles","previous_headings":"","what":"Example Breeding Program","title":"Introduction to AlphaSimR","text":"simplified animal breeding program modeling 20 discrete generations selection. generation consists 1000 animals, 500 male 500 female. generation, best 25 males selected basis genetic value single polygenic trait mated females produce 1000 replacement animals. quantitative trait selection modeled controlled 10,000 QTL. QTL equally split across 10 chromosome groups 1,000 QTL per chromosome. mean genetic value individuals generation recorded construct plot genetic gain per generation.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/articles/intro.html","id":"creating-founder-haplotypes","dir":"Articles","previous_headings":"","what":"Creating Founder Haplotypes","title":"Introduction to AlphaSimR","text":"first step simulation creating set founder haplotypes. founder haplotypes used form genome genotypes animals first generation. genotypes descendants derived haplotypes using simulated mating genetic recombination. simulation, single line code needed create haplotypes, given . code uses quickHaplo function generate initial haplotypes. quickHaplo function generates haplotypes randomly sampling 1s 0s. approach equivalent modeling population linkage Hardy-Weinberg equilibrium allele frequencies 0.5. approach rapid generate realistic haplotypes. makes approach great prototyping code, ill-suited types simulations. preferred choice simulating realistic haplotypes use runMacs function. runMacs function wrapper MaCS software, coalescent simulation program included within distribution AlphaSimR (Chen, Marjoram, Wall 2009). MaCS software used AlphaSimR simulate bi-allelic genome sequences according population demographic history. runMacs function allows user specify one several predefined population histories supply population history. list currently available population histories can found runMacs help document. alternative choice providing realistic initial haplotypes import newMapPop function. function allows user import haplotypes can generated another software package taken directly real marker data.","code":"founderPop = quickHaplo(nInd=1000, nChr=10, segSites=1000)"},{"path":"https://gaynorr.github.io/AlphaSimR/articles/intro.html","id":"setting-simulation-parameters","dir":"Articles","previous_headings":"","what":"Setting Simulation Parameters","title":"Introduction to AlphaSimR","text":"second step setting global parameters simulation. can done three lines code. first line initializes object containing simulation parameters. object must initialized founder haplotypes created previous step code given . output function object class SimParam saved name SP. name SP almost always used, many AlphaSimR functions use argument called “simParam” default value NULL. leave value NULL, functions search global environment object called SP use function’s argument. means use SP, won’t need specify value “simParam” argument. next line code defines quantitative trait used selection. mentioned previous section, trait controlled 1000 QTL per chromosome. rest function arguments left defaults, include trait mean zero variance one unit. ‘’ end SP$addTraitA indicates trait’s QTL additive effects. traits AlphaSimR include additive effects. Traits may also include combination three additional types effects: dominance (“D”), epistasis (“E”), genotype--environment (“G”). specific combination trait effects requested using function appropriate letter ending. example, trait additive epistasis effects can requested using SP$addTraitAE. following trait types currently offered: “”, “AD”, “AE”, “AG”, “ADE”, “ADG”, “AEG”, “ADEG”. final line code defines sexes determined simulation. Sex systematically assigned (.e. male, female, male, …). Systematic assignment used ensure always equal numbers males females.","code":"SP = SimParam$new(founderPop) SP$addTraitA(nQtlPerChr=1000) SP$setSexes(\"yes_sys\")"},{"path":"https://gaynorr.github.io/AlphaSimR/articles/intro.html","id":"modeling-the-breeding-program","dir":"Articles","previous_headings":"","what":"Modeling the Breeding Program","title":"Introduction to AlphaSimR","text":"now ready start modeling breeding program. begin, need generate initial population animals. step take haplotypes founderPop information SP create object Pop-class. Pop-class object represents population individuals. population important units AlphaSimR, AlphaSimR functions use one populations argument. regard, AlphaSimR can thought modeling discrete populations basic unit. contrasts predecessor, used discrete generations. Populations fixed unit AlphaSimR. Many functions AlphaSimR take population argument, modify population, return modified population. Populations can also used “directly”. example, can pull individuals form new (sub-)populations using [] can merge populations together using c(). functionality particularly useful performing tasks AlphaSimR lacks built-function. However, example breeding program presented easily modeled using built-functions. continuing model breeding program, first think data ’ll need examining results next stage. must expressly request relevant data saved. AlphaSimR designed way increased speed reduced memory usage. example plot generation mean time desired. needed construct plot vector containing mean generation. start vector, mean current generation saved “genMean”. subsequent generation, mean generation added “genMean”. Measuring mean current generation accomplished code . final lines code modeling 20 generations selection mating. AlphaSimR host functions modeling selection mating. example selectCross function used, efficiently combines selection mating single function call. function actually uses two separate function AlphaSimR, selectInd randCross selection mating, respectively. model multiple generations selection, function call placed within loop line code tracking population mean. Using loop makes code easier read avoids needless duplication. loop “pop” overwritten generation. keeps memory usage low keeps code simple. However, user needed retain older populations several alternative approaches adopted. approaches include giving population unique name, storing populations elements list, dynamically growing populations c(). code loop given .","code":"pop = newPop(founderPop) genMean = meanG(pop) for(generation in 1:20){   pop = selectCross(pop=pop, nFemale=500, nMale=25, use=\"gv\", nCrosses=1000)   genMean = c(genMean, meanG(pop)) }"},{"path":"https://gaynorr.github.io/AlphaSimR/articles/intro.html","id":"examining-the-results","dir":"Articles","previous_headings":"","what":"Examining the Results","title":"Introduction to AlphaSimR","text":"last step simulation examining results. example one result: vector population means generation. examine result, code produce basic line plot.","code":"plot(0:20, genMean, xlab=\"Generation\", ylab=\"Mean Genetic Value\", type=\"l\")"},{"path":"https://gaynorr.github.io/AlphaSimR/articles/intro.html","id":"full-code","dir":"Articles","previous_headings":"","what":"Full Code","title":"Introduction to AlphaSimR","text":"","code":"library(AlphaSimR) # Creating Founder Haplotypes founderPop = quickHaplo(nInd=1000, nChr=10, segSites=1000)  # Setting Simulation Parameters SP = SimParam$new(founderPop) SP$addTraitA(nQtlPerChr=1000) SP$setSexes(\"yes_sys\")  # Modeling the Breeding Program pop = newPop(founderPop) genMean = meanG(pop) for(generation in 1:20){   pop = selectCross(pop=pop, nFemale=500, nMale=25, use=\"gv\", nCrosses=1000)   genMean = c(genMean, meanG(pop)) }  # Examining the Results plot(0:20, genMean, xlab=\"Generation\", ylab=\"Mean Genetic Value\", type=\"l\")"},{"path":[]},{"path":"https://gaynorr.github.io/AlphaSimR/articles/traits.html","id":"genotype-dosage-scaling","dir":"Articles","previous_headings":"","what":"Genotype Dosage Scaling","title":"Traits in AlphaSimR","text":"AlphaSimR defines individual’s raw genotype dosage number copies “1” allele locus. Since loci AlphaSimR biallelic alleles “0” “1”, definition raw genotype dosage fully explains individual’s genotype. number copies “0” allele just individual’s ploidy level minus raw genotype dosage. usually rather irrelevant detail, user want model diploid organism whose ploidy level always two. However, AlphaSimR can also used model wide range autopolyploid organisms even allows mixing ploidy levels within simulation. means allowable range raw genotype dosage fixed value software must account fact. AlphaSimR accounts different levels ploidy scaling organism’s genotype dosage accordance ploidy level. primary motivation using scaled dosages unify user inputs. use scaled dosages can also make easier compare simulations different levels ploidy. However, user must use care making comparisons, underlying assumptions used model may valid. use scaled genotype dosages implies individual’s genetic value depends relative ratio alleles independent organism’s ploidy level. traits organisms evidence support assumption least reject , also plenty evidence clearly rejecting assumption traits (Gallais 2003). Thus, direct comparisons possible AlphaSimR always biologically relevant. However, vast majority users won’t running simulation depends assumption, information presented solely purpose understanding functions presented following sections. two types scaled genotype dosages AlphaSimR: additive dominance. explanation given . followed table providing example dosage scaling diploid autotetraploid organisms. scaled additive genotype dosage (\\(x_A\\)) shown equation (2). equation linearly scales relative dosage set values opposing homozygotes -1 1. \\[\\begin{equation} x_A = \\big( x - \\tfrac{ploidy}{2} \\big) \\big( \\tfrac{2}{ploidy} \\big) \\end{equation}\\] scaled dominance genotype dosage (\\(x_D\\)) shown equation (3). equation uses non-linear scaling fit value opposing homozygotes 0 middlemost heterozygote 1. middlemost heterozygote genotype equal ratio “0” “1” alleles. diploid organism, scaled dominance genotype dosage matches classic parameterization dominance. autopolyploid organisms, scaled dominance genotype dosage consistent digenic dominance (discussed later). \\[\\begin{equation} x_D = x \\big( ploidy - x \\big) \\big( \\tfrac{2}{ploidy} \\big)^2 \\end{equation}\\] Table 1 provides example raw scaled genotype dosages diploid autotetraploid organism. diploid tetraploid columns represent raw genotype dosages respective organisms. additive dominance columns represent corresponding scaled genotype dosages. table shows 0, 1 2 genotypes diploid organism treated equivalent 0, 2 4 genotypes autotetraploid organism.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/articles/traits.html","id":"additive-effects","dir":"Articles","previous_headings":"","what":"Additive Effects","title":"Traits in AlphaSimR","text":"\\[\\begin{equation} (x) = \\sum x_A \\end{equation}\\] function additive effects given equation (4). right-hand side summation QTL product additive effect (\\(\\)) scaled additive dosage (\\(x_A\\)). equation equivalent parameterizations classic quantitative trait models. unique aspect additive effects AlphaSimR sampling effects. Additive effects sampled two stages. first stage involves sampling initial values similar methods used stochastic simulation software programs. second stage unique. stage involves scaling magnitude initial values achieve desired genetic variance, either total additive genetic variance. first stage sampling additive effects setting initial values effects. Initial values sampled either standard normal distribution gamma distribution. using gamma distribution, user specifies shape parameter scale parameter set 1. deviates sampled gamma distribution randomly assigned either positive negative sign. Random assignment sign results expected distribution symmetric distribution mean 0. second stage scaling magnitude effects achieve user specified genetic variance. user specified genetic variance can either total additive. scaling procedure involves just additive effect, also dominance epistatic effects trait includes effects well. procedure works first calculating variance founder population using initially sampled effects calculating scaling constant applied effects achieve desired variance founder population. scaling constant equals square-root target genetic variance (total additive) divided square-root initial genetic variance (total additive). Note founder population population user uses initialize simulation parameters object. Scaling magnitude effects allows AlphaSimR build simulations trait values matching real-world counterparts. example, user simulating grain yield plant species likely estimates means variances tons per hectare. user can use create simulation values. primary benefit matching values make interpretation simulation results intuitive. significance results apparent user can work scale familiar . also allows user easily identify potential flaws simulation values move outside range biologically acceptable values.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/articles/traits.html","id":"dominance-effects","dir":"Articles","previous_headings":"","what":"Dominance Effects","title":"Traits in AlphaSimR","text":"\\[\\begin{equation} D(x) = \\sum d x_D \\end{equation}\\] function dominance effects given equation (5). right-hand side equation summation QTL product dominance effect (\\(d\\)) scaled dominance dosage (\\(x_D\\)). equation equivalent parameterization dominance classic quantitative trait models diploid organisms. additive effects, method sampling dominance effects AlphaSimR requires special attention. Dominance effects calculated AlphaSimR using concept dominance degrees. formula calculation given equation (6). equation shows dominance effect (\\(d\\)) locus dominance degree (\\(\\delta\\)) locus times absolute value additive effect (\\(\\)). \\[\\begin{equation} d = \\delta \\left| \\right| \\end{equation}\\] rationale behind using dominance degrees intuitive biological interpretation diploid organisms. example, dominance degree 0 represents dominance additive model. dominance degree 1 corresponds complete dominance. Dominance degrees 0 1 correspond partial dominance, values 1 correspond -dominance. Dominance effects, additive effects, sampled two stages. first stage sampling initial values second stage scaling magnitude values. sampling initial effects involves two user supplied parameters, mean variance normal distribution used sample dominance degrees. dominance degrees used conjunction additive effects calculate dominance effects. scaling procedure performed described additive effects section calculate scaling constant. scaling constant directly applied dominance effects. Note scaling changes value dominance effect, change value dominance degree. means specification dominance degree distribution independent requested genetic variance. Dominance effects become complicated discussing polyploid organisms. polyploids additional heterozygous genotypes. example, autotetraploid organism two homozygous genotypes (0 4) three heterozygous genotypes (1, 2 3). additional heterozygous genotype requires additional dominance parameter obtain fully parameterized model. Several different parameterizations used polyploids full discussion parameterizations outside scope document. Interested readers refer Gallais’s textbook details (2003). AlphaSimR include additional term dominance model polyploids, make use fully parameterized model. Instead, AlphaSimR uses digenic dominance model ploidy levels due use scaled dominance genotype dosages. model chosen provides consistency user interface internal coding regardless ploidy level provides reasonable approximation partial dominance highly polygenic traits. unfortunate side effect dominance model polyploids previously described interpretation dominance degrees breaks. Consider single QTL additive effect 1 dominance degree 1. genotypes genetic values example diploid autotetraploid organism given Table 2. diploid organism, heterozygous genotype equivalent best homozygote, dominance degree 1 indicates complete dominance. However, autotetraploid organism three heterozygous genotypes. value middlemost heterozygous genotype equivalent best homozygote, heterozygous genotype highest value. heterozygous genotype highest value better best homozygote, dominance degree 1 actually represents -dominance autotetraploid.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/articles/traits.html","id":"epistatic-effects","dir":"Articles","previous_headings":"","what":"Epistatic Effects","title":"Traits in AlphaSimR","text":"\\[\\begin{equation} E(x) = \\sum e x_{A_1} x_{A_2} \\end{equation}\\] function epistatic effects given equation (7). summation right-hand side pairs QTLs, AlphaSimR uses simplified model epistasis restricts epistatic interactions pairs loci. QTL must present one one pair, number pairs equal half number QTL. remaining elements right-hand side equation (7) epistatic effects (\\(e\\)), scaled additive dosage first locus pair (\\(x_{A_1}\\)) scaled additive dosage second locus pair (\\(x_{A_2}\\)). epistatic model equation (7) somewhat constrained. model allows epistasis pairs loci models additive--additive epistasis. motivation behind using constrained model maintain computational tractability using large numbers QTL. dominance model, model considered reasonable approximation complicated reality. sampling epistatic effects similar sampling additive effects one additional user specified parameter relative ratio additive--additive epistatic variance. relative ratio refers ratio additive--additive epistatic variance additive variance. parameter sets variance epistatic effects. Specifically, variance effects set value expected achieve desired ratio random mating population whose QTL linkage equilibrium allele frequency 0.5. Note populations, including simulated populations, meet assumptions, observed relative ratio additive additive--additive epistatic variance unlikely match requested ratio. observed additive--additive epistatic variance typically smaller, value maximized allele frequency 0.5. Note unselected bi-parental populations derived inbred parents expected allele frequencies 0.5 segregating alleles. Thus, populations ideal estimating reasonable value relative ratio additive--additive epistatic variance.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/articles/traits.html","id":"genotype-by-environment-effects","dir":"Articles","previous_headings":"","what":"Genotype-by-Environment Effects","title":"Traits in AlphaSimR","text":"\\[\\begin{equation} G(x, w) = w b(x) \\end{equation}\\] \\[\\begin{equation} b(x) = \\mu_G + \\sum g x_A \\end{equation}\\] function genotype--environment effects given equations (8) (9). right-hand side equation (8) contains two parts: environmental covariate (\\(w\\)) genotype specific slope (\\(b(x)\\)). formula genotype specific slope shown equation (9). right-hand side equation includes intercept value (\\(\\mu_G\\)) summation QTL product genotype--environment effect (\\(g\\)) scaled additive dosage (\\(x_A\\)). following paragraphs explain equations model genotype--environment interactions. Initially, explanation cover case population genotype--environment interaction variance, environmental variance. explanation parameters equations changed model genotype--environment interaction variance environmental variance given next section. begin, description variables equations sampled needed. much easier understand formulas come together model genotype--environment interactions understood variables represent. environmental covariate (\\(w\\)) equation (8) represents environmental component genotype--environment interaction. value environmental covariate randomly sampled standard normal distribution. definition, means average value environmental covariate zero variance one. average value environmental covariate considered target environment. Thus, value equation (8) target environment always zero. genotype specific slope equation (9) represents genetic component genotype--environment interaction. astute reader notice equation similar equation additive trait. Indeed, genotype specific slope really just additive trait. term \\(\\mu_G\\) serves similar role \\(\\mu\\) equation (1) summation right-hand side equation (9) similar function additive effects equation (4). Also like additive trait, effects genotype specific slope scaled achieve specific mean variance founder population. case, mean set zero variance set user specified genotype--environment interaction variance. understand environmental covariate genotype specific slope model genotype--environment interactions helps review properties variables. environmental covariate just random variable mean zero variance one. genotype specific slope also random variable, regards founder population, mean zero variance equal genotype--environment variance. means equation (8) just product two random variables. random variables independent, formula variance product given equation . \\[\\begin{equation} Var(w b) = E[w]^2 Var(b) + Var(w) E[b]^2 + Var(w) Var(b) \\end{equation}\\] Equation (10) gives variance product \\(w\\) \\(b\\) equation (8). term \\(Var()\\) indicates variance variable term \\(E[]\\) indicates expectation (mean) variable. founder population, expectations \\(w\\) \\(b\\) zero, first two terms right-hand side equation drop . Equation (10) reduces product two variances. variance \\(w\\) one variance \\(b\\) equals genotype--environment interaction variance, variance equation (8) equals genotype--environment interaction variance equivalent variance genotype specific slopes. must repeated description limited founder population. important point, mean variance genotype specific slope can different populations since genetic control.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/articles/traits.html","id":"adding-environmental-variance","dir":"Articles","previous_headings":"Genotype-by-Environment Effects","what":"Adding Environmental Variance","title":"Traits in AlphaSimR","text":"genotype--environment effects model described altered model founder population non-zero environmental variance. equations remain relevant altered model sampling distributions effects equations changed. Specifically, variance environmental covariate set environmental variance (\\(\\sigma_E^2\\)) genotype specific slope set different mean variance. mean genotype specific slope set one variance set genotype--environment interaction variance divided environmental variance (\\(\\tfrac{\\sigma_{GE}^2}{\\sigma_E^2}\\)). logic behind modifications becomes clear examination equation (10). right-hand side equation (10) contains three terms. first term equals zero, environmental covariate mean zero (.e. \\(E[w] = 0\\)). second term equals environmental variance, mean genotype specific slope equals one variance environmental covariate equals environmental variance (.e. \\(E[b] = 1\\) \\(Var(w) = \\sigma_E^2\\)). Finally, value last term equals genotype--environment interaction variance (.e. \\(Var(w) Var(b) = \\sigma_E^2 \\tfrac{\\sigma_{GE}^2}{\\sigma_E^2} = \\sigma_{GE}^2\\)). examination equation (10) also shows environmental genotype--environment interaction variances populations specific parameters genetic control. example, population higher average genotype specific slope also higher value second term equation (10). population thus higher environmental variance even though environment changed. Likewise, amount genotype--environment interaction variance depends variance genotype specific slope.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/articles/traits.html","id":"relationship-to-finlay-wilkinson-regression","dir":"Articles","previous_headings":"Genotype-by-Environment Effects","what":"Relationship to Finlay-Wilkinson Regression","title":"Traits in AlphaSimR","text":"AlphaSimR’s model genotype--environment effects effectively biological model Finlay-Wilkinson regression. Finlay-Wilkinson regression classic technique analyzing genotype--environment interactions (Finlay Wilkinson 1963). simplest form, individual’s genotype--environment interaction reduced intercept slope. slope Finlay-Wilkinson regression roughly equivalent genotype specific slope equation (9). intercept Finlay-Wilkinson regression roughly equivalent genetic value individual target environment. Initially, similarity two models intentional. model used AlphaSimR originates model used Gaynor et al. (2017). model treated QTL’s additive effect random variable whose value depended value environmental covariate. model roughly equivalent AlphaSimR’s model founder population zero environmental variance. difference models AlphaSimR scales effects exactly achieve desired variance Gaynor et al. model randomly sampled effects expectation sampled effects equaled desired variance. realized later slight change model, described , introduce specified amount environmental variance modifications result model properties matching measured Finlay-Wilkinson regression.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/articles/traits.html","id":"user-interaction","dir":"Articles","previous_headings":"Genotype-by-Environment Effects","what":"User Interaction","title":"Traits in AlphaSimR","text":"AlphaSimR users directly observe set value environmental covariate. Instead, indirectly set value providing randomly sampled p-value environment. AlphaSimR uses p-value calculate appropriate value \\(w\\) level environmental variance. Users note p-values follow uniform distribution range zero one, recommended users randomly generate p-values using R’s built-runif function. p-value 0.5 corresponds \\(w\\) equaling zero equivalent target environment. user supply p-value, AlphaSimR sample one random. Genetic values genetic variances reported AlphaSimR always target environment. Since target environment corresponds \\(w\\) equaling zero, equation (8) effectively ignored calculations. values phenotypes phenotypic variance ever reflect contribution genotype--environment interaction.","code":""},{"path":[]},{"path":"https://gaynorr.github.io/AlphaSimR/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Chris Gaynor. Author, maintainer. Gregor Gorjanc. Contributor. John Hickey. Contributor. Daniel Money. Contributor. David Wilson. Contributor. Thiago Oliveira. Contributor. Audrey Martin. Contributor. Philip Greenspoon. Contributor.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Gaynor RC, Gorjanc G, Hickey JM (2021). “AlphaSimR: R package breeding program simulations.” G3 Gene|Genomes|Genetics, 11(jkaa07). https://doi.org/10.1093/g3journal/jkaa017.","code":"@Article{,   title = {AlphaSimR: an R package for breeding program simulations},   author = {R Chris Gaynor and Gregor Gorjanc and John M Hickey},   journal = {G3 Gene|Genomes|Genetics},   year = {2021},   volume = {11},   number = {jkaa07},   issue = {2},   url = {https://doi.org/10.1093/g3journal/jkaa017}, }"},{"path":"https://gaynorr.github.io/AlphaSimR/index.html","id":"readme","dir":"","previous_headings":"","what":"Breeding Program Simulations","title":"Breeding Program Simulations","text":"successor ‘AlphaSim’ software breeding program simulation (Faux et al., 2016; https://doi.org/10.3835/plantgenome2016.02.0013). Used stochastic simulations breeding programs level DNA sequence every individual. Contained wide range functions modeling common tasks breeding program, selection crossing. functions allow constructing simulations highly complex plant animal breeding programs via scripting R software environment. simulations can used evaluate overall breeding program performance conduct research breeding program design, implementation genomic selection. Included ‘Markovian Coalescent Simulator’ (‘MaCS’) fast simulation biallelic sequences according population demographic history (Chen et al., 2009; https://doi.org/10.1101/gr.083634.108).","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/index.html","id":"publication","dir":"","previous_headings":"","what":"Publication","title":"Breeding Program Simulations","text":"Gaynor, R. Chris, Gregor Gorjanc, John M. Hickey. 2021. AlphaSimR: R package breeding program simulations. G3 Gene|Genomes|Genetics 11(2):jkaa017. https://doi.org/10.1093/g3journal/jkaa017.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/index.html","id":"download","dir":"","previous_headings":"","what":"Download","title":"Breeding Program Simulations","text":"AlphaSimR available CRAN. install use: development version AlphaSimR (potentially unstable) can accessed devel branch GitHub. install use: install vignettes use:","code":"install.packages('AlphaSimR') devtools::install_github(repo=\"gaynorr/AlphaSimR@devel\") devtools::install_github(repo=\"gaynorr/AlphaSimR@devel\", build_vignettes=TRUE)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/AlphaSimR-package.html","id":null,"dir":"Reference","previous_headings":"","what":"AlphaSimR: Breeding Program Simulations — AlphaSimR-package","title":"AlphaSimR: Breeding Program Simulations — AlphaSimR-package","text":"successor 'AlphaSim' software breeding program  simulation [Faux et al. (2016) <doi:10.3835/plantgenome2016.02.0013>].  Used stochastic simulations breeding programs level DNA  sequence every individual. Contained wide range functions  modeling common tasks breeding program, selection crossing.  functions allow constructing simulations highly complex plant  animal breeding programs via scripting R software environment.  simulations can used evaluate overall breeding program performance  conduct research breeding program design, implementation  genomic selection. Included 'Markovian Coalescent Simulator' ('MaCS')  fast simulation biallelic sequences according population  demographic history [Chen et al. (2009) <doi:10.1101/gr.083634.108>]. Please see introductory vignette instructions using package.  vignette can viewed using following command:  vignette(\"intro\",package=\"AlphaSimR\")","code":""},{"path":[]},{"path":"https://gaynorr.github.io/AlphaSimR/reference/AlphaSimR-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"AlphaSimR: Breeding Program Simulations — AlphaSimR-package","text":"Maintainer: Chris Gaynor gaynor.robert@hotmail.com (ORCID) contributors: Gregor Gorjanc (ORCID) [contributor] John Hickey (ORCID) [contributor] Daniel Money (ORCID) [contributor] David Wilson [contributor] Thiago Oliveira (ORCID) [contributor] Audrey Martin (ORCID) [contributor] Philip Greenspoon (ORCID) [contributor]","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/HybridPop-class.html","id":null,"dir":"Reference","previous_headings":"","what":"Hybrid population — HybridPop-class","title":"Hybrid population — HybridPop-class","text":"lightweight version Pop-class hybrid lines. Memory saved storing genotypic data.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/HybridPop-class.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Hybrid population — HybridPop-class","text":"","code":"# S4 method for HybridPop [(x, i)  # S4 method for HybridPop c(x, ...)  isHybridPop(x)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/HybridPop-class.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Hybrid population — HybridPop-class","text":"x 'HybridPop' index individuals ... additional 'HybridPop' objects","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/HybridPop-class.html","id":"methods-by-generic-","dir":"Reference","previous_headings":"","what":"Methods (by generic)","title":"Hybrid population — HybridPop-class","text":"[: Extract HybridPop using index id c(HybridPop): Combine multiple HybridPops","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/HybridPop-class.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Hybrid population — HybridPop-class","text":"isHybridPop(): Test object HybridPop class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/HybridPop-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"Hybrid population — HybridPop-class","text":"nInd number individuals id individual's identifier mother identifier individual's mother father identifier individual's father nTraits number traits gv matrix genetic values. using GxE traits, gv reflects gv p=0.5. Dimensions nInd nTraits. pheno matrix phenotypic values. Dimensions nInd nTraits. gxe list containing GxE slopes GxE traits","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/LociMap-class.html","id":null,"dir":"Reference","previous_headings":"","what":"Loci metadata — LociMap-class","title":"Loci metadata — LociMap-class","text":"used SNPs QTLs","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/LociMap-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"Loci metadata — LociMap-class","text":"nLoci total number loci lociPerChr number loci per chromosome lociLoc physical position loci name optional name LociMap object","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/MapPop-class.html","id":null,"dir":"Reference","previous_headings":"","what":"Raw population with genetic map — MapPop-class","title":"Raw population with genetic map — MapPop-class","text":"Extends RawPop-class add genetic map. first object created simulation. used creating initial populations setting traits SimParam.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/MapPop-class.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Raw population with genetic map — MapPop-class","text":"","code":"# S4 method for MapPop [(x, i)  # S4 method for MapPop c(x, ...)  isMapPop(x)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/MapPop-class.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Raw population with genetic map — MapPop-class","text":"x 'MapPop' object index individuals ... additional 'MapPop' objects","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/MapPop-class.html","id":"methods-by-generic-","dir":"Reference","previous_headings":"","what":"Methods (by generic)","title":"Raw population with genetic map — MapPop-class","text":"[: Extract MapPop index c(MapPop): Combine multiple MapPops","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/MapPop-class.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Raw population with genetic map — MapPop-class","text":"isMapPop(): Test object MapPop class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/MapPop-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"Raw population with genetic map — MapPop-class","text":"genMap list chromosome genetic maps centromere vector centromere positions inbred indicates whether individuals fully inbred","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/MultiPop-class.html","id":null,"dir":"Reference","previous_headings":"","what":"Multi-Population — MultiPop-class","title":"Multi-Population — MultiPop-class","text":"mega-population represents population populations. designed behave like list populations.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/MultiPop-class.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Multi-Population — MultiPop-class","text":"","code":"# S4 method for MultiPop [(x, i)  # S4 method for MultiPop [[(x, i)  # S4 method for MultiPop c(x, ...)  isMultiPop(x)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/MultiPop-class.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Multi-Population — MultiPop-class","text":"x 'MultiPop' object index populations mega-populations ... additional 'MultiPop' 'Pop' objects","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/MultiPop-class.html","id":"methods-by-generic-","dir":"Reference","previous_headings":"","what":"Methods (by generic)","title":"Multi-Population — MultiPop-class","text":"[: Extract MultiPop index [[: Extract Pop index c(MultiPop): Combine multiple MultiPops","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/MultiPop-class.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Multi-Population — MultiPop-class","text":"isMultiPop(): Test object MultiPop class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/MultiPop-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"Multi-Population — MultiPop-class","text":"pops list Pop-class /MultiPop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/NamedMapPop-class.html","id":null,"dir":"Reference","previous_headings":"","what":"Raw population with genetic map and id — NamedMapPop-class","title":"Raw population with genetic map and id — NamedMapPop-class","text":"Extends MapPop-class add id, mother father.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/NamedMapPop-class.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Raw population with genetic map and id — NamedMapPop-class","text":"","code":"# S4 method for NamedMapPop [(x, i)  # S4 method for NamedMapPop c(x, ...)  isNamedMapPop(x)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/NamedMapPop-class.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Raw population with genetic map and id — NamedMapPop-class","text":"x 'NamedMapPop' object index individuals ... additional 'NamedMapPop' objects","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/NamedMapPop-class.html","id":"methods-by-generic-","dir":"Reference","previous_headings":"","what":"Methods (by generic)","title":"Raw population with genetic map and id — NamedMapPop-class","text":"[: Extract NamedMapPop index c(NamedMapPop): Combine multiple NamedMapPops","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/NamedMapPop-class.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Raw population with genetic map and id — NamedMapPop-class","text":"isNamedMapPop(): Test object NamedMapPop class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/NamedMapPop-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"Raw population with genetic map and id — NamedMapPop-class","text":"id individual's identifier mother identifier individual's mother father identifier individual's father","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/Pop-class.html","id":null,"dir":"Reference","previous_headings":"","what":"Population — Pop-class","title":"Population — Pop-class","text":"Extends RawPop-class add sex, genetic values, phenotypes, pedigrees.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/Pop-class.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Population — Pop-class","text":"","code":"# S4 method for Pop [(x, i)  # S4 method for Pop c(x, ...)  # S4 method for Pop show(object)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/Pop-class.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Population — Pop-class","text":"x 'Pop' object index individuals ... additional 'Pop' objects object 'Pop' object","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/Pop-class.html","id":"methods-by-generic-","dir":"Reference","previous_headings":"","what":"Methods (by generic)","title":"Population — Pop-class","text":"[: Extract Pop index id c(Pop): Combine multiple Pops show(Pop): Show population summary","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/Pop-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"Population — Pop-class","text":"id individual's identifier iid individual's internal identifier mother identifier individual's mother father identifier individual's father sex sex individuals: \"M\" males, \"F\" females, \"H\" hermaphrodites nTraits number traits gv matrix genetic values. using GxE traits, gv reflects gv p=0.5. Dimensions nInd nTraits. pheno matrix phenotypic values. Dimensions nInd nTraits. ebv matrix estimated breeding values. Dimensions nInd rows variable number columns. gxe list containing GxE slopes GxE traits fixEff fixed effect relating phenotype. Used genomic selection models otherwise ignored. misc list whose elements correspond individuals population. list normally empty exists solely open slot available uses store extra information individuals. miscPop list length containing optional meta data  population. list empty unless information supplied user. Note list emptied every time population subsetted.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUP.html","id":null,"dir":"Reference","previous_headings":"","what":"RR-BLUP Model — RRBLUP","title":"RR-BLUP Model — RRBLUP","text":"Fits RR-BLUP model genomic predictions.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUP.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"RR-BLUP Model — RRBLUP","text":"","code":"RRBLUP(   pop,   traits = 1,   use = \"pheno\",   snpChip = 1,   useQtl = FALSE,   maxIter = 1000L,   simParam = NULL,   ... )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUP.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"RR-BLUP Model — RRBLUP","text":"pop Pop-class serve training population traits integer indicating trait traits model, vector trait names,  function traits returning single value. use train model using phenotypes \"pheno\", genetic values \"gv\",  estimated breeding values \"ebv\", breeding values \"bv\", randomly \"rand\" snpChip integer indicating SNP chip genotype  use useQtl QTL genotypes used instead SNP chip.  TRUE, snpChip specifies trait's QTL use, thus  QTL may match QTL underlying phenotype supplied traits. maxIter maximum number iterations. used  number traits greater 1. simParam object SimParam ... additional arguments using function  traits","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUP.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"RR-BLUP Model — RRBLUP","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=20)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitA(10) SP$setVarE(h2=0.5) SP$addSnpChip(10)  #Create population pop = newPop(founderPop, simParam=SP)  #Run GS model and set EBV ans = RRBLUP(pop, simParam=SP) pop = setEBV(pop, ans, simParam=SP)  #Evaluate accuracy cor(gv(pop), ebv(pop)) #>        est_GV_Trait1 #> Trait1     0.7377476"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUP2.html","id":null,"dir":"Reference","previous_headings":"","what":"RR-BLUP Model 2 — RRBLUP2","title":"RR-BLUP Model 2 — RRBLUP2","text":"Fits RR-BLUP model genomic predictions. implementation  meant situations RRBLUP slow. Note  RRBLUP2 faster certain situations, see details .  users use RRBLUP.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUP2.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"RR-BLUP Model 2 — RRBLUP2","text":"","code":"RRBLUP2(   pop,   traits = 1,   use = \"pheno\",   snpChip = 1,   useQtl = FALSE,   maxIter = 10,   Vu = NULL,   Ve = NULL,   useEM = TRUE,   tol = 1e-06,   simParam = NULL,   ... )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUP2.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"RR-BLUP Model 2 — RRBLUP2","text":"pop Pop-class serve training population traits integer indicating trait model, trait name, function traits returning single value. Unlike RRBLUP,  univariate models supported. use train model using phenotypes \"pheno\", genetic values \"gv\",  estimated breeding values \"ebv\", breeding values \"bv\", randomly \"rand\" snpChip integer indicating SNP chip genotype  use useQtl QTL genotypes used instead SNP chip.  TRUE, snpChip specifies trait's QTL use, thus  QTL may match QTL underlying phenotype supplied traits. maxIter maximum number iterations. Vu marker effect variance. value NULL,  reasonable starting point chosen automatically. Ve error variance. value NULL,  reasonable starting point chosen automatically. useEM use EM solve variance components. false,  initial values considered true. tol tolerance EM algorithm convergence simParam object SimParam ... additional arguments using function  traits","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUP2.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"RR-BLUP Model 2 — RRBLUP2","text":"RRBLUP2 function works best number markers  large. solves RR-BLUP problem setting  solving Henderson's mixed model equations. Solving equations  involves square matrix dimensions equal number fixed  effects plus number random effects (markers). Whereas RRBLUP  function solves RR-BLUP problem using EMMA approach. approach involves  square matrix dimensions equal number phenotypic records. means  RRBLUP2 function uses less memory RRBLUP number markers  approximately equal smaller number phenotypic records. RRBLUP2 function recommend cases variance components  unknown. uses EM algorithm solve unknown variance components,  generally considerably slower EMMA approach RRBLUP.  number iterations EM algorithm set maxIter. default value  typically small convergence. algorithm fails converge  warning displayed, results given last iteration. results may  \"good enough\". However make claim effect, can generalize  possible use cases. RRBLUP2 function can quickly solve mixed model equations without estimating variance  components. variance components set defining Vu Ve. Estimation components  suppressed setting useEM false. may useful model retrained  multiple times simulation. run RRBLUP function first  time model trained, use variance components output  future runs RRBLUP2 functions. , can make claim general robustness  approach.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUP2.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"RR-BLUP Model 2 — RRBLUP2","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=20)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitA(10) SP$setVarE(h2=0.5) SP$addSnpChip(10)  #Create population pop = newPop(founderPop, simParam=SP)  #Run GS model and set EBV ans = RRBLUP2(pop, simParam=SP) pop = setEBV(pop, ans, simParam=SP)  #Evaluate accuracy cor(gv(pop), ebv(pop)) #>        est_GV_Trait1 #> Trait1     0.7056706"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUPMemUse.html","id":null,"dir":"Reference","previous_headings":"","what":"RRBLUP Memory Usage — RRBLUPMemUse","title":"RRBLUP Memory Usage — RRBLUPMemUse","text":"Estimates amount RAM needed run RRBLUP related functions given training population size.  Note function may underestimate total usage.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUPMemUse.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"RRBLUP Memory Usage — RRBLUPMemUse","text":"","code":"RRBLUPMemUse(nInd, nMarker, model = \"REG\")"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUPMemUse.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"RRBLUP Memory Usage — RRBLUPMemUse","text":"nInd number individuals training population nMarker number markers per individual model either \"REG\", \"GCA\", \"SCA\" RRBLUP  RRBLUP_GCA RRBLUP_SCA respectively.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUPMemUse.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"RRBLUP Memory Usage — RRBLUPMemUse","text":"Returns estimate required gigabytes RAM","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUPMemUse.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"RRBLUP Memory Usage — RRBLUPMemUse","text":"","code":"RRBLUPMemUse(nInd=1000, nMarker=5000) #> [1] 0.06412"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUP_D.html","id":null,"dir":"Reference","previous_headings":"","what":"RR-BLUP Model with Dominance — RRBLUP_D","title":"RR-BLUP Model with Dominance — RRBLUP_D","text":"Fits RR-BLUP model genomic predictions includes  dominance effects.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUP_D.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"RR-BLUP Model with Dominance — RRBLUP_D","text":"","code":"RRBLUP_D(   pop,   traits = 1,   use = \"pheno\",   snpChip = 1,   useQtl = FALSE,   maxIter = 40L,   simParam = NULL,   ... )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUP_D.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"RR-BLUP Model with Dominance — RRBLUP_D","text":"pop Pop-class serve training population traits integer indicating trait model, trait name, function traits returning single value. use train model using phenotypes \"pheno\", genetic values \"gv\",  estimated breeding values \"ebv\", breeding values \"bv\", randomly \"rand\" snpChip integer indicating SNP chip genotype  use useQtl QTL genotypes used instead SNP chip.  TRUE, snpChip specifies trait's QTL use, thus  QTL may match QTL underlying phenotype supplied traits. maxIter maximum number iterations. used  number traits greater 1. simParam object SimParam ... additional arguments using function  traits","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUP_D.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"RR-BLUP Model with Dominance — RRBLUP_D","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=20)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitAD(10, meanDD=0.5) SP$setVarE(h2=0.5) SP$addSnpChip(10)  #Create population pop = newPop(founderPop, simParam=SP)  #Run GS model and set EBV ans = RRBLUP_D(pop, simParam=SP) #> Warning: Reached maxIter without converging pop = setEBV(pop, ans, simParam=SP)  #Evaluate accuracy cor(gv(pop), ebv(pop)) #>        est_GV_Trait1 #> Trait1     0.7802633"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUP_D2.html","id":null,"dir":"Reference","previous_headings":"","what":"RR-BLUP with Dominance Model 2 — RRBLUP_D2","title":"RR-BLUP with Dominance Model 2 — RRBLUP_D2","text":"Fits RR-BLUP model genomic predictions includes  dominance effects. implementation meant situations  RRBLUP_D slow. Note RRBLUP_D2  faster certain situations. users use  RRBLUP_D.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUP_D2.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"RR-BLUP with Dominance Model 2 — RRBLUP_D2","text":"","code":"RRBLUP_D2(   pop,   traits = 1,   use = \"pheno\",   snpChip = 1,   useQtl = FALSE,   maxIter = 10,   Va = NULL,   Vd = NULL,   Ve = NULL,   useEM = TRUE,   tol = 1e-06,   simParam = NULL,   ... )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUP_D2.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"RR-BLUP with Dominance Model 2 — RRBLUP_D2","text":"pop Pop-class serve training population traits integer indicating trait model, trait name, function traits returning single value. use train model using phenotypes \"pheno\", genetic values \"gv\",  estimated breeding values \"ebv\", breeding values \"bv\", randomly \"rand\" snpChip integer indicating SNP chip genotype  use useQtl QTL genotypes used instead SNP chip.  TRUE, snpChip specifies trait's QTL use, thus  QTL may match QTL underlying phenotype supplied traits. maxIter maximum number iterations. used  number traits greater 1. Va marker effect variance additive effects. value NULL,  reasonable starting point chosen automatically. Vd marker effect variance dominance effects. value NULL,  reasonable starting point chosen automatically. Ve error variance. value NULL,  reasonable starting point chosen automatically. useEM use EM solve variance components. false,  initial values considered true. tol tolerance EM algorithm convergence simParam object SimParam ... additional arguments using function  traits","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUP_D2.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"RR-BLUP with Dominance Model 2 — RRBLUP_D2","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=20)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitAD(10, meanDD=0.5) SP$setVarE(h2=0.5) SP$addSnpChip(10)  #Create population pop = newPop(founderPop, simParam=SP)  #Run GS model and set EBV ans = RRBLUP_D2(pop, simParam=SP) pop = setEBV(pop, ans, simParam=SP)  #Evaluate accuracy cor(gv(pop), ebv(pop)) #>        est_GV_Trait1 #> Trait1     0.8385404"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUP_GCA.html","id":null,"dir":"Reference","previous_headings":"","what":"RR-BLUP GCA Model — RRBLUP_GCA","title":"RR-BLUP GCA Model — RRBLUP_GCA","text":"Fits RR-BLUP model estimates seperate marker effects females males. Useful predicting GCA parents single cross hybrids. Can also predict performance specific  single cross hybrids.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUP_GCA.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"RR-BLUP GCA Model — RRBLUP_GCA","text":"","code":"RRBLUP_GCA(   pop,   traits = 1,   use = \"pheno\",   snpChip = 1,   useQtl = FALSE,   maxIter = 40L,   simParam = NULL,   ... )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUP_GCA.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"RR-BLUP GCA Model — RRBLUP_GCA","text":"pop Pop-class serve training population traits integer indicating trait model, trait name, function traits returning single value. use train model using phenotypes \"pheno\", genetic values \"gv\",  estimated breeding values \"ebv\", breeding values \"bv\", randomly \"rand\" snpChip integer indicating SNP chip genotype  use useQtl QTL genotypes used instead SNP chip.  TRUE, snpChip specifies trait's QTL use, thus  QTL may match QTL underlying phenotype supplied traits. maxIter maximum number iterations convergence. simParam object SimParam ... additional arguments using function  traits","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUP_GCA.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"RR-BLUP GCA Model — RRBLUP_GCA","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=20)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitA(10) SP$setVarE(h2=0.5) SP$addSnpChip(10)  #Create population pop = newPop(founderPop, simParam=SP)  #Run GS model and set EBV ans = RRBLUP_GCA(pop, simParam=SP) pop = setEBV(pop, ans, simParam=SP)  #Evaluate accuracy cor(gv(pop), ebv(pop)) #>        est_GV_Trait1 #> Trait1     0.4269091"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUP_GCA2.html","id":null,"dir":"Reference","previous_headings":"","what":"RR-BLUP GCA Model 2 — RRBLUP_GCA2","title":"RR-BLUP GCA Model 2 — RRBLUP_GCA2","text":"Fits RR-BLUP model estimates seperate marker effects females males. implementation meant situations  RRBLUP_GCA slow. Note RRBLUP_GCA2  faster certain situations. users use  RRBLUP_GCA.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUP_GCA2.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"RR-BLUP GCA Model 2 — RRBLUP_GCA2","text":"","code":"RRBLUP_GCA2(   pop,   traits = 1,   use = \"pheno\",   snpChip = 1,   useQtl = FALSE,   maxIter = 10,   VuF = NULL,   VuM = NULL,   Ve = NULL,   useEM = TRUE,   tol = 1e-06,   simParam = NULL,   ... )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUP_GCA2.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"RR-BLUP GCA Model 2 — RRBLUP_GCA2","text":"pop Pop-class serve training population traits integer indicating trait model, trait name, function traits returning single value. use train model using phenotypes \"pheno\", genetic values \"gv\",  estimated breeding values \"ebv\", breeding values \"bv\", randomly \"rand\" snpChip integer indicating SNP chip genotype  use useQtl QTL genotypes used instead SNP chip.  TRUE, snpChip specifies trait's QTL use, thus  QTL may match QTL underlying phenotype supplied traits. maxIter maximum number iterations convergence. VuF marker effect variance females. value NULL,  reasonable starting point chosen automatically. VuM marker effect variance males. value NULL,  reasonable starting point chosen automatically. Ve error variance. value NULL,  reasonable starting point chosen automatically. useEM use EM solve variance components. false,  initial values considered true. tol tolerance EM algorithm convergence simParam object SimParam ... additional arguments using function  traits","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUP_GCA2.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"RR-BLUP GCA Model 2 — RRBLUP_GCA2","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=20)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitA(10) SP$setVarE(h2=0.5) SP$addSnpChip(10)  #Create population pop = newPop(founderPop, simParam=SP)  #Run GS model and set EBV ans = RRBLUP_GCA2(pop, simParam=SP) pop = setEBV(pop, ans, simParam=SP)  #Evaluate accuracy cor(gv(pop), ebv(pop)) #>        est_GV_Trait1 #> Trait1     0.7978478"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUP_SCA.html","id":null,"dir":"Reference","previous_headings":"","what":"RR-BLUP SCA Model — RRBLUP_SCA","title":"RR-BLUP SCA Model — RRBLUP_SCA","text":"extention RRBLUP_GCA adds dominance effects.  Note seen consistent benefit model  RRBLUP_GCA.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUP_SCA.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"RR-BLUP SCA Model — RRBLUP_SCA","text":"","code":"RRBLUP_SCA(   pop,   traits = 1,   use = \"pheno\",   snpChip = 1,   useQtl = FALSE,   maxIter = 40L,   simParam = NULL,   ... )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUP_SCA.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"RR-BLUP SCA Model — RRBLUP_SCA","text":"pop Pop-class serve training population traits integer indicating trait model, trait name, function traits returning single value. use train model using phenotypes \"pheno\", genetic values \"gv\",  estimated breeding values \"ebv\", breeding values \"bv\", randomly \"rand\" snpChip integer indicating SNP chip genotype  use useQtl QTL genotypes used instead SNP chip.  TRUE, snpChip specifies trait's QTL use, thus  QTL may match QTL underlying phenotype supplied traits. maxIter maximum number iterations convergence. simParam object SimParam ... additional arguments using function  traits","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUP_SCA.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"RR-BLUP SCA Model — RRBLUP_SCA","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=2, nChr=1, segSites=20)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitA(10) SP$setVarE(h2=0.5) SP$addSnpChip(10)  #Create population pop = newPop(founderPop, simParam=SP)  #Run GS model and set EBV ans = RRBLUP_SCA(pop, simParam=SP) pop = setEBV(pop, ans, simParam=SP)  #Evaluate accuracy cor(gv(pop), ebv(pop)) #>        est_GV_Trait1 #> Trait1            NA"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUP_SCA2.html","id":null,"dir":"Reference","previous_headings":"","what":"RR-BLUP SCA Model 2 — RRBLUP_SCA2","title":"RR-BLUP SCA Model 2 — RRBLUP_SCA2","text":"Fits RR-BLUP model estimates seperate additive effects females males dominance effect. implementation meant  situations RRBLUP_SCA slow. Note  RRBLUP_SCA2 faster certain situations. users use  RRBLUP_SCA.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUP_SCA2.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"RR-BLUP SCA Model 2 — RRBLUP_SCA2","text":"","code":"RRBLUP_SCA2(   pop,   traits = 1,   use = \"pheno\",   snpChip = 1,   useQtl = FALSE,   maxIter = 10,   VuF = NULL,   VuM = NULL,   VuD = NULL,   Ve = NULL,   useEM = TRUE,   tol = 1e-06,   simParam = NULL,   ... )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUP_SCA2.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"RR-BLUP SCA Model 2 — RRBLUP_SCA2","text":"pop Pop-class serve training population traits integer indicating trait model, trait name, function traits returning single value. use train model using phenotypes \"pheno\", genetic values \"gv\",  estimated breeding values \"ebv\", breeding values \"bv\", randomly \"rand\" snpChip integer indicating SNP chip genotype  use useQtl QTL genotypes used instead SNP chip.  TRUE, snpChip specifies trait's QTL use, thus  QTL may match QTL underlying phenotype supplied traits. maxIter maximum number iterations convergence. VuF marker effect variance females. value NULL,  reasonable starting point chosen automatically. VuM marker effect variance males. value NULL,  reasonable starting point chosen automatically. VuD marker effect variance dominance. value NULL,  reasonable starting point chosen automatically. Ve error variance. value NULL,  reasonable starting point chosen automatically. useEM use EM solve variance components. false,  initial values considered true. tol tolerance EM algorithm convergence simParam object SimParam ... additional arguments using function  traits","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRBLUP_SCA2.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"RR-BLUP SCA Model 2 — RRBLUP_SCA2","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=20)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitA(10) SP$setVarE(h2=0.5) SP$addSnpChip(10)  #Create population pop = newPop(founderPop, simParam=SP)  #Run GS model and set EBV ans = RRBLUP_SCA2(pop, simParam=SP) pop = setEBV(pop, ans, simParam=SP)  #Evaluate accuracy cor(gv(pop), ebv(pop)) #>        est_GV_Trait1 #> Trait1     0.6495195"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRsol-class.html","id":null,"dir":"Reference","previous_headings":"","what":"RR-BLUP Solution — RRsol-class","title":"RR-BLUP Solution — RRsol-class","text":"Contains output AlphaSimR's genomic  selection functions.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RRsol-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"RR-BLUP Solution — RRsol-class","text":"gv Trait(s) estimating genetic values bv Trait(s) estimating breeding values female Trait(s) estimating GCA female pool male Trait(s) estimating GCA male pool Vu Estimated marker variance(s) Ve Estimated error variance","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RawPop-class.html","id":null,"dir":"Reference","previous_headings":"","what":"Raw Population — RawPop-class","title":"Raw Population — RawPop-class","text":"raw population class contains genotype data.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RawPop-class.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Raw Population — RawPop-class","text":"","code":"# S4 method for RawPop [(x, i)  # S4 method for RawPop c(x, ...)  # S4 method for RawPop show(object)  isRawPop(x)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RawPop-class.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Raw Population — RawPop-class","text":"x 'RawPop' object index individuals ... additional 'RawPop' objects object 'RawPop' object","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RawPop-class.html","id":"methods-by-generic-","dir":"Reference","previous_headings":"","what":"Methods (by generic)","title":"Raw Population — RawPop-class","text":"[: Extract RawPop index c(RawPop): Combine multiple RawPops show(RawPop): Show population summary","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RawPop-class.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Raw Population — RawPop-class","text":"isRawPop(): Test object RawPop class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/RawPop-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"Raw Population — RawPop-class","text":"nInd number individuals nChr number chromosomes ploidy level ploidy nLoci number loci per chromosome geno list nChr length containing chromosome genotypes. element three dimensional array raw values. array dimensions nLoci ploidy nInd.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":null,"dir":"Reference","previous_headings":"","what":"Simulation parameters — SimParam","title":"Simulation parameters — SimParam","text":"Container global simulation parameters. Saving object SP allow accessed function defaults.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Simulation parameters — SimParam","text":"default founder population population used initalize SimParam object. population can changed replacing population founderPop slot. must run resetPop existing populations obtain new trait values.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"Simulation parameters — SimParam","text":"nThreads number threads used platforms OpenMP support snpChips list SNP chips invalidQtl list segregating sites valid QTL invalidSnp list segregating sites valid SNP founderPop founder population used variance scaling finalizePop function applied newly created populations. Currently nothing changed expert users. allowEmptyPop true, population arguments nInd=0 return empty population warning instead error. v crossover interference parameter gamma model recombination. value 1 indicates crossover interference (e.g. Haldane mapping function). value 2.6 approximates degree crossover interference implied Kosambi mapping function. (default 2.6) p proportion crossovers coming non-interfering pathway. (default 0) quadProb probability quadrivalent pairing autopolyploid. (default 0)","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"active-bindings","dir":"Reference","previous_headings":"","what":"Active bindings","title":"Simulation parameters — SimParam","text":"traitNames vector trait names snpChipNames vector chip names traits list traits nChr number chromosomes nTraits number traits nSnpChips number SNP chips segSites segregating sites per chromosome sexes sexes used mating sepMap seperate genetic maps males females genMap \"matrix\" chromosome genetic maps femaleMap \"matrix\" chromosome genetic maps females maleMap \"matrix\" chromosome genetic maps males centromere position centromeres genetic map femaleCentromere position centromeres female genetic map maleCentromere position centromeres male genetic map lastId last ID number assigned isTrackPed pedigree tracked pedigree pedigree matrix individuals isTrackRec recombination tracked recHist list historic recombination events haplotypes list computed IBD haplotypes varA additive genetic variance founderPop varG total genetic variance founderPop varE default error variance version version AlphaSimR used generate object","code":""},{"path":[]},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"Simulation parameters — SimParam","text":"SimParam$new() SimParam$setTrackPed() SimParam$setTrackRec() SimParam$resetPed() SimParam$restrSegSites() SimParam$setSexes() SimParam$setFounderHap() SimParam$addSnpChip() SimParam$addSnpChipByName() SimParam$addStructuredSnpChip() SimParam$addTraitA() SimParam$addTraitAD() SimParam$altAddTraitAD() SimParam$addTraitAG() SimParam$addTraitADG() SimParam$addTraitAE() SimParam$addTraitADE() SimParam$addTraitAEG() SimParam$addTraitADEG() SimParam$manAddTrait() SimParam$importTrait() SimParam$switchTrait() SimParam$removeTrait() SimParam$setVarE() SimParam$setCorE() SimParam$rescaleTraits() SimParam$setRecombRatio() SimParam$switchGenMap() SimParam$switchFemaleMap() SimParam$switchMaleMap() SimParam$addToRec() SimParam$ibdHaplo() SimParam$updateLastId() SimParam$addToPed() SimParam$clone()","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"Simulation parameters — SimParam","text":"Starts process building new simulation creating new SimParam object assigning founder population class. recommended save object name \"SP\", subsequent functions check global environment object name simParam arguments NULL. allows call functions without explicitly supplying simParam argument every call.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulation parameters — SimParam","text":"","code":"SimParam$new(founderPop)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulation parameters — SimParam","text":"founderPop object MapPop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Simulation parameters — SimParam","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"method-settrackped-","dir":"Reference","previous_headings":"","what":"Method setTrackPed()","title":"Simulation parameters — SimParam","text":"Sets pedigree tracking simulation. default pedigree tracking turned . turned , pedigree individuals created tracked, except created hybridCross. Turning pedigree tracking turn recombination tracking turned .","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulation parameters — SimParam","text":"","code":"SimParam$setTrackPed(isTrackPed, force = FALSE)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulation parameters — SimParam","text":"isTrackPed pedigree tracking . force check running simulation ignored. set TRUE know .","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"examples-1","dir":"Reference","previous_headings":"","what":"Examples","title":"Simulation parameters — SimParam","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) \\dontshow{SP$nThreads = 1L} SP$setTrackPed(TRUE)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"method-settrackrec-","dir":"Reference","previous_headings":"","what":"Method setTrackRec()","title":"Simulation parameters — SimParam","text":"Sets recombination tracking simulation. default recombination tracking turned . turned recombination tracking also turn pedigree tracking. Recombination tracking keeps records individuals created, except created hybridCross, pedigree tracked.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulation parameters — SimParam","text":"","code":"SimParam$setTrackRec(isTrackRec, force = FALSE)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulation parameters — SimParam","text":"isTrackRec recombination tracking . force check running simulation ignored. set TRUE know .","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"examples-2","dir":"Reference","previous_headings":"","what":"Examples","title":"Simulation parameters — SimParam","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) \\dontshow{SP$nThreads = 1L} SP$setTrackRec(TRUE)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"method-resetped-","dir":"Reference","previous_headings":"","what":"Method resetPed()","title":"Simulation parameters — SimParam","text":"Resets internal lastId, pedigree recombination tracking (use) supplied lastId. careful using function may introduce bug use individuals deleted portion pedigree.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulation parameters — SimParam","text":"","code":"SimParam$resetPed(lastId = 0L)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"arguments-3","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulation parameters — SimParam","text":"lastId last ID include pedigree","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"examples-3","dir":"Reference","previous_headings":"","what":"Examples","title":"Simulation parameters — SimParam","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) \\dontshow{SP$nThreads = 1L}  #Create population pop = newPop(founderPop, simParam=SP) pop@id # 1:10  #Create another population after reseting pedigree SP$resetPed() pop2 = newPop(founderPop, simParam=SP) pop2@id # 1:10"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"method-restrsegsites-","dir":"Reference","previous_headings":"","what":"Method restrSegSites()","title":"Simulation parameters — SimParam","text":"Sets restrictions segregating sites can serve SNP /QTL.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"usage-4","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulation parameters — SimParam","text":"","code":"SimParam$restrSegSites(   minQtlPerChr = NULL,   minSnpPerChr = NULL,   excludeQtl = NULL,   excludeSnp = NULL,   overlap = FALSE,   minSnpFreq = NULL )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"arguments-4","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulation parameters — SimParam","text":"minQtlPerChr minimum number segregating sites  QTLs. Can single value vector values chromosome. minSnpPerChr minimum number segregating sites SNPs. Can single value vector values chromosome. excludeQtl optional vector segregating site names  exclude consideration viable QTL. excludeSnp optional vector segregating site names  exclude consideration viable SNP. overlap SNP QTL sites allowed overlap. minSnpFreq minimum allowable frequency SNP loci. minimum SNP frequency used value NULL.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"examples-4","dir":"Reference","previous_headings":"","what":"Examples","title":"Simulation parameters — SimParam","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) \\dontshow{SP$nThreads = 1L} SP$restrSegSites(minQtlPerChr=5, minSnpPerChr=5)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"method-setsexes-","dir":"Reference","previous_headings":"","what":"Method setSexes()","title":"Simulation parameters — SimParam","text":"Changes sexes determined simulation. default sexes \"\", indicating individuals hermaphrodites. add sexes simulation, run function \"yes_sys\" \"yes_rand\". value \"yes_sys\" systematically assign sexes newly created individuals first male female. Populations odd number individuals one male female. value \"yes_rand\" randomly assign sex individual.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"usage-5","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulation parameters — SimParam","text":"","code":"SimParam$setSexes(sexes, force = FALSE)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"arguments-5","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulation parameters — SimParam","text":"sexes acceptable value \"\", \"yes_sys\", \"yes_rand\" force check running simulation ignored. set TRUE know .","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"examples-5","dir":"Reference","previous_headings":"","what":"Examples","title":"Simulation parameters — SimParam","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) \\dontshow{SP$nThreads = 1L} SP$setSexes(\"yes_sys\")"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"method-setfounderhap-","dir":"Reference","previous_headings":"","what":"Method setFounderHap()","title":"Simulation parameters — SimParam","text":"Allows manual setting founder haplotypes. functionality  fully documented, still experimental.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"usage-6","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulation parameters — SimParam","text":"","code":"SimParam$setFounderHap(hapMap)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"arguments-6","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulation parameters — SimParam","text":"hapMap list founder haplotypes","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"method-addsnpchip-","dir":"Reference","previous_headings":"","what":"Method addSnpChip()","title":"Simulation parameters — SimParam","text":"Randomly assigns eligible SNPs SNP chip","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"usage-7","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulation parameters — SimParam","text":"","code":"SimParam$addSnpChip(nSnpPerChr, minSnpFreq = NULL, refPop = NULL, name = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"arguments-7","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulation parameters — SimParam","text":"nSnpPerChr number SNPs per chromosome. Can single value nChr values. minSnpFreq minimum allowable frequency SNP loci. NULL, minimum frequency used. refPop reference population calculating SNP frequency. NULL, founder population used. name optional name chip","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"examples-6","dir":"Reference","previous_headings":"","what":"Examples","title":"Simulation parameters — SimParam","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) \\dontshow{SP$nThreads = 1L} SP$addSnpChip(10)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"method-addsnpchipbyname-","dir":"Reference","previous_headings":"","what":"Method addSnpChipByName()","title":"Simulation parameters — SimParam","text":"Assigns SNPs SNP chip supplying marker names. function  check excluded SNPs add SNPs list  excluded QTL purpose avoiding overlap SNPs QTL.  Excluding SNPs used QTL can accomplished using  excludeQtl argument SimParam's restrSegSites function.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"usage-8","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulation parameters — SimParam","text":"","code":"SimParam$addSnpChipByName(markers, name = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"arguments-8","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulation parameters — SimParam","text":"markers vector names markers name optional name chip","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"examples-7","dir":"Reference","previous_headings":"","what":"Examples","title":"Simulation parameters — SimParam","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$addSnpChipByName(c(\"1_1\",\"1_3\"))"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"method-addstructuredsnpchip-","dir":"Reference","previous_headings":"","what":"Method addStructuredSnpChip()","title":"Simulation parameters — SimParam","text":"Randomly selects number snps structure assigns chips based structure","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"usage-9","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulation parameters — SimParam","text":"","code":"SimParam$addStructuredSnpChip(nSnpPerChr, structure, force = FALSE)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"arguments-9","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulation parameters — SimParam","text":"nSnpPerChr number SNPs per chromosome. Can single value nChr values. structure matrix.  Rows snp chips, columns chips. value true snp chip. force check running simulation ignored. set TRUE know .","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"method-addtraita-","dir":"Reference","previous_headings":"","what":"Method addTraitA()","title":"Simulation parameters — SimParam","text":"Randomly assigns eligible QTLs one additive traits. simulating one trait, traits pleiotropic correlated additive effects.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"usage-10","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulation parameters — SimParam","text":"","code":"SimParam$addTraitA(   nQtlPerChr,   mean = 0,   var = 1,   corA = NULL,   gamma = FALSE,   shape = 1,   force = FALSE,   name = NULL )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"arguments-10","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulation parameters — SimParam","text":"nQtlPerChr number QTLs per chromosome. Can single value nChr values. mean vector desired mean genetic values one traits var vector desired genetic variances one traits corA matrix correlations additive effects gamma gamma distribution used instead normal shape shape parameter gamma distribution (rate/scale parameter gamma distribution accounted via desired level genetic variance, var argument) force check running simulation ignored. set TRUE know . name optional name trait(s)","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"examples-8","dir":"Reference","previous_headings":"","what":"Examples","title":"Simulation parameters — SimParam","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) \\dontshow{SP$nThreads = 1L} SP$addTraitA(10)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"method-addtraitad-","dir":"Reference","previous_headings":"","what":"Method addTraitAD()","title":"Simulation parameters — SimParam","text":"Randomly assigns eligible QTLs one traits dominance. simulating one trait, traits pleiotropic correlated effects.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"usage-11","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulation parameters — SimParam","text":"","code":"SimParam$addTraitAD(   nQtlPerChr,   mean = 0,   var = 1,   meanDD = 0,   varDD = 0,   corA = NULL,   corDD = NULL,   useVarA = TRUE,   gamma = FALSE,   shape = 1,   force = FALSE,   name = NULL )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"arguments-11","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulation parameters — SimParam","text":"nQtlPerChr number QTLs per chromosome. Can single value nChr values. mean vector desired mean genetic values one traits var vector desired genetic variances one traits meanDD mean dominance degree varDD variance dominance degree corA matrix correlations additive effects corDD matrix correlations dominance degrees useVarA tune according additive genetic variance true. FALSE, tuning performed according total genetic variance. gamma gamma distribution used instead normal shape shape parameter gamma distribution (rate/scale parameter gamma distribution accounted via desired level genetic variance, var argument) force check running simulation ignored. set TRUE know . name optional name trait(s)","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"examples-9","dir":"Reference","previous_headings":"","what":"Examples","title":"Simulation parameters — SimParam","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) \\dontshow{SP$nThreads = 1L} SP$addTraitAD(10, meanDD=0.5)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"method-altaddtraitad-","dir":"Reference","previous_headings":"","what":"Method altAddTraitAD()","title":"Simulation parameters — SimParam","text":"alternative method adding trait additive  dominance effects  AlphaSimR simulation. function attempts create trait matching  user defined values number QTL, inbreeding depression, additive genetic  variance dominance genetic variance.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"usage-12","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulation parameters — SimParam","text":"","code":"SimParam$altAddTraitAD(   nQtlPerChr,   mean = 0,   varA = 1,   varD = 0,   inbrDepr = 0,   limMeanDD = c(0, 1.5),   limVarDD = c(0, 0.5),   silent = FALSE,   force = FALSE,   name = NULL )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"arguments-12","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulation parameters — SimParam","text":"nQtlPerChr number QTLs per chromosome.  Can single value nChr values. mean desired mean trait varA desired additive variance varD desired dominance variance inbrDepr desired inbreeding depression, see details limMeanDD limits meanDD, see details limVarDD limits varDD, see details silent summary details printed console force check running simulation ignored. set TRUE know . name optional name trait","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Simulation parameters — SimParam","text":"function always add trait 'SimParam', unless error occurs  picking QTLs. resulting trait always desired mean  additive genetic variance. However, may desired values  inbreeding depression dominance variance. Thus, strongly recommended  check output printed console determine close trait's  parameters came desired values. mean additive genetic variance always achieved exactly.  function attempts achieve desired dominance variance inbreeding  depression staying within user supplied constraints  acceptable range dominance degree mean variance. desired values achieved, acceptable range need increased / number QTL may need increased. limits setting  range dominance degree mean variance, care taken  regards biological feasibility limits supplied.  default limits somewhat arbitrarily set, make claim  reasonable limits routine use. Inbreeding depression function defined difference mean  genetic value population allele frequency  reference population (population used initialize SimParam)  Hardy-Weinberg equilibrium compared population allele  frequency fully inbred. equivalent amount mean  population increases going inbreeding coefficient 1 (fully  inbred) population inbreeding coefficient 0 (Hardy-Weinberg  equilibrium). Note sign value (usually) positive.  corresponds detrimental effect inbreeding higher values  trait considered biologically beneficial. Summary information trait printed console silent=FALSE.  summary information reports inbreeding depression dominance  variance population well dominance degree mean variance  applied trait.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"examples-10","dir":"Reference","previous_headings":"","what":"Examples","title":"Simulation parameters — SimParam","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) \\dontshow{SP$nThreads = 1L} SP$altAddTraitAD(nQtlPerChr=10, mean=0, varA=1, varD=0.05, inbrDepr=0.2)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"method-addtraitag-","dir":"Reference","previous_headings":"","what":"Method addTraitAG()","title":"Simulation parameters — SimParam","text":"Randomly assigns eligible QTLs one additive GxE traits. simulating one trait, traits pleiotropic correlated effects.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"usage-13","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulation parameters — SimParam","text":"","code":"SimParam$addTraitAG(   nQtlPerChr,   mean = 0,   var = 1,   varGxE = 1e-06,   varEnv = 0,   corA = NULL,   corGxE = NULL,   gamma = FALSE,   shape = 1,   force = FALSE,   name = NULL )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"arguments-13","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulation parameters — SimParam","text":"nQtlPerChr number QTLs per chromosome. Can single value nChr values. mean vector desired mean genetic values one traits var vector desired genetic variances one traits varGxE vector total genotype--environment variances traits varEnv vector environmental variances one traits corA matrix correlations additive effects corGxE matrix correlations GxE effects gamma gamma distribution used instead normal shape shape parameter gamma distribution (rate/scale parameter gamma distribution accounted via desired level genetic variance, var argument) force check running simulation ignored. set TRUE know . name optional name trait(s)","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"examples-11","dir":"Reference","previous_headings":"","what":"Examples","title":"Simulation parameters — SimParam","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) \\dontshow{SP$nThreads = 1L} SP$addTraitAG(10, varGxE=2)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"method-addtraitadg-","dir":"Reference","previous_headings":"","what":"Method addTraitADG()","title":"Simulation parameters — SimParam","text":"Randomly assigns eligible QTLs trait dominance GxE.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"usage-14","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulation parameters — SimParam","text":"","code":"SimParam$addTraitADG(   nQtlPerChr,   mean = 0,   var = 1,   varEnv = 0,   varGxE = 1e-06,   meanDD = 0,   varDD = 0,   corA = NULL,   corDD = NULL,   corGxE = NULL,   useVarA = TRUE,   gamma = FALSE,   shape = 1,   force = FALSE,   name = NULL )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"arguments-14","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulation parameters — SimParam","text":"nQtlPerChr number QTLs per chromosome. Can single value nChr values. mean vector desired mean genetic values one traits var vector desired genetic variances one traits varEnv vector environmental variances one traits varGxE vector total genotype--environment variances traits meanDD mean dominance degree varDD variance dominance degree corA matrix correlations additive effects corDD matrix correlations dominance degrees corGxE matrix correlations GxE effects useVarA tune according additive genetic variance true gamma gamma distribution used instead normal shape shape parameter gamma distribution (rate/scale parameter gamma distribution accounted via desired level genetic variance, var argument) force check running simulation ignored. set TRUE know . name optional name trait(s)","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"examples-12","dir":"Reference","previous_headings":"","what":"Examples","title":"Simulation parameters — SimParam","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) \\dontshow{SP$nThreads = 1L} SP$addTraitADG(10, meanDD=0.5, varGxE=2)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"method-addtraitae-","dir":"Reference","previous_headings":"","what":"Method addTraitAE()","title":"Simulation parameters — SimParam","text":"Randomly assigns eligible QTLs one additive epistasis traits. simulating one trait, traits pleiotropic correlated additive effects.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"usage-15","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulation parameters — SimParam","text":"","code":"SimParam$addTraitAE(   nQtlPerChr,   mean = 0,   var = 1,   relAA = 0,   corA = NULL,   corAA = NULL,   useVarA = TRUE,   gamma = FALSE,   shape = 1,   force = FALSE,   name = NULL )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"arguments-15","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulation parameters — SimParam","text":"nQtlPerChr number QTLs per chromosome. Can single value nChr values. mean vector desired mean genetic values one traits var vector desired genetic variances one traits relAA relative value additive--additive variance compared additive variance diploid organism allele frequency 0.5 corA matrix correlations additive effects corAA matrix correlations additive--additive effects useVarA tune according additive genetic variance true. FALSE, tuning performed according total genetic variance. gamma gamma distribution used instead normal shape shape parameter gamma distribution (rate/scale parameter gamma distribution accounted via desired level genetic variance, var argument) force check running simulation ignored. set TRUE know . name optional name trait(s)","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"examples-13","dir":"Reference","previous_headings":"","what":"Examples","title":"Simulation parameters — SimParam","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) \\dontshow{SP$nThreads = 1L} SP$addTraitAE(10, relAA=0.1)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"method-addtraitade-","dir":"Reference","previous_headings":"","what":"Method addTraitADE()","title":"Simulation parameters — SimParam","text":"Randomly assigns eligible QTLs one traits dominance epistasis. simulating one trait, traits pleiotropic correlated effects.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"usage-16","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulation parameters — SimParam","text":"","code":"SimParam$addTraitADE(   nQtlPerChr,   mean = 0,   var = 1,   meanDD = 0,   varDD = 0,   relAA = 0,   corA = NULL,   corDD = NULL,   corAA = NULL,   useVarA = TRUE,   gamma = FALSE,   shape = 1,   force = FALSE,   name = NULL )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"arguments-16","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulation parameters — SimParam","text":"nQtlPerChr number QTLs per chromosome. Can single value nChr values. mean vector desired mean genetic values one traits var vector desired genetic variances one traits meanDD mean dominance degree varDD variance dominance degree relAA relative value additive--additive variance compared additive variance diploid organism allele frequency 0.5 corA matrix correlations additive effects corDD matrix correlations dominance degrees corAA matrix correlations additive--additive effects useVarA tune according additive genetic variance true. FALSE, tuning performed according total genetic variance. gamma gamma distribution used instead normal shape shape parameter gamma distribution (rate/scale parameter gamma distribution accounted via desired level genetic variance, var argument) force check running simulation ignored. set TRUE know . name optional name trait(s)","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"examples-14","dir":"Reference","previous_headings":"","what":"Examples","title":"Simulation parameters — SimParam","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) \\dontshow{SP$nThreads = 1L} SP$addTraitADE(10)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"method-addtraitaeg-","dir":"Reference","previous_headings":"","what":"Method addTraitAEG()","title":"Simulation parameters — SimParam","text":"Randomly assigns eligible QTLs one additive epistasis GxE traits. simulating one trait, traits pleiotropic correlated effects.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"usage-17","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulation parameters — SimParam","text":"","code":"SimParam$addTraitAEG(   nQtlPerChr,   mean = 0,   var = 1,   relAA = 0,   varGxE = 1e-06,   varEnv = 0,   corA = NULL,   corAA = NULL,   corGxE = NULL,   useVarA = TRUE,   gamma = FALSE,   shape = 1,   force = FALSE,   name = NULL )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"arguments-17","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulation parameters — SimParam","text":"nQtlPerChr number QTLs per chromosome. Can single value nChr values. mean vector desired mean genetic values one traits var vector desired genetic variances one traits relAA relative value additive--additive variance compared additive variance diploid organism allele frequency 0.5 varGxE vector total genotype--environment variances traits varEnv vector environmental variances one traits corA matrix correlations additive effects corAA matrix correlations additive--additive effects corGxE matrix correlations GxE effects useVarA tune according additive genetic variance true. FALSE, tuning performed according total genetic variance. gamma gamma distribution used instead normal shape shape parameter gamma distribution (rate/scale parameter gamma distribution accounted via desired level genetic variance, var argument) force check running simulation ignored. set TRUE know . name optional name trait(s)","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"examples-15","dir":"Reference","previous_headings":"","what":"Examples","title":"Simulation parameters — SimParam","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) \\dontshow{SP$nThreads = 1L} SP$addTraitAEG(10, varGxE=2)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"method-addtraitadeg-","dir":"Reference","previous_headings":"","what":"Method addTraitADEG()","title":"Simulation parameters — SimParam","text":"Randomly assigns eligible QTLs trait dominance, epistasis GxE.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"usage-18","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulation parameters — SimParam","text":"","code":"SimParam$addTraitADEG(   nQtlPerChr,   mean = 0,   var = 1,   varEnv = 0,   varGxE = 1e-06,   meanDD = 0,   varDD = 0,   relAA = 0,   corA = NULL,   corDD = NULL,   corAA = NULL,   corGxE = NULL,   useVarA = TRUE,   gamma = FALSE,   shape = 1,   force = FALSE,   name = NULL )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"arguments-18","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulation parameters — SimParam","text":"nQtlPerChr number QTLs per chromosome. Can single value nChr values. mean vector desired mean genetic values one traits var vector desired genetic variances one traits varEnv vector environmental variances one traits varGxE vector total genotype--environment variances traits meanDD mean dominance degree varDD variance dominance degree relAA relative value additive--additive variance compared additive variance diploid organism allele frequency 0.5 corA matrix correlations additive effects corDD matrix correlations dominance degrees corAA matrix correlations additive--additive effects corGxE matrix correlations GxE effects useVarA tune according additive genetic variance true gamma gamma distribution used instead normal shape shape parameter gamma distribution (rate/scale parameter gamma distribution accounted via desired level genetic variance, var argument) force check running simulation ignored. set TRUE know . name optional name trait(s)","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"examples-16","dir":"Reference","previous_headings":"","what":"Examples","title":"Simulation parameters — SimParam","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) \\dontshow{SP$nThreads = 1L} SP$addTraitADEG(10, meanDD=0.5, varGxE=2)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"method-manaddtrait-","dir":"Reference","previous_headings":"","what":"Method manAddTrait()","title":"Simulation parameters — SimParam","text":"Manually add new trait simulation. Trait must formatted LociMap-class. trait already formatted, consider using importTrait.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"usage-19","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulation parameters — SimParam","text":"","code":"SimParam$manAddTrait(lociMap, varE = NA_real_, force = FALSE)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"arguments-19","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulation parameters — SimParam","text":"lociMap new object descended LociMap-class varE default error variance phenotype, optional force check running simulation ignored. set TRUE know ","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"method-importtrait-","dir":"Reference","previous_headings":"","what":"Method importTrait()","title":"Simulation parameters — SimParam","text":"Manually add new trait(s) simulation. Unlike manAddTrait function, function require formatting trait LociMap-class. formatting performed automatically user, user friendly data.frames matrices taken inputs. function works AD trait types.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"usage-20","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulation parameters — SimParam","text":"","code":"SimParam$importTrait(   markerNames,   addEff,   domEff = NULL,   intercept = NULL,   name = NULL,   varE = NULL,   force = FALSE )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"arguments-20","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulation parameters — SimParam","text":"markerNames vector names QTL addEff matrix additive effects (nLoci x nTraits). Alternatively, vector length nLoci can supplied single trait. domEff optional dominance effects locus intercept optional intercepts trait name optional name(s) trait(s) varE default error variance phenotype, optional force check running simulation ignored. set TRUE know ","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"method-switchtrait-","dir":"Reference","previous_headings":"","what":"Method switchTrait()","title":"Simulation parameters — SimParam","text":"Switch trait simulation.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"usage-21","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulation parameters — SimParam","text":"","code":"SimParam$switchTrait(traitPos, lociMap, varE = NA_real_, force = FALSE)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"arguments-21","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulation parameters — SimParam","text":"traitPos integer indicate trait switch lociMap new object descended LociMap-class varE default error variance phenotype, optional force check running simulation ignored. set TRUE know ","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"method-removetrait-","dir":"Reference","previous_headings":"","what":"Method removeTrait()","title":"Simulation parameters — SimParam","text":"Remove trait simulation","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"usage-22","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulation parameters — SimParam","text":"","code":"SimParam$removeTrait(traits, force = FALSE)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"arguments-22","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulation parameters — SimParam","text":"traits integer vector indicating traits remove force check running simulation ignored. set TRUE know ","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"method-setvare-","dir":"Reference","previous_headings":"","what":"Method setVarE()","title":"Simulation parameters — SimParam","text":"Defines default values error variances used setPheno. defaults  used automatically generate phenotypes new  populations created. See details section setPheno information arguments  used.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"usage-23","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulation parameters — SimParam","text":"","code":"SimParam$setVarE(h2 = NULL, H2 = NULL, varE = NULL, corE = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"arguments-23","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulation parameters — SimParam","text":"h2 vector desired narrow-sense heritabilities H2 vector desired broad-sense heritabilities varE vector matrix error variances corE optional matrix error correlations","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"examples-17","dir":"Reference","previous_headings":"","what":"Examples","title":"Simulation parameters — SimParam","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) \\dontshow{SP$nThreads = 1L} SP$addTraitA(10) SP$setVarE(h2=0.5)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"method-setcore-","dir":"Reference","previous_headings":"","what":"Method setCorE()","title":"Simulation parameters — SimParam","text":"Defines correlation structure default error variances. must call setVarE first define default error variances.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"usage-24","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulation parameters — SimParam","text":"","code":"SimParam$setCorE(corE)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"arguments-24","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulation parameters — SimParam","text":"corE correlation matrix error variances","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"examples-18","dir":"Reference","previous_headings":"","what":"Examples","title":"Simulation parameters — SimParam","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) \\dontshow{SP$nThreads = 1L} SP$addTraitA(10, mean=c(0,0), var=c(1,1), corA=diag(2)) SP$setVarE(varE=c(1,1)) E = 0.5*diag(2)+0.5 #Positively correlated error SP$setCorE(E)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"method-rescaletraits-","dir":"Reference","previous_headings":"","what":"Method rescaleTraits()","title":"Simulation parameters — SimParam","text":"Linearly scales traits achieve desired values means variances founder population.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"usage-25","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulation parameters — SimParam","text":"","code":"SimParam$rescaleTraits(   mean = 0,   var = 1,   varEnv = 0,   varGxE = 1e-06,   useVarA = TRUE )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"arguments-25","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulation parameters — SimParam","text":"mean vector new trait means var vector new trait variances varEnv vector new environmental variances varGxE vector new GxE variances useVarA tune according additive genetic variance true","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"examples-19","dir":"Reference","previous_headings":"","what":"Examples","title":"Simulation parameters — SimParam","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$addTraitA(10)  #Create population pop = newPop(founderPop, simParam=SP) meanG(pop)  #Change mean to 1 SP$rescaleTraits(mean=1) \\dontshow{SP$nThreads = 1L} #Run resetPop for change to take effect pop = resetPop(pop, simParam=SP) meanG(pop)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"method-setrecombratio-","dir":"Reference","previous_headings":"","what":"Method setRecombRatio()","title":"Simulation parameters — SimParam","text":"Set relative recombination rates males females. allows sex-specific recombination rates, assumption equivalent recombination landscapes.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"usage-26","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulation parameters — SimParam","text":"","code":"SimParam$setRecombRatio(femaleRatio)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"arguments-26","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulation parameters — SimParam","text":"femaleRatio relative ratio recombination females compared males. value 2 indicate twice much recombination females. value must greater 0. (default 1)","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"examples-20","dir":"Reference","previous_headings":"","what":"Examples","title":"Simulation parameters — SimParam","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) \\dontshow{SP$nThreads = 1L} SP$setRecombRatio(2) #Twice as much recombination in females"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"method-switchgenmap-","dir":"Reference","previous_headings":"","what":"Method switchGenMap()","title":"Simulation parameters — SimParam","text":"Replaces existing genetic map.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"usage-27","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulation parameters — SimParam","text":"","code":"SimParam$switchGenMap(genMap, centromere = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"arguments-27","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulation parameters — SimParam","text":"genMap list length nChr containing numeric vectors position segregating site chromosome. centromere numeric vector centromere positions. NULL, centromere assumed metacentric.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"method-switchfemalemap-","dir":"Reference","previous_headings":"","what":"Method switchFemaleMap()","title":"Simulation parameters — SimParam","text":"Replaces existing female genetic map.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"usage-28","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulation parameters — SimParam","text":"","code":"SimParam$switchFemaleMap(genMap, centromere = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"arguments-28","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulation parameters — SimParam","text":"genMap list length nChr containing numeric vectors position segregating site chromosome. centromere numeric vector centromere positions. NULL, centromere assumed metacentric.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"method-switchmalemap-","dir":"Reference","previous_headings":"","what":"Method switchMaleMap()","title":"Simulation parameters — SimParam","text":"Replaces existing male genetic map.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"usage-29","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulation parameters — SimParam","text":"","code":"SimParam$switchMaleMap(genMap, centromere = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"arguments-29","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulation parameters — SimParam","text":"genMap list length nChr containing numeric vectors position segregating site chromosome. centromere numeric vector centromere positions. NULL, centromere assumed metacentric.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"method-addtorec-","dir":"Reference","previous_headings":"","what":"Method addToRec()","title":"Simulation parameters — SimParam","text":"internal use .","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"usage-30","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulation parameters — SimParam","text":"","code":"SimParam$addToRec(lastId, id, mother, father, isDH, hist, ploidy)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"arguments-30","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulation parameters — SimParam","text":"lastId ID last individual id name individual mother vector mother iids father vector father iids isDH indicator DH lines hist new recombination history ploidy ploidy level","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"method-ibdhaplo-","dir":"Reference","previous_headings":"","what":"Method ibdHaplo()","title":"Simulation parameters — SimParam","text":"internal use .","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"usage-31","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulation parameters — SimParam","text":"","code":"SimParam$ibdHaplo(iid)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"arguments-31","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulation parameters — SimParam","text":"iid internal ID","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"method-updatelastid-","dir":"Reference","previous_headings":"","what":"Method updateLastId()","title":"Simulation parameters — SimParam","text":"internal use .","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"usage-32","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulation parameters — SimParam","text":"","code":"SimParam$updateLastId(lastId)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"arguments-32","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulation parameters — SimParam","text":"lastId last ID assigned","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"method-addtoped-","dir":"Reference","previous_headings":"","what":"Method addToPed()","title":"Simulation parameters — SimParam","text":"internal use .","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"usage-33","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulation parameters — SimParam","text":"","code":"SimParam$addToPed(lastId, id, mother, father, isDH)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"arguments-33","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulation parameters — SimParam","text":"lastId ID last individual id name individual mother vector mother iids father vector father iids isDH indicator DH lines","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"Simulation parameters — SimParam","text":"objects class cloneable method.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"usage-34","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulation parameters — SimParam","text":"","code":"SimParam$clone(deep = FALSE)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"arguments-34","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulation parameters — SimParam","text":"deep Whether make deep clone.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/SimParam.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Simulation parameters — SimParam","text":"","code":"## ------------------------------------------------ ## Method `SimParam$new` ## ------------------------------------------------  #Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop)  ## ------------------------------------------------ ## Method `SimParam$setTrackPed` ## ------------------------------------------------  #Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$setTrackPed(TRUE)  ## ------------------------------------------------ ## Method `SimParam$setTrackRec` ## ------------------------------------------------  #Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$setTrackRec(TRUE)  ## ------------------------------------------------ ## Method `SimParam$resetPed` ## ------------------------------------------------  #Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L  #Create population pop = newPop(founderPop, simParam=SP) pop@id # 1:10 #>  [1] \"1\"  \"2\"  \"3\"  \"4\"  \"5\"  \"6\"  \"7\"  \"8\"  \"9\"  \"10\"  #Create another population after reseting pedigree SP$resetPed() pop2 = newPop(founderPop, simParam=SP) pop2@id # 1:10 #>  [1] \"1\"  \"2\"  \"3\"  \"4\"  \"5\"  \"6\"  \"7\"  \"8\"  \"9\"  \"10\"  ## ------------------------------------------------ ## Method `SimParam$restrSegSites` ## ------------------------------------------------  #Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$restrSegSites(minQtlPerChr=5, minSnpPerChr=5)  ## ------------------------------------------------ ## Method `SimParam$setSexes` ## ------------------------------------------------  #Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$setSexes(\"yes_sys\")  ## ------------------------------------------------ ## Method `SimParam$addSnpChip` ## ------------------------------------------------  #Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addSnpChip(10)  ## ------------------------------------------------ ## Method `SimParam$addSnpChipByName` ## ------------------------------------------------  #Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$addSnpChipByName(c(\"1_1\",\"1_3\"))  ## ------------------------------------------------ ## Method `SimParam$addTraitA` ## ------------------------------------------------  #Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitA(10)  ## ------------------------------------------------ ## Method `SimParam$addTraitAD` ## ------------------------------------------------  #Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitAD(10, meanDD=0.5)  ## ------------------------------------------------ ## Method `SimParam$altAddTraitAD` ## ------------------------------------------------  #Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$altAddTraitAD(nQtlPerChr=10, mean=0, varA=1, varD=0.05, inbrDepr=0.2) #> A new trait called Trait1 was added.  #>    varD = 0.01267706  #>    inbrDepr = 0.249998  #>    meanDD = 0.1500681  #>    varDD = 0   ## ------------------------------------------------ ## Method `SimParam$addTraitAG` ## ------------------------------------------------  #Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitAG(10, varGxE=2)  ## ------------------------------------------------ ## Method `SimParam$addTraitADG` ## ------------------------------------------------  #Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitADG(10, meanDD=0.5, varGxE=2)  ## ------------------------------------------------ ## Method `SimParam$addTraitAE` ## ------------------------------------------------  #Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitAE(10, relAA=0.1)  ## ------------------------------------------------ ## Method `SimParam$addTraitADE` ## ------------------------------------------------  #Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitADE(10)  ## ------------------------------------------------ ## Method `SimParam$addTraitAEG` ## ------------------------------------------------  #Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitAEG(10, varGxE=2)  ## ------------------------------------------------ ## Method `SimParam$addTraitADEG` ## ------------------------------------------------  #Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitADEG(10, meanDD=0.5, varGxE=2)  ## ------------------------------------------------ ## Method `SimParam$setVarE` ## ------------------------------------------------  #Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitA(10) SP$setVarE(h2=0.5)  ## ------------------------------------------------ ## Method `SimParam$setCorE` ## ------------------------------------------------  #Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitA(10, mean=c(0,0), var=c(1,1), corA=diag(2)) SP$setVarE(varE=c(1,1)) E = 0.5*diag(2)+0.5 #Positively correlated error SP$setCorE(E) #> Warning: This function has been deprecated. Use simParam$setVarE instead.  ## ------------------------------------------------ ## Method `SimParam$rescaleTraits` ## ------------------------------------------------  #Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$addTraitA(10)  #Create population pop = newPop(founderPop, simParam=SP) meanG(pop) #>       Trait1  #> 3.330669e-17   #Change mean to 1 SP$rescaleTraits(mean=1) SP$nThreads = 1L #Run resetPop for change to take effect pop = resetPop(pop, simParam=SP) meanG(pop) #> Trait1  #>      1   ## ------------------------------------------------ ## Method `SimParam$setRecombRatio` ## ------------------------------------------------  #Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$setRecombRatio(2) #Twice as much recombination in females"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/TraitA-class.html","id":null,"dir":"Reference","previous_headings":"","what":"Additive trait — TraitA-class","title":"Additive trait — TraitA-class","text":"Extends LociMap-class model additive traits","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/TraitA-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"Additive trait — TraitA-class","text":"addEff additive effects intercept adjustment factor gv","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/TraitA2-class.html","id":null,"dir":"Reference","previous_headings":"","what":"Sex specific additive trait — TraitA2-class","title":"Sex specific additive trait — TraitA2-class","text":"Extends TraitA-class model seperate additive effects parent origin. Used exclusively genomic selection.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/TraitA2-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"Sex specific additive trait — TraitA2-class","text":"addEffMale additive effects","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/TraitA2D-class.html","id":null,"dir":"Reference","previous_headings":"","what":"Sex specific additive and dominance trait — TraitA2D-class","title":"Sex specific additive and dominance trait — TraitA2D-class","text":"Extends TraitA2-class add dominance","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/TraitA2D-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"Sex specific additive and dominance trait — TraitA2D-class","text":"domEff dominance effects","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/TraitAD-class.html","id":null,"dir":"Reference","previous_headings":"","what":"Additive and dominance trait — TraitAD-class","title":"Additive and dominance trait — TraitAD-class","text":"Extends TraitA-class add dominance","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/TraitAD-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"Additive and dominance trait — TraitAD-class","text":"domEff dominance effects","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/TraitADE-class.html","id":null,"dir":"Reference","previous_headings":"","what":"Additive, dominance, and epistatic trait — TraitADE-class","title":"Additive, dominance, and epistatic trait — TraitADE-class","text":"Extends TraitAD-class add epistasis","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/TraitADE-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"Additive, dominance, and epistatic trait — TraitADE-class","text":"epiEff epistatic effects","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/TraitADEG-class.html","id":null,"dir":"Reference","previous_headings":"","what":"Additive, dominance, epistasis, and GxE trait — TraitADEG-class","title":"Additive, dominance, epistasis, and GxE trait — TraitADEG-class","text":"Extends TraitADE-class add GxE effects","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/TraitADEG-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"Additive, dominance, epistasis, and GxE trait — TraitADEG-class","text":"gxeEff GxE effects gxeInt GxE intercept envVar Environmental variance","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/TraitADG-class.html","id":null,"dir":"Reference","previous_headings":"","what":"Additive, dominance and GxE trait — TraitADG-class","title":"Additive, dominance and GxE trait — TraitADG-class","text":"Extends TraitAD-class add GxE effects","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/TraitADG-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"Additive, dominance and GxE trait — TraitADG-class","text":"gxeEff GxE effects gxeInt GxE intercept envVar Environmental variance","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/TraitAE-class.html","id":null,"dir":"Reference","previous_headings":"","what":"Additive and epistatic trait — TraitAE-class","title":"Additive and epistatic trait — TraitAE-class","text":"Extends TraitA-class add epistasis","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/TraitAE-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"Additive and epistatic trait — TraitAE-class","text":"epiEff epistatic effects","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/TraitAEG-class.html","id":null,"dir":"Reference","previous_headings":"","what":"Additive, epistasis and GxE trait — TraitAEG-class","title":"Additive, epistasis and GxE trait — TraitAEG-class","text":"Extends TraitAE-class add GxE effects","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/TraitAEG-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"Additive, epistasis and GxE trait — TraitAEG-class","text":"gxeEff GxE effects gxeInt GxE intercept envVar Environmental variance","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/TraitAG-class.html","id":null,"dir":"Reference","previous_headings":"","what":"Additive and GxE trait — TraitAG-class","title":"Additive and GxE trait — TraitAG-class","text":"Extends TraitA-class add GxE effects","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/TraitAG-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"Additive and GxE trait — TraitAG-class","text":"gxeEff GxE effects gxeInt GxE intercept envVar Environmental variance","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/aa.html","id":null,"dir":"Reference","previous_headings":"","what":"Additive-by-additive epistatic deviations — aa","title":"Additive-by-additive epistatic deviations — aa","text":"Returns additive--additive epistatic deviations traits","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/aa.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Additive-by-additive epistatic deviations — aa","text":"","code":"aa(pop, simParam = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/aa.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Additive-by-additive epistatic deviations — aa","text":"pop object Pop-class simParam object SimParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/aa.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Additive-by-additive epistatic deviations — aa","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$addTraitAD(10, meanDD=0.5) SP$setVarE(h2=0.5) SP$nThreads = 1L  #Create population pop = newPop(founderPop, simParam=SP) aa(pop, simParam=SP) #>       Trait1 #>  [1,]      0 #>  [2,]      0 #>  [3,]      0 #>  [4,]      0 #>  [5,]      0 #>  [6,]      0 #>  [7,]      0 #>  [8,]      0 #>  [9,]      0 #> [10,]      0"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/addSegSite.html","id":null,"dir":"Reference","previous_headings":"","what":"Add segregating site to MapPop — addSegSite","title":"Add segregating site to MapPop — addSegSite","text":"function allows adding new  segregating site user supplied genotypes MapPop.  position site set using genetic map position.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/addSegSite.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add segregating site to MapPop — addSegSite","text":"","code":"addSegSite(mapPop, siteName, chr, mapPos, haplo)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/addSegSite.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add segregating site to MapPop — addSegSite","text":"mapPop object MapPop-class siteName name give segregating site chr chromosome add site mapPos genetic map position site Morgans haplo haplotypes site","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/addSegSite.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add segregating site to MapPop — addSegSite","text":"object MapPop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/addSegSite.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add segregating site to MapPop — addSegSite","text":"","code":"# Creates a populations of 10 outbred individuals # Their genome consists of 1 chromosome and 2 segregating sites founderPop = quickHaplo(nInd=10,nChr=1,segSites=2)  # Add a locus a the 0.5 Morgan map position haplo = matrix(sample(x=0:1, size=20, replace=TRUE), ncol=1)  founderPop2 = addSegSite(founderPop, siteName=\"x\", chr=1, mapPos=0.5, haplo=haplo)  pullSegSiteHaplo(founderPop2) #>      1_1 x 1_2 #> 1_1    0 0   0 #> 1_2    0 0   1 #> 2_1    0 1   0 #> 2_2    0 0   0 #> 3_1    0 1   1 #> 3_2    0 0   0 #> 4_1    0 0   0 #> 4_2    0 1   0 #> 5_1    1 0   0 #> 5_2    1 1   1 #> 6_1    0 1   0 #> 6_2    1 1   1 #> 7_1    0 0   0 #> 7_2    0 1   0 #> 8_1    0 0   0 #> 8_2    0 1   0 #> 9_1    0 1   1 #> 9_2    0 1   1 #> 10_1   0 0   1 #> 10_2   1 1   0"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/attrition.html","id":null,"dir":"Reference","previous_headings":"","what":"Lose individuals at random — attrition","title":"Lose individuals at random — attrition","text":"Samples individuals random remove population.  user supplies probability individuals  removed population.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/attrition.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Lose individuals at random — attrition","text":"","code":"attrition(pop, p)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/attrition.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Lose individuals at random — attrition","text":"pop object Pop-class p expected proportion individuals lost attrition.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/attrition.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Lose individuals at random — attrition","text":"object Pop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/attrition.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Lose individuals at random — attrition","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=100, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L  #Create population pop = newPop(founderPop, simParam=SP)  #Lose an expected 5% of individuals pop = attrition(pop, p=0.05)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/bv.html","id":null,"dir":"Reference","previous_headings":"","what":"Breeding value — bv","title":"Breeding value — bv","text":"Returns breeding values traits","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/bv.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Breeding value — bv","text":"","code":"bv(pop, simParam = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/bv.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Breeding value — bv","text":"pop object Pop-class simParam object SimParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/bv.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Breeding value — bv","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$addTraitAD(10, meanDD=0.5) SP$setVarE(h2=0.5) SP$nThreads = 1L  #Create population pop = newPop(founderPop, simParam=SP) bv(pop, simParam=SP) #>           Trait1 #>  [1,] -0.5819010 #>  [2,] -0.6447681 #>  [3,]  1.1362233 #>  [4,]  0.1896749 #>  [5,]  1.1721026 #>  [6,] -2.2595757 #>  [7,]  0.9043475 #>  [8,]  0.3135806 #>  [9,]  0.3834670 #> [10,] -0.6131512"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/cChr.html","id":null,"dir":"Reference","previous_headings":"","what":"Combine MapPop chromosomes — cChr","title":"Combine MapPop chromosomes — cChr","text":"Merges chromosomes multiple MapPop-class NamedMapPop-class objects. MapPop must number chromosomes","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/cChr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Combine MapPop chromosomes — cChr","text":"","code":"cChr(...)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/cChr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Combine MapPop chromosomes — cChr","text":"... MapPop-class NamedMapPop-class objects combined","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/cChr.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Combine MapPop chromosomes — cChr","text":"Returns object MapPop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/cChr.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Combine MapPop chromosomes — cChr","text":"","code":"pop1 = quickHaplo(nInd=10, nChr=1, segSites=10) pop2 = quickHaplo(nInd=10, nChr=1, segSites=10)  combinedPop = cChr(pop1, pop2)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/calcGCA.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate GCA — calcGCA","title":"Calculate GCA — calcGCA","text":"Calculate general combining ability test crosses. Intended output hybridCross using \"testcross\" option, work population.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/calcGCA.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate GCA — calcGCA","text":"","code":"calcGCA(pop, use = \"pheno\")"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/calcGCA.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate GCA — calcGCA","text":"pop object Pop-class HybridPop-class use tabulate either genetic values \"gv\", estimated breeding values \"ebv\", phenotypes \"pheno\"","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/calcGCA.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate GCA — calcGCA","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10, inbred=TRUE)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitA(10)  #Create population pop = newPop(founderPop, simParam=SP)  #Make crosses for full diallele pop2 = hybridCross(pop, pop, simParam=SP) GCA = calcGCA(pop2, use=\"gv\")"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/dd.html","id":null,"dir":"Reference","previous_headings":"","what":"Dominance deviations — dd","title":"Dominance deviations — dd","text":"Returns dominance deviations traits","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/dd.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Dominance deviations — dd","text":"","code":"dd(pop, simParam = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/dd.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Dominance deviations — dd","text":"pop object Pop-class simParam object SimParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/dd.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Dominance deviations — dd","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$addTraitAD(10, meanDD=0.5) SP$setVarE(h2=0.5) SP$nThreads = 1L  #Create population pop = newPop(founderPop, simParam=SP) dd(pop, simParam=SP) #>            Trait1 #>  [1,] -0.10503553 #>  [2,]  0.73076413 #>  [3,]  0.01139845 #>  [4,]  0.40533407 #>  [5,]  0.22873377 #>  [6,] -0.59229218 #>  [7,]  0.04563734 #>  [8,] -1.01899456 #>  [9,] -0.02762519 #> [10,]  0.32207968"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/dot-newPop.html","id":null,"dir":"Reference","previous_headings":"","what":"Create new population (internal) — .newPop","title":"Create new population (internal) — .newPop","text":"Creates new Pop-class object Pop superclass.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/dot-newPop.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create new population (internal) — .newPop","text":"","code":".newPop(   rawPop,   id = NULL,   mother = NULL,   father = NULL,   iMother = NULL,   iFather = NULL,   isDH = NULL,   femaleParentPop = NULL,   maleParentPop = NULL,   hist = NULL,   simParam = NULL,   ... )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/dot-newPop.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create new population (internal) — .newPop","text":"rawPop object pop superclass id optional id new individuals mother optional id mothers father optional id fathers iMother optional internal id mothers iFather optional internal id fathers isDH optional indicator DH/inbred individuals femaleParentPop optional population female parents maleParentPop optional population male parents hist optional recombination history simParam object SimParam ... additional arguments passed finalizePop function simParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/dot-newPop.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create new population (internal) — .newPop","text":"Returns object Pop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/doubleGenome.html","id":null,"dir":"Reference","previous_headings":"","what":"Double the ploidy of individuals — doubleGenome","title":"Double the ploidy of individuals — doubleGenome","text":"Creates new individuals twice ploidy.  function created model formation tetraploid  potatoes diploid potatoes. function work  population.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/doubleGenome.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Double the ploidy of individuals — doubleGenome","text":"","code":"doubleGenome(pop, keepParents = TRUE, simParam = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/doubleGenome.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Double the ploidy of individuals — doubleGenome","text":"pop object 'Pop' superclass keepParents previous parents used mother  father. simParam object 'SimParam' class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/doubleGenome.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Double the ploidy of individuals — doubleGenome","text":"Returns object Pop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/doubleGenome.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Double the ploidy of individuals — doubleGenome","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=2, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L  #Create population pop = newPop(founderPop, simParam=SP)  #Create individuals with doubled ploidy pop2 = doubleGenome(pop, simParam=SP)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/ebv.html","id":null,"dir":"Reference","previous_headings":"","what":"Estimated breeding value — ebv","title":"Estimated breeding value — ebv","text":"wrapper accessing ebv slot","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/ebv.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Estimated breeding value — ebv","text":"","code":"ebv(pop)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/ebv.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Estimated breeding value — ebv","text":"pop Pop-class similar object","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/ebv.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Estimated breeding value — ebv","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitAD(10, meanDD=0.5) SP$setVarE(h2=0.5)  #Create population pop = newPop(founderPop, simParam=SP) pop@ebv = matrix(rnorm(pop@nInd), nrow=pop@nInd, ncol=1) ebv(pop) #>             [,1] #>  [1,]  0.3040397 #>  [2,] -1.0463369 #>  [3,]  0.5035516 #>  [4,] -0.3157750 #>  [5,]  0.1527558 #>  [6,]  0.3604446 #>  [7,] -1.3172457 #>  [8,]  1.9060921 #>  [9,] -0.2842742 #> [10,]  0.4744226"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/editGenome.html","id":null,"dir":"Reference","previous_headings":"","what":"Edit genome — editGenome","title":"Edit genome — editGenome","text":"Edits selected loci selected individuals homozygous  state either 1 0 allele. gv slot recalculated  reflect changes due editing, slots remain .","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/editGenome.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Edit genome — editGenome","text":"","code":"editGenome(pop, ind, chr, segSites, allele, simParam = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/editGenome.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Edit genome — editGenome","text":"pop object Pop-class ind vector individuals edit chr vector chromosomes edit.  Length must match length segSites. segSites vector segregating sites edit. Length must  match length chr. allele either 0 1 desired allele simParam object SimParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/editGenome.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Edit genome — editGenome","text":"Returns object Pop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/editGenome.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Edit genome — editGenome","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=2, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitA(10)  #Create population pop = newPop(founderPop, simParam=SP)  #Change individual 1 to homozygous for the 1 allele  #at locus 1, chromosome 1 pop2 = editGenome(pop, ind=1, chr=1, segSites=1,                    allele=1, simParam=SP)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/editGenomeTopQtl.html","id":null,"dir":"Reference","previous_headings":"","what":"Edit genome - the top QTL — editGenomeTopQtl","title":"Edit genome - the top QTL — editGenomeTopQtl","text":"Edits top QTL (largest additive effect) homozygous  state allele increasing. nonfixed QTL edited gv slot recalculated reflect changes due editing, slots remain .","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/editGenomeTopQtl.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Edit genome - the top QTL — editGenomeTopQtl","text":"","code":"editGenomeTopQtl(pop, ind, nQtl, trait = 1, increase = TRUE, simParam = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/editGenomeTopQtl.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Edit genome - the top QTL — editGenomeTopQtl","text":"pop object Pop-class ind vector individuals edit nQtl number QTL edit trait trait effects guide selection top QTL increase trait value increased decreased simParam object SimParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/editGenomeTopQtl.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Edit genome - the top QTL — editGenomeTopQtl","text":"Returns object Pop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/editGenomeTopQtl.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Edit genome - the top QTL — editGenomeTopQtl","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=2, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitA(10)  #Create population pop = newPop(founderPop, simParam=SP)  #Change up to 10 loci for individual 1  pop2 = editGenomeTopQtl(pop, ind=1, nQtl=10, simParam=SP)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/fastRRBLUP.html","id":null,"dir":"Reference","previous_headings":"","what":"Fast RR-BLUP — fastRRBLUP","title":"Fast RR-BLUP — fastRRBLUP","text":"Solves RR-BLUP model genomic predictions given known variance  components. implementation meant fast low memory  alternative RRBLUP RRBLUP2. Unlike  functions, fastRRBLUP fit fixed effects ( intercept) account unequal replication.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/fastRRBLUP.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fast RR-BLUP — fastRRBLUP","text":"","code":"fastRRBLUP(   pop,   traits = 1,   use = \"pheno\",   snpChip = 1,   useQtl = FALSE,   maxIter = 1000,   Vu = NULL,   Ve = NULL,   simParam = NULL,   ... )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/fastRRBLUP.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fast RR-BLUP — fastRRBLUP","text":"pop Pop-class serve training population traits integer indicating trait model, trait name,  function traits returning single value. univariate models  supported. use train model using phenotypes \"pheno\", genetic values \"gv\",  estimated breeding values \"ebv\", breeding values \"bv\", randomly \"rand\" snpChip integer indicating SNP chip genotype  use useQtl QTL genotypes used instead SNP chip.  TRUE, snpChip specifies trait's QTL use, thus  QTL may match QTL underlying phenotype supplied traits. maxIter maximum number iterations. Vu marker effect variance. value NULL,  reasonable value chosen automatically. Ve error variance. value NULL,  reasonable value chosen automatically. simParam object SimParam ... additional arguments using function  traits","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/fastRRBLUP.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Fast RR-BLUP — fastRRBLUP","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=20)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitA(10) SP$setVarE(h2=0.5) SP$addSnpChip(10)  #Create population pop = newPop(founderPop, simParam=SP)  #Run GS model and set EBV ans = fastRRBLUP(pop, simParam=SP) pop = setEBV(pop, ans, simParam=SP)  #Evaluate accuracy cor(gv(pop), ebv(pop)) #>        est_GV_Trait1 #> Trait1     0.8202796"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/genParam.html","id":null,"dir":"Reference","previous_headings":"","what":"Sumarize genetic parameters — genParam","title":"Sumarize genetic parameters — genParam","text":"Calculates genetic genic additive dominance variances object Pop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/genParam.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sumarize genetic parameters — genParam","text":"","code":"genParam(pop, simParam = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/genParam.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sumarize genetic parameters — genParam","text":"pop object Pop-class simParam object SimParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/genParam.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Sumarize genetic parameters — genParam","text":"varA nTrait nTrait matrix additive genetic variances varD nTrait nTrait matrix dominance genetic variances varAA nTrait nTrait matrix additive--additive genetic variances varG nTrait nTrait matrix total genetic variances genicVarA nTrait vector additive genic variances genicVarD nTrait vector dominance genic variances genicVarAA nTrait vector additive--additive genic variances genicVarG nTrait vector total genic variances covA_HW nTrait vector additive covariances due non-random mating covD_HW nTrait vector dominance covariances due non-random mating covAA_HW nTrait vector additive--additive covariances due non-random mating covG_HW nTrait vector total genic covariances due non-random mating covA_L nTrait vector additive covariances due linkage disequilibrium covD_L nTrait vector dominance covariances due linkage disequilibrium covAA_L nTrait vector additive--additive covariances due linkage disequilibrium covAD_L nTrait vector additive dominance covariances due linkage disequilibrium covAAA_L nTrait vector additive additive--additive covariances due linkage disequilibrium covDAA_L nTrait vector dominance additive--additive covariances due linkage disequilibrium covG_L nTrait vector total genic covariances due linkage disequilibrium mu nTrait vector trait means mu_HW nTrait vector expected trait means random mating gv matrix genetic values dimensions nInd nTraits bv matrix breeding values dimensions nInd nTraits dd matrix dominance deviations dimensions nInd nTraits aa matrix additive--additive epistatic deviations dimensions nInd nTraits gv_mu nTrait vector intercepts dimensions nInd nTraits gv_a matrix additive genetic values dimensions nInd nTraits gv_d matrix dominance genetic values dimensions nInd nTraits gv_aa matrix additive--additive genetic values dimensions nInd nTraits","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/genParam.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Sumarize genetic parameters — genParam","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$addTraitAD(10, meanDD=0.5) SP$setVarE(h2=0.5) SP$nThreads = 1L  #Create population pop = newPop(founderPop, simParam=SP) ans = genParam(pop, simParam=SP)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/genicVarA.html","id":null,"dir":"Reference","previous_headings":"","what":"Additive genic variance — genicVarA","title":"Additive genic variance — genicVarA","text":"Returns additive genic variance traits","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/genicVarA.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Additive genic variance — genicVarA","text":"","code":"genicVarA(pop, simParam = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/genicVarA.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Additive genic variance — genicVarA","text":"pop object Pop-class simParam object SimParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/genicVarA.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Additive genic variance — genicVarA","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$addTraitAD(10, meanDD=0.5) SP$setVarE(h2=0.5) SP$nThreads = 1L  #Create population pop = newPop(founderPop, simParam=SP) genicVarA(pop, simParam=SP) #>    Trait1  #> 0.7557754"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/genicVarAA.html","id":null,"dir":"Reference","previous_headings":"","what":"Additive-by-additive genic variance — genicVarAA","title":"Additive-by-additive genic variance — genicVarAA","text":"Returns additive--additive epistatic genic variance traits","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/genicVarAA.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Additive-by-additive genic variance — genicVarAA","text":"","code":"genicVarAA(pop, simParam = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/genicVarAA.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Additive-by-additive genic variance — genicVarAA","text":"pop object Pop-class simParam object SimParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/genicVarAA.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Additive-by-additive genic variance — genicVarAA","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$addTraitAD(10, meanDD=0.5) SP$setVarE(h2=0.5) SP$nThreads = 1L  #Create population pop = newPop(founderPop, simParam=SP) genicVarAA(pop, simParam=SP) #> Trait1  #>      0"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/genicVarD.html","id":null,"dir":"Reference","previous_headings":"","what":"Dominance genic variance — genicVarD","title":"Dominance genic variance — genicVarD","text":"Returns dominance genic variance traits","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/genicVarD.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Dominance genic variance — genicVarD","text":"","code":"genicVarD(pop, simParam = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/genicVarD.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Dominance genic variance — genicVarD","text":"pop object Pop-class simParam object SimParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/genicVarD.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Dominance genic variance — genicVarD","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$addTraitAD(10, meanDD=0.5) SP$setVarE(h2=0.5) SP$nThreads = 1L  #Create population pop = newPop(founderPop, simParam=SP) genicVarD(pop, simParam=SP) #>    Trait1  #> 0.1549891"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/genicVarG.html","id":null,"dir":"Reference","previous_headings":"","what":"Total genic variance — genicVarG","title":"Total genic variance — genicVarG","text":"Returns total genic variance traits","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/genicVarG.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Total genic variance — genicVarG","text":"","code":"genicVarG(pop, simParam = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/genicVarG.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Total genic variance — genicVarG","text":"pop object Pop-class simParam object SimParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/genicVarG.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Total genic variance — genicVarG","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$addTraitAD(10, meanDD=0.5) SP$setVarE(h2=0.5) SP$nThreads = 1L  #Create population pop = newPop(founderPop, simParam=SP) genicVarG(pop, simParam=SP) #>   Trait1  #> 1.714605"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/getGenMap.html","id":null,"dir":"Reference","previous_headings":"","what":"Get genetic map — getGenMap","title":"Get genetic map — getGenMap","text":"Retrieves genetic map loci.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/getGenMap.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get genetic map — getGenMap","text":"","code":"getGenMap(object = NULL, sex = \"A\")"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/getGenMap.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get genetic map — getGenMap","text":"object retrieve genetic map.  Can object SimParam  MapPop-class. NULL, function  look SimParam object called \"SP\"  global environment. sex determines sex specific map  returned. Options \"\" average map, \"F\"  female map, \"M\" male map. options  equivalent using sex specific maps using  pulling MapPop.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/getGenMap.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get genetic map — getGenMap","text":"Returns data.frame : id Unique identifier locus chr Chromosome containing locus pos Genetic map position","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/getGenMap.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get genetic map — getGenMap","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters getGenMap(founderPop) #>      id chr       pos #> 1   1_1   1 0.0000000 #> 2   1_2   1 0.1111111 #> 3   1_3   1 0.2222222 #> 4   1_4   1 0.3333333 #> 5   1_5   1 0.4444444 #> 6   1_6   1 0.5555556 #> 7   1_7   1 0.6666667 #> 8   1_8   1 0.7777778 #> 9   1_9   1 0.8888889 #> 10 1_10   1 1.0000000"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/getMisc.html","id":null,"dir":"Reference","previous_headings":"","what":"Get miscelaneous information in a population — getMisc","title":"Get miscelaneous information in a population — getMisc","text":"Get miscelaneous information population","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/getMisc.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get miscelaneous information in a population — getMisc","text":"","code":"getMisc(x, node = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/getMisc.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get miscelaneous information in a population — getMisc","text":"x Pop-class node character, name node get x@misc slot; NULL whole x@misc slot returned","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/getMisc.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get miscelaneous information in a population — getMisc","text":"x@misc slot nodes x@misc[[*]][[node]]","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/getMisc.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get miscelaneous information in a population — getMisc","text":"","code":"founderGenomes <- quickHaplo(nInd = 3, nChr = 1, segSites = 100) SP <- SimParam$new(founderGenomes) SP$nThreads = 1L basePop <- newPop(founderGenomes) #> Error in get(\"SP\", envir = .GlobalEnv): object 'SP' not found  basePop <- setMisc(basePop, node = \"info\", value = 1) #> Error in eval(expr, envir, enclos): object 'basePop' not found basePop@misc #> Error in eval(expr, envir, enclos): object 'basePop' not found getMisc(x = basePop, node = \"info\") #> Error in eval(expr, envir, enclos): object 'basePop' not found  basePop <- setMisc(basePop, node = \"info2\", value = c(\"A\", \"B\", \"C\")) #> Error in eval(expr, envir, enclos): object 'basePop' not found basePop@misc #> Error in eval(expr, envir, enclos): object 'basePop' not found getMisc(x = basePop, node = \"info2\") #> Error in eval(expr, envir, enclos): object 'basePop' not found  n <- nInd(basePop) #> Error in eval(expr, envir, enclos): object 'basePop' not found location <- vector(mode = \"list\", length = n) #> Error in eval(expr, envir, enclos): object 'n' not found for (ind in seq_len(n)) {   location[[ind]] <- runif(n = 2, min = 0, max = 100) } #> Error in eval(expr, envir, enclos): object 'n' not found location #> Error in eval(expr, envir, enclos): object 'location' not found basePop <- setMisc(basePop, node = \"location\", value = location) #> Error in eval(expr, envir, enclos): object 'basePop' not found basePop@misc #> Error in eval(expr, envir, enclos): object 'basePop' not found getMisc(x = basePop, node = \"location\") #> Error in eval(expr, envir, enclos): object 'basePop' not found  n <- nInd(basePop) #> Error in eval(expr, envir, enclos): object 'basePop' not found location <- vector(mode = \"list\", length = n) #> Error in eval(expr, envir, enclos): object 'n' not found for (ind in c(1, 3)) {   location[[ind]] <- runif(n = 2, min = 0, max = 100) } #> Error: object 'location' not found location #> Error in eval(expr, envir, enclos): object 'location' not found basePop <- setMisc(basePop, node = \"location\", value = location) #> Error in eval(expr, envir, enclos): object 'basePop' not found basePop@misc #> Error in eval(expr, envir, enclos): object 'basePop' not found getMisc(x = basePop, node = \"location\") #> Error in eval(expr, envir, enclos): object 'basePop' not found  getMisc(x = basePop) #> Error in eval(expr, envir, enclos): object 'basePop' not found"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/getNumThreads.html","id":null,"dir":"Reference","previous_headings":"","what":"Number of available threads — getNumThreads","title":"Number of available threads — getNumThreads","text":"Gets number available threads calling OpenMP function omp_get_max_threads()","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/getNumThreads.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Number of available threads — getNumThreads","text":"","code":"getNumThreads()"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/getNumThreads.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Number of available threads — getNumThreads","text":"integer","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/getNumThreads.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Number of available threads — getNumThreads","text":"","code":"getNumThreads() #> [1] 4"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/getPed.html","id":null,"dir":"Reference","previous_headings":"","what":"Get pedigree — getPed","title":"Get pedigree — getPed","text":"Returns population's pedigree stored  id, mother father slots. NULL returned  input population lacks required.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/getPed.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get pedigree — getPed","text":"","code":"getPed(pop)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/getPed.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get pedigree — getPed","text":"pop population","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/getPed.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get pedigree — getPed","text":"","code":"# Create a founder population founderPop = quickHaplo(2,1,2)  # Set simulation parameters SP = SimParam$new(founderPop)  # Create a population pop = newPop(founderPop, simParam=SP)  # Get the pedigree getPed(pop) #>   id mother father #> 1  1      0      0 #> 2  2      0      0  # Returns NULL when a population lacks a pedigree getPed(founderPop) #> NULL"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/getQtlMap.html","id":null,"dir":"Reference","previous_headings":"","what":"Get QTL genetic map — getQtlMap","title":"Get QTL genetic map — getQtlMap","text":"Retrieves genetic map  QTL given trait.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/getQtlMap.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get QTL genetic map — getQtlMap","text":"","code":"getQtlMap(trait = 1, sex = \"A\", simParam = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/getQtlMap.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get QTL genetic map — getQtlMap","text":"trait integer sex determines sex specific map  returned. Options \"\" average map, \"F\"  female map, \"M\" male map. options  equivalent using sex specific maps. simParam object SimParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/getQtlMap.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get QTL genetic map — getQtlMap","text":"Returns data.frame : id Unique identifier QTL chr Chromosome containing QTL site Segregating site chromosome pos Genetic map position","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/getQtlMap.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get QTL genetic map — getQtlMap","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitA(5)  #Pull SNP map getQtlMap(trait=1, simParam=SP) #>        id chr site       pos #> 1_1   1_1   1    1 0.0000000 #> 1_3   1_3   1    3 0.2222222 #> 1_7   1_7   1    7 0.6666667 #> 1_9   1_9   1    9 0.8888889 #> 1_10 1_10   1   10 1.0000000"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/getSnpMap.html","id":null,"dir":"Reference","previous_headings":"","what":"Get SNP genetic map — getSnpMap","title":"Get SNP genetic map — getSnpMap","text":"Retrieves genetic map  given SNP chip.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/getSnpMap.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get SNP genetic map — getSnpMap","text":"","code":"getSnpMap(snpChip = 1, sex = \"A\", simParam = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/getSnpMap.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get SNP genetic map — getSnpMap","text":"snpChip integer. Indicates SNP chip's map retrieve. sex determines sex specific map  returned. Options \"\" average map, \"F\"  female map, \"M\" male map. options  equivalent using sex specific maps. simParam object SimParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/getSnpMap.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get SNP genetic map — getSnpMap","text":"Returns data.frame : id Unique identifier SNP chr Chromosome containing SNP site Segregating site chromosome pos Genetic map position","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/getSnpMap.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get SNP genetic map — getSnpMap","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addSnpChip(5)  #Pull SNP map getSnpMap(snpChip=1, simParam=SP) #>      id chr site       pos #> 1_1 1_1   1    1 0.0000000 #> 1_2 1_2   1    2 0.1111111 #> 1_5 1_5   1    5 0.4444444 #> 1_8 1_8   1    8 0.7777778 #> 1_9 1_9   1    9 0.8888889"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/gv.html","id":null,"dir":"Reference","previous_headings":"","what":"Genetic value — gv","title":"Genetic value — gv","text":"wrapper accessing gv slot","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/gv.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Genetic value — gv","text":"","code":"gv(pop)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/gv.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Genetic value — gv","text":"pop Pop-class similar object","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/gv.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Genetic value — gv","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$addTraitAD(10, meanDD=0.5) SP$setVarE(h2=0.5) SP$nThreads = 1L  #Create population pop = newPop(founderPop, simParam=SP) gv(pop) #>            Trait1 #>  [1,]  0.71484047 #>  [2,] -0.07815592 #>  [3,]  1.37265706 #>  [4,]  0.13208771 #>  [5,]  0.95704027 #>  [6,]  0.82209630 #>  [7,] -1.25105844 #>  [8,] -0.47357585 #>  [9,] -2.04039868 #> [10,] -0.15553291"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/hybridCross.html","id":null,"dir":"Reference","previous_headings":"","what":"Hybrid crossing — hybridCross","title":"Hybrid crossing — hybridCross","text":"convience function hybrid plant breeding simulations. Allows easy specification test cross scheme /creation object HybridPop-class. Note HybridPop-class used parents created using makeDH function newPop using inbred founders. id new individuals [mother_id]_[father_id]","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/hybridCross.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Hybrid crossing — hybridCross","text":"","code":"hybridCross(   females,   males,   crossPlan = \"testcross\",   returnHybridPop = FALSE,   simParam = NULL )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/hybridCross.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Hybrid crossing — hybridCross","text":"females female population, object Pop-class males male population, object Pop-class crossPlan either \"testcross\" possible combinantions matrix two columns designed crosses returnHybridPop results returned HybridPop-class. false returns results Pop-class. Population must fully inbred TRUE. simParam object SimParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/hybridCross.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Hybrid crossing — hybridCross","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=2, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L  #Create population pop = newPop(founderPop, simParam=SP)  #Make crosses for full diallele pop2 = hybridCross(pop, pop, simParam=SP)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/importGenMap.html","id":null,"dir":"Reference","previous_headings":"","what":"Import genetic map — importGenMap","title":"Import genetic map — importGenMap","text":"Formats genetic map stored data.frame AlphaSimR's internal format. Map positions must  Morgans.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/importGenMap.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Import genetic map — importGenMap","text":"","code":"importGenMap(genMap)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/importGenMap.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Import genetic map — importGenMap","text":"genMap genetic map data.frame. first three columns must : marker name, chromosome,  map position (Morgans). Marker name chromosome  coerced using .character.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/importGenMap.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Import genetic map — importGenMap","text":"list named vectors","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/importGenMap.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Import genetic map — importGenMap","text":"","code":"genMap = data.frame(markerName=letters[1:5],                     chromosome=c(1,1,1,2,2),                     position=c(0,0.5,1,0.15,0.4))  asrMap = importGenMap(genMap=genMap)  str(asrMap) #> List of 2 #>  $ 1: Named num [1:3] 0 0.5 1 #>   ..- attr(*, \"names\")= chr [1:3] \"a\" \"b\" \"c\" #>  $ 2: Named num [1:2] 0 0.25 #>   ..- attr(*, \"names\")= chr [1:2] \"d\" \"e\""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/importHaplo.html","id":null,"dir":"Reference","previous_headings":"","what":"Import haplotypes — importHaplo","title":"Import haplotypes — importHaplo","text":"Formats haplotype matrix format  AlphaSimR population can used  initialize simulation. function serves  wrapper newMapPop  utilizes user friendly input format.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/importHaplo.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Import haplotypes — importHaplo","text":"","code":"importHaplo(haplo, genMap, ploidy = 2L, ped = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/importHaplo.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Import haplotypes — importHaplo","text":"haplo matrix haplotypes genMap genetic map data.frame. first three columns must : marker name, chromosome,  map position (Morgans). Marker name chromosome  coerced using .character. See importGenMap ploidy ploidy level organism ped optional pedigree supplied  genotypes. See details.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/importHaplo.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Import haplotypes — importHaplo","text":"MapPop-class ped NULL, otherwise NamedMapPop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/importHaplo.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Import haplotypes — importHaplo","text":"optional pedigree can data.frame, matrix vector.  object data.frame matrix, first three  columns must include information following order: id,  mother, father. values coerced using  .character. object vector, assumed  include id. case, mother father set  \"0\" individuals.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/importHaplo.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Import haplotypes — importHaplo","text":"","code":"haplo = rbind(c(1,1,0,1,0),               c(1,1,0,1,0),               c(0,1,1,0,0),               c(0,1,1,0,0)) colnames(haplo) = letters[1:5]  genMap = data.frame(markerName=letters[1:5],                     chromosome=c(1,1,1,2,2),                     position=c(0,0.5,1,0.15,0.4))  ped = data.frame(id=c(\"a\",\"b\"),                  mother=c(0,0),                  father=c(0,0))  founderPop = importHaplo(haplo=haplo,                           genMap=genMap,                          ploidy=2L,                          ped=ped)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/importInbredGeno.html","id":null,"dir":"Reference","previous_headings":"","what":"Import inbred, diploid genotypes — importInbredGeno","title":"Import inbred, diploid genotypes — importInbredGeno","text":"Formats genotypes inbred, diploid lines  AlphaSimR population can used  initialize simulation. attempt made  automatically detect 0,1,2 -1,0,1 genotype coding.  Heterozygotes probabilistic genotypes allowed,  coerced nearest homozygote. Pedigree  information optional provided  passed population easier identification  simulation.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/importInbredGeno.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Import inbred, diploid genotypes — importInbredGeno","text":"","code":"importInbredGeno(geno, genMap, ped = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/importInbredGeno.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Import inbred, diploid genotypes — importInbredGeno","text":"geno matrix genotypes genMap genetic map data.frame. first three columns must : marker name, chromosome,  map position (Morgans). Marker name chromosome  coerced using .character. See importGenMap ped optional pedigree supplied  genotypes. See details.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/importInbredGeno.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Import inbred, diploid genotypes — importInbredGeno","text":"MapPop-class ped NULL, otherwise NamedMapPop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/importInbredGeno.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Import inbred, diploid genotypes — importInbredGeno","text":"optional pedigree can data.frame, matrix vector.  object data.frame matrix, first three  columns must include information following order: id,  mother, father. values coerced using  .character. object vector, assumed  include id. case, mother father set  \"0\" individuals.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/importInbredGeno.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Import inbred, diploid genotypes — importInbredGeno","text":"","code":"geno = rbind(c(2,2,0,2,0),              c(0,2,2,0,0)) colnames(geno) = letters[1:5]  genMap = data.frame(markerName=letters[1:5],                     chromosome=c(1,1,1,2,2),                     position=c(0,0.5,1,0.15,0.4))  ped = data.frame(id=c(\"a\",\"b\"),                  mother=c(0,0),                  father=c(0,0))  founderPop = importInbredGeno(geno=geno,                               genMap=genMap,                               ped=ped)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/isFemale.html","id":null,"dir":"Reference","previous_headings":"","what":"Test if individuals of a population are female or male — isFemale","title":"Test if individuals of a population are female or male — isFemale","text":"Test individuals population female male","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/isFemale.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Test if individuals of a population are female or male — isFemale","text":"","code":"isFemale(x)  isMale(x)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/isFemale.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Test if individuals of a population are female or male — isFemale","text":"x Pop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/isFemale.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Test if individuals of a population are female or male — isFemale","text":"logical","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/isFemale.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Test if individuals of a population are female or male — isFemale","text":"isMale(): Test individuals population female male","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/isFemale.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Test if individuals of a population are female or male — isFemale","text":"","code":"founderGenomes <- quickHaplo(nInd = 3, nChr = 1, segSites = 100) SP <- SimParam$new(founderGenomes) SP$setSexes(sexes = \"yes_sys\") pop <- newPop(founderGenomes) #> Error in get(\"SP\", envir = .GlobalEnv): object 'SP' not found  isFemale(pop) #> Error in eval(expr, envir, enclos): object 'pop' not found isMale(pop) #> Error in eval(expr, envir, enclos): object 'pop' not found  pop[isFemale(pop)] #> Error in eval(expr, envir, enclos): object 'pop' not found pop[isFemale(pop)]@sex #> Error in eval(expr, envir, enclos): object 'pop' not found"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/isPop.html","id":null,"dir":"Reference","previous_headings":"","what":"Test if object is of a Population class — isPop","title":"Test if object is of a Population class — isPop","text":"Utilify function test object Population class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/isPop.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Test if object is of a Population class — isPop","text":"","code":"isPop(x)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/isPop.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Test if object is of a Population class — isPop","text":"x Pop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/isPop.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Test if object is of a Population class — isPop","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=2, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$addTraitA(10)  #Create population pop = newPop(founderPop, simParam=SP) isPop(pop) #> [1] TRUE isPop(SP) #> [1] FALSE"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/makeCross.html","id":null,"dir":"Reference","previous_headings":"","what":"Make designed crosses — makeCross","title":"Make designed crosses — makeCross","text":"Makes crosses within population using user supplied crossing plan.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/makeCross.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make designed crosses — makeCross","text":"","code":"makeCross(pop, crossPlan, nProgeny = 1, simParam = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/makeCross.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make designed crosses — makeCross","text":"pop object Pop-class crossPlan matrix two column representing female male parents. Either integers position population character strings IDs. nProgeny number progeny per cross simParam object SimParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/makeCross.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make designed crosses — makeCross","text":"Returns object Pop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/makeCross.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Make designed crosses — makeCross","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L  #Create population pop = newPop(founderPop, simParam=SP)  #Cross individual 1 with individual 10 crossPlan = matrix(c(1,10), nrow=1, ncol=2) pop2 = makeCross(pop, crossPlan, simParam=SP)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/makeCross2.html","id":null,"dir":"Reference","previous_headings":"","what":"Make designed crosses — makeCross2","title":"Make designed crosses — makeCross2","text":"Makes crosses two populations using user supplied crossing plan.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/makeCross2.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make designed crosses — makeCross2","text":"","code":"makeCross2(females, males, crossPlan, nProgeny = 1, simParam = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/makeCross2.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make designed crosses — makeCross2","text":"females object Pop-class female parents. males object Pop-class male parents. crossPlan matrix two column representing female male parents. Either integers position population character strings IDs. nProgeny number progeny per cross simParam object SimParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/makeCross2.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make designed crosses — makeCross2","text":"Returns object Pop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/makeCross2.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Make designed crosses — makeCross2","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L  #Create population pop = newPop(founderPop, simParam=SP)  #Cross individual 1 with individual 10 crossPlan = matrix(c(1,10), nrow=1, ncol=2) pop2 = makeCross2(pop, pop, crossPlan, simParam=SP)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/makeDH.html","id":null,"dir":"Reference","previous_headings":"","what":"Generates DH lines — makeDH","title":"Generates DH lines — makeDH","text":"Creates DH lines individual population. works diploid individuals. polyploids, use reduceGenome doubleGenome.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/makeDH.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generates DH lines — makeDH","text":"","code":"makeDH(pop, nDH = 1, useFemale = TRUE, keepParents = TRUE, simParam = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/makeDH.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generates DH lines — makeDH","text":"pop object 'Pop' superclass nDH total number DH lines per individual useFemale female recombination rates used. keepParents previous parents used mother father. simParam object 'SimParam' class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/makeDH.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generates DH lines — makeDH","text":"Returns object Pop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/makeDH.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Generates DH lines — makeDH","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=2, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L  #Create population pop = newPop(founderPop, simParam=SP)  #Create 1 DH for each individual pop2 = makeDH(pop, simParam=SP)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/meanG.html","id":null,"dir":"Reference","previous_headings":"","what":"Mean genetic values — meanG","title":"Mean genetic values — meanG","text":"Returns mean genetic values traits","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/meanG.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Mean genetic values — meanG","text":"","code":"meanG(pop)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/meanG.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Mean genetic values — meanG","text":"pop object Pop-class HybridPop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/meanG.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Mean genetic values — meanG","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$addTraitA(10) SP$setVarE(h2=0.5) SP$nThreads = 1L  #Create population pop = newPop(founderPop, simParam=SP) meanG(pop) #>       Trait1  #> 6.245005e-17"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/meanP.html","id":null,"dir":"Reference","previous_headings":"","what":"Mean phenotypic values — meanP","title":"Mean phenotypic values — meanP","text":"Returns mean phenotypic values traits","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/meanP.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Mean phenotypic values — meanP","text":"","code":"meanP(pop)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/meanP.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Mean phenotypic values — meanP","text":"pop object Pop-class HybridPop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/meanP.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Mean phenotypic values — meanP","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$addTraitA(10) SP$setVarE(h2=0.5) SP$nThreads = 1L  #Create population pop = newPop(founderPop, simParam=SP) meanP(pop) #>     Trait1  #> -0.5176546"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/mergeGenome.html","id":null,"dir":"Reference","previous_headings":"","what":"Combine genomes of individuals — mergeGenome","title":"Combine genomes of individuals — mergeGenome","text":"function designed model pairing gametes. male female individuals treated gametes, ploidy newly  created individuals sum parents.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/mergeGenome.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Combine genomes of individuals — mergeGenome","text":"","code":"mergeGenome(females, males, crossPlan, simParam = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/mergeGenome.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Combine genomes of individuals — mergeGenome","text":"females object Pop-class female parents. males object Pop-class male parents. crossPlan matrix two column representing female male parents. Either integers position population character strings IDs. simParam object SimParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/mergeGenome.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Combine genomes of individuals — mergeGenome","text":"Returns object Pop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/mergeGenome.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Combine genomes of individuals — mergeGenome","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L  #Create population pop = newPop(founderPop, simParam=SP)  #Cross individual 1 with individual 10 crossPlan = matrix(c(1,10), nrow=1, ncol=2) pop2 = mergeGenome(pop, pop, crossPlan, simParam=SP)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/mergePops.html","id":null,"dir":"Reference","previous_headings":"","what":"Merge list of populations — mergePops","title":"Merge list of populations — mergePops","text":"Rapidly merges list populations single population","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/mergePops.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Merge list of populations — mergePops","text":"","code":"mergePops(popList)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/mergePops.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Merge list of populations — mergePops","text":"popList list containing Pop-class elements MultiPop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/mergePops.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Merge list of populations — mergePops","text":"Returns Pop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/mergePops.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Merge list of populations — mergePops","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L  #Create a list of populations and merge list pop = newPop(founderPop, simParam=SP) popList = list(pop, pop) pop2 = mergePops(popList)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/mutate.html","id":null,"dir":"Reference","previous_headings":"","what":"Add Random Mutations — mutate","title":"Add Random Mutations — mutate","text":"Adds random mutations individuals  population. Note existing phenotypes  EBVs kept. Thus, user need run  setPheno /setEBV  generate new phenotypes EBVs reflect  changes introduced new mutations.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/mutate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add Random Mutations — mutate","text":"","code":"mutate(pop, mutRate = 2.5e-08, returnPos = FALSE, simParam = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/mutate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add Random Mutations — mutate","text":"pop object Pop-class mutRate rate new mutations returnPos positions mutations returned simParam object SimParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/mutate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add Random Mutations — mutate","text":"object Pop-class  returnPos=FALSE list containing  Pop-class data.frame containing  postions mutations returnPos=TRUE","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/mutate.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add Random Mutations — mutate","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=2, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitA(10)  #Create population pop = newPop(founderPop, simParam=SP)  #Introduce mutations pop = mutate(pop, simParam=SP)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/nInd.html","id":null,"dir":"Reference","previous_headings":"","what":"Number of individuals — nInd","title":"Number of individuals — nInd","text":"wrapper accessing nInd slot","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/nInd.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Number of individuals — nInd","text":"","code":"nInd(pop)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/nInd.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Number of individuals — nInd","text":"pop Pop-class similar object","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/nInd.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Number of individuals — nInd","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitAD(10, meanDD=0.5) SP$setVarE(h2=0.5)  #Create population pop = newPop(founderPop, simParam=SP) nInd(pop) #> [1] 10"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/newEmptyPop.html","id":null,"dir":"Reference","previous_headings":"","what":"Creates an empty population — newEmptyPop","title":"Creates an empty population — newEmptyPop","text":"Creates empty Pop-class object user defined ploidy parameters taken simParam.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/newEmptyPop.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Creates an empty population — newEmptyPop","text":"","code":"newEmptyPop(ploidy = 2L, simParam = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/newEmptyPop.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Creates an empty population — newEmptyPop","text":"ploidy ploidy population simParam object SimParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/newEmptyPop.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Creates an empty population — newEmptyPop","text":"Returns object Pop-class zero individuals","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/newEmptyPop.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Creates an empty population — newEmptyPop","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=2, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$addTraitA(10)  #Create empty population pop = newEmptyPop(simParam=SP) isPop(pop) #> [1] TRUE"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/newMapPop.html","id":null,"dir":"Reference","previous_headings":"","what":"New MapPop — newMapPop","title":"New MapPop — newMapPop","text":"Creates new MapPop-class user supplied  genetic maps haplotypes.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/newMapPop.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"New MapPop — newMapPop","text":"","code":"newMapPop(genMap, haplotypes, inbred = FALSE, ploidy = 2L)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/newMapPop.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"New MapPop — newMapPop","text":"genMap list genetic maps haplotypes list matrices data.frames  can coerced matrices. See details. inbred individuals fully inbred ploidy ploidy level organism","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/newMapPop.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"New MapPop — newMapPop","text":"object MapPop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/newMapPop.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"New MapPop — newMapPop","text":"item genMap must vector ordered genetic lengths  Morgans. first value must zero. length vector  determines number segregating sites chromosome. item haplotypes must coercible matrix. columns  matrix correspond segregating sites. number rows  must match number individuals times ploidy using  inbred=FALSE. using inbred=TRUE, number rows must equal  number individuals. haplotypes can stored numeric,  integer raw. underlying C++ function use raw.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/newMapPop.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"New MapPop — newMapPop","text":"","code":"# Create genetic map for two chromosomes, each 1 Morgan long # Each chromosome contains 11 equally spaced segregating sites genMap = list(seq(0,1,length.out=11),                seq(0,1,length.out=11))                 # Create haplotypes for 10 outbred individuals chr1 = sample(x=0:1,size=20*11,replace=TRUE) chr1 = matrix(chr1,nrow=20,ncol=11) chr2 = sample(x=0:1,size=20*11,replace=TRUE) chr2 = matrix(chr2,nrow=20,ncol=11) haplotypes = list(chr1,chr2)  founderPop = newMapPop(genMap=genMap, haplotypes=haplotypes)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/newMultiPop.html","id":null,"dir":"Reference","previous_headings":"","what":"Create new Multi Population — newMultiPop","title":"Create new Multi Population — newMultiPop","text":"Creates new MultiPop-class one Pop-class /MultiPop-class objects.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/newMultiPop.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create new Multi Population — newMultiPop","text":"","code":"newMultiPop(...)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/newMultiPop.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create new Multi Population — newMultiPop","text":"... one Pop-class /MultiPop-class objects.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/newMultiPop.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create new Multi Population — newMultiPop","text":"Returns object MultiPop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/newMultiPop.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create new Multi Population — newMultiPop","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=2, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$addTraitA(10)  #Create population pop = newPop(founderPop, simParam=SP) megaPop = newMultiPop(pop=pop) isMultiPop(megaPop) #> [1] TRUE"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/newPop.html","id":null,"dir":"Reference","previous_headings":"","what":"Create new population — newPop","title":"Create new population — newPop","text":"Creates initial Pop-class object MapPop-class NamedMapPop-class. function intended us output functions runMacs, newMapPop, quickHaplo.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/newPop.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create new population — newPop","text":"","code":"newPop(rawPop, simParam = NULL, ...)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/newPop.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create new population — newPop","text":"rawPop object MapPop-class NamedMapPop-class simParam object SimParam ... additional arguments used internally","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/newPop.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create new population — newPop","text":"Returns object Pop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/newPop.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create new population — newPop","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=2, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$addTraitA(10)  #Create population pop = newPop(founderPop, simParam=SP) isPop(pop) #> [1] TRUE"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pedigreeCross.html","id":null,"dir":"Reference","previous_headings":"","what":"Pedigree cross — pedigreeCross","title":"Pedigree cross — pedigreeCross","text":"Creates Pop-class generic pedigree set founder individuals. way user supplied pedigree used depends value matchID. matchID TRUE, IDs user supplied pedigree matched founderNames. matchID FALSE, founder individuals user supplied pedigree randomly sampled founderPop.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pedigreeCross.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pedigree cross — pedigreeCross","text":"","code":"pedigreeCross(   founderPop,   id,   mother,   father,   matchID = FALSE,   maxCycle = 100,   DH = NULL,   nSelf = NULL,   useFemale = TRUE,   simParam = NULL )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pedigreeCross.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pedigree cross — pedigreeCross","text":"founderPop Pop-class id vector unique identifiers individuals pedigree. values IDs seperate IDs founderPop matchID=FALSE. mother vector identifiers mothers individuals pedigree. Must match one elements id vector treated unknown. father vector identifiers fathers individuals pedigree. Must match one elements id vector treated unknown. matchID indicates IDs founderPop matched id argument. See details. maxCycle maximum number loops make pedigree sort . DH optional vector indicating individual made doubled haploid. nSelf optional vector indicating many generations individual selfed. useFemale creating DH lines, female recombination rates used. parameter effect , recombRatio=1. simParam object 'SimParam' class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pedigreeCross.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Pedigree cross — pedigreeCross","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=2, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L  #Create population pop = newPop(founderPop, simParam=SP)  #Pedigree for a biparental cross with 7 generations of selfing id = 1:10 mother = c(0,0,1,3:9) father = c(0,0,2,3:9) pop2 = pedigreeCross(pop, id, mother, father, simParam=SP)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pheno.html","id":null,"dir":"Reference","previous_headings":"","what":"Phenotype — pheno","title":"Phenotype — pheno","text":"wrapper accessing pheno slot","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pheno.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Phenotype — pheno","text":"","code":"pheno(pop)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pheno.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Phenotype — pheno","text":"pop Pop-class similar object","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pheno.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Phenotype — pheno","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$addTraitAD(10, meanDD=0.5) SP$setVarE(h2=0.5) SP$nThreads = 1L  #Create population pop = newPop(founderPop, simParam=SP) pheno(pop) #>            Trait1 #>  [1,]  1.67656264 #>  [2,]  0.06400970 #>  [3,]  0.10327339 #>  [4,]  0.34523187 #>  [5,] -2.79961555 #>  [6,] -1.65236691 #>  [7,]  1.48035829 #>  [8,] -0.06125746 #>  [9,] -0.23027332 #> [10,] -0.87406848"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/popVar.html","id":null,"dir":"Reference","previous_headings":"","what":"Population variance — popVar","title":"Population variance — popVar","text":"Calculates population variance matrix  opposed sample variance matrix calculated  var. .e. divides n instead  n-1","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/popVar.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Population variance — popVar","text":"","code":"popVar(X)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/popVar.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Population variance — popVar","text":"X n m matrix","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/popVar.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Population variance — popVar","text":"m m variance-covariance matrix","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullIbdHaplo.html","id":null,"dir":"Reference","previous_headings":"","what":"Pull IBD haplotypes — pullIbdHaplo","title":"Pull IBD haplotypes — pullIbdHaplo","text":"Retrieves IBD haplotype data","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullIbdHaplo.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pull IBD haplotypes — pullIbdHaplo","text":"","code":"pullIbdHaplo(pop, chr = NULL, snpChip = NULL, simParam = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullIbdHaplo.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pull IBD haplotypes — pullIbdHaplo","text":"pop object Pop-class chr vector chromosomes retrieve. NULL, chromosomes retrieved. snpChip integer indicating SNP array loci  retrieved. NULL, sites retrieved. simParam object SimParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullIbdHaplo.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pull IBD haplotypes — pullIbdHaplo","text":"Returns matrix IBD haplotypes.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullIbdHaplo.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Pull IBD haplotypes — pullIbdHaplo","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=15)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitA(10) SP$addSnpChip(5) SP$setTrackRec(TRUE)  #Create population pop = newPop(founderPop, simParam=SP) pullIbdHaplo(pop, simParam=SP) #>      1_1 1_2 1_3 1_4 1_5 1_6 1_7 1_8 1_9 1_10 1_11 1_12 1_13 1_14 1_15 #> 1_1    1   1   1   1   1   1   1   1   1    1    1    1    1    1    1 #> 1_2    2   2   2   2   2   2   2   2   2    2    2    2    2    2    2 #> 2_1    3   3   3   3   3   3   3   3   3    3    3    3    3    3    3 #> 2_2    4   4   4   4   4   4   4   4   4    4    4    4    4    4    4 #> 3_1    5   5   5   5   5   5   5   5   5    5    5    5    5    5    5 #> 3_2    6   6   6   6   6   6   6   6   6    6    6    6    6    6    6 #> 4_1    7   7   7   7   7   7   7   7   7    7    7    7    7    7    7 #> 4_2    8   8   8   8   8   8   8   8   8    8    8    8    8    8    8 #> 5_1    9   9   9   9   9   9   9   9   9    9    9    9    9    9    9 #> 5_2   10  10  10  10  10  10  10  10  10   10   10   10   10   10   10 #> 6_1   11  11  11  11  11  11  11  11  11   11   11   11   11   11   11 #> 6_2   12  12  12  12  12  12  12  12  12   12   12   12   12   12   12 #> 7_1   13  13  13  13  13  13  13  13  13   13   13   13   13   13   13 #> 7_2   14  14  14  14  14  14  14  14  14   14   14   14   14   14   14 #> 8_1   15  15  15  15  15  15  15  15  15   15   15   15   15   15   15 #> 8_2   16  16  16  16  16  16  16  16  16   16   16   16   16   16   16 #> 9_1   17  17  17  17  17  17  17  17  17   17   17   17   17   17   17 #> 9_2   18  18  18  18  18  18  18  18  18   18   18   18   18   18   18 #> 10_1  19  19  19  19  19  19  19  19  19   19   19   19   19   19   19 #> 10_2  20  20  20  20  20  20  20  20  20   20   20   20   20   20   20"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullMarkerGeno.html","id":null,"dir":"Reference","previous_headings":"","what":"Pull marker genotypes — pullMarkerGeno","title":"Pull marker genotypes — pullMarkerGeno","text":"Retrieves genotype data user specified loci","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullMarkerGeno.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pull marker genotypes — pullMarkerGeno","text":"","code":"pullMarkerGeno(pop, markers, asRaw = FALSE, simParam = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullMarkerGeno.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pull marker genotypes — pullMarkerGeno","text":"pop object RawPop-class MapPop-class markers character vector. Indicates names loci retrieved. asRaw return raw (byte) format simParam object SimParam,  used pop MapPop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullMarkerGeno.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pull marker genotypes — pullMarkerGeno","text":"Returns matrix genotypes.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullMarkerGeno.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Pull marker genotypes — pullMarkerGeno","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=15)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitA(10) SP$addSnpChip(5)  #Create population pop = newPop(founderPop, simParam=SP)  #Pull genotype data for first two markers on chromosome one. #Marker name is consistent with default naming in AlphaSimR. pullMarkerGeno(pop, markers=c(\"1_1\",\"1_2\"), simParam=SP) #>    1_1 1_2 #> 1    0   0 #> 2    0   1 #> 3    1   2 #> 4    2   2 #> 5    1   1 #> 6    1   1 #> 7    0   2 #> 8    0   1 #> 9    2   0 #> 10   1   1"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullMarkerHaplo.html","id":null,"dir":"Reference","previous_headings":"","what":"Pull marker haplotypes — pullMarkerHaplo","title":"Pull marker haplotypes — pullMarkerHaplo","text":"Retrieves haplotype data user specified loci","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullMarkerHaplo.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pull marker haplotypes — pullMarkerHaplo","text":"","code":"pullMarkerHaplo(pop, markers, haplo = \"all\", asRaw = FALSE, simParam = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullMarkerHaplo.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pull marker haplotypes — pullMarkerHaplo","text":"pop object RawPop-class MapPop-class markers character vector. Indicates names loci retrieved haplo either \"\" haplotypes integer single set haplotypes. Use value 1 female haplotypes value 2 male haplotypes diploids. asRaw return raw (byte) format simParam object SimParam,  used pop MapPop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullMarkerHaplo.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pull marker haplotypes — pullMarkerHaplo","text":"Returns matrix genotypes.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullMarkerHaplo.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Pull marker haplotypes — pullMarkerHaplo","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=15)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitA(10) SP$addSnpChip(5) SP$setTrackRec(TRUE)  #Create population pop = newPop(founderPop, simParam=SP)  #Pull haplotype data for first two markers on chromosome one. #Marker name is consistent with default naming in AlphaSimR. pullMarkerHaplo(pop, markers=c(\"1_1\",\"1_2\"), simParam=SP) #>      1_1 1_2 #> 1_1    0   1 #> 1_2    0   0 #> 2_1    1   1 #> 2_2    0   1 #> 3_1    1   1 #> 3_2    0   0 #> 4_1    1   1 #> 4_2    1   1 #> 5_1    0   1 #> 5_2    0   0 #> 6_1    1   1 #> 6_2    0   1 #> 7_1    0   0 #> 7_2    1   0 #> 8_1    1   0 #> 8_2    1   1 #> 9_1    0   0 #> 9_2    1   1 #> 10_1   0   0 #> 10_2   0   0"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullQtlGeno.html","id":null,"dir":"Reference","previous_headings":"","what":"Pull QTL genotypes — pullQtlGeno","title":"Pull QTL genotypes — pullQtlGeno","text":"Retrieves QTL genotype data","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullQtlGeno.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pull QTL genotypes — pullQtlGeno","text":"","code":"pullQtlGeno(pop, trait = 1, chr = NULL, asRaw = FALSE, simParam = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullQtlGeno.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pull QTL genotypes — pullQtlGeno","text":"pop object Pop-class trait integer. Indicates trait's QTL genotypes retrieve. chr vector chromosomes retrieve. NULL, chromosome retrieved. asRaw return raw (byte) format simParam object SimParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullQtlGeno.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pull QTL genotypes — pullQtlGeno","text":"Returns matrix QTL genotypes.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullQtlGeno.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Pull QTL genotypes — pullQtlGeno","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=15)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitA(10) SP$addSnpChip(5)  #Create population pop = newPop(founderPop, simParam=SP) pullQtlGeno(pop, simParam=SP) #>    1_2 1_3 1_4 1_6 1_7 1_10 1_11 1_13 1_14 1_15 #> 1    0   1   0   2   2    0    0    2    1    2 #> 2    1   0   0   2   0    0    1    2    0    0 #> 3    2   1   1   2   2    1    1    0    1    1 #> 4    2   0   2   1   0    2    1    1    1    1 #> 5    2   0   1   2   0    0    0    2    0    1 #> 6    1   2   1   1   1    1    1    0    1    1 #> 7    0   0   2   0   0    0    1    1    0    2 #> 8    1   0   1   1   0    1    1    1    1    1 #> 9    1   2   2   0   1    1    1    1    2    1 #> 10   0   1   0   0   1    2    1    1    1    1"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullQtlHaplo.html","id":null,"dir":"Reference","previous_headings":"","what":"Pull QTL haplotypes — pullQtlHaplo","title":"Pull QTL haplotypes — pullQtlHaplo","text":"Retrieves QTL haplotype data","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullQtlHaplo.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pull QTL haplotypes — pullQtlHaplo","text":"","code":"pullQtlHaplo(   pop,   trait = 1,   haplo = \"all\",   chr = NULL,   asRaw = FALSE,   simParam = NULL )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullQtlHaplo.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pull QTL haplotypes — pullQtlHaplo","text":"pop object Pop-class trait integer. Indicates trait's QTL haplotypes retrieve. haplo either \"\" haplotypes integer single set haplotypes. Use value 1 female haplotypes value 2 male haplotypes diploids. chr vector chromosomes retrieve. NULL, chromosome retrieved. asRaw return raw (byte) format simParam object SimParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullQtlHaplo.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pull QTL haplotypes — pullQtlHaplo","text":"Returns matrix QTL haplotypes.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullQtlHaplo.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Pull QTL haplotypes — pullQtlHaplo","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=15)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitA(10) SP$addSnpChip(5)  #Create population pop = newPop(founderPop, simParam=SP) pullQtlHaplo(pop, simParam=SP) #>      1_1 1_2 1_3 1_4 1_7 1_9 1_11 1_12 1_13 1_15 #> 1_1    1   1   0   1   1   1    0    0    0    1 #> 1_2    1   0   0   1   0   1    0    1    1    0 #> 2_1    1   1   1   0   1   1    0    0    1    1 #> 2_2    0   1   0   1   1   0    0    0    1    0 #> 3_1    1   1   1   1   0   1    0    0    1    1 #> 3_2    1   0   1   0   0   1    1    0    1    0 #> 4_1    1   0   0   0   1   0    0    0    1    0 #> 4_2    0   0   0   0   0   1    1    1    0    0 #> 5_1    0   0   1   0   1   0    0    1    1    1 #> 5_2    1   0   1   1   1   0    1    1    0    0 #> 6_1    0   1   0   0   1   1    0    0    1    0 #> 6_2    0   1   0   1   1   1    1    1    0    1 #> 7_1    0   0   0   0   1   1    1    1    1    0 #> 7_2    1   1   1   0   0   0    0    1    1    0 #> 8_1    1   0   0   1   0   1    1    0    0    1 #> 8_2    1   1   1   0   0   1    1    1    1    0 #> 9_1    0   0   1   0   1   0    1    1    1    0 #> 9_2    0   0   0   1   1   0    0    0    0    1 #> 10_1   1   1   1   0   0   1    0    0    0    0 #> 10_2   1   0   0   0   1   0    1    0    1    0"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullSegSiteGeno.html","id":null,"dir":"Reference","previous_headings":"","what":"Pull segregating site genotypes — pullSegSiteGeno","title":"Pull segregating site genotypes — pullSegSiteGeno","text":"Retrieves genotype data segregating sites","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullSegSiteGeno.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pull segregating site genotypes — pullSegSiteGeno","text":"","code":"pullSegSiteGeno(pop, chr = NULL, asRaw = FALSE, simParam = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullSegSiteGeno.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pull segregating site genotypes — pullSegSiteGeno","text":"pop object RawPop-class MapPop-class chr vector chromosomes retrieve. NULL, chromosome retrieved. asRaw return raw (byte) format simParam object SimParam,  used pop MapPop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullSegSiteGeno.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pull segregating site genotypes — pullSegSiteGeno","text":"Returns matrix genotypes","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullSegSiteGeno.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Pull segregating site genotypes — pullSegSiteGeno","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=15)  #Set simulation parameters SP = SimParam$new(founderPop) SP$addTraitA(10) SP$addSnpChip(5)  #Create population pop = newPop(founderPop, simParam=SP) pullSegSiteGeno(pop, simParam=SP) #>    1_1 1_2 1_3 1_4 1_5 1_6 1_7 1_8 1_9 1_10 1_11 1_12 1_13 1_14 1_15 #> 1    2   1   2   2   0   2   2   0   1    1    1    0    1    1    1 #> 2    1   1   2   0   1   1   0   0   1    0    1    0    1    0    1 #> 3    0   1   2   0   2   1   1   2   1    1    1    1    2    0    0 #> 4    1   1   1   2   2   2   1   1   2    1    1    1    1    1    2 #> 5    2   0   1   2   1   1   0   1   1    0    1    0    2    1    1 #> 6    1   0   2   2   1   1   1   1   1    0    2    1    0    1    2 #> 7    0   0   1   0   1   1   1   0   0    1    2    2    2    2    2 #> 8    0   2   1   0   1   1   1   2   0    2    2    1    1    0    1 #> 9    2   1   1   0   1   1   0   0   1    2    1    2    0    1    0 #> 10   1   1   1   2   0   1   1   1   1    2    2    1    0    1    0"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullSegSiteHaplo.html","id":null,"dir":"Reference","previous_headings":"","what":"Pull seg site haplotypes — pullSegSiteHaplo","title":"Pull seg site haplotypes — pullSegSiteHaplo","text":"Retrieves haplotype data segregating sites","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullSegSiteHaplo.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pull seg site haplotypes — pullSegSiteHaplo","text":"","code":"pullSegSiteHaplo(   pop,   haplo = \"all\",   chr = NULL,   asRaw = FALSE,   simParam = NULL )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullSegSiteHaplo.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pull seg site haplotypes — pullSegSiteHaplo","text":"pop object RawPop-class MapPop-class haplo either \"\" haplotypes integer single set haplotypes. Use value 1 female haplotypes value 2 male haplotypes diploids. chr vector chromosomes retrieve. NULL, chromosome retrieved. asRaw return raw (byte) format simParam object SimParam,  used pop MapPop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullSegSiteHaplo.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pull seg site haplotypes — pullSegSiteHaplo","text":"Returns matrix haplotypes","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullSegSiteHaplo.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Pull seg site haplotypes — pullSegSiteHaplo","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=15)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitA(10) SP$addSnpChip(5)  #Create population pop = newPop(founderPop, simParam=SP) pullSegSiteHaplo(pop, simParam=SP) #>      1_1 1_2 1_3 1_4 1_5 1_6 1_7 1_8 1_9 1_10 1_11 1_12 1_13 1_14 1_15 #> 1_1    1   0   0   1   1   1   1   0   1    1    0    0    0    1    1 #> 1_2    1   1   1   0   1   0   0   0   0    1    0    0    1    1    0 #> 2_1    0   0   0   0   0   1   1   0   0    1    0    0    0    0    0 #> 2_2    0   0   1   0   0   1   1   0   1    0    0    0    1    0    0 #> 3_1    1   1   0   0   0   0   1   0   0    0    0    0    0    1    0 #> 3_2    1   0   0   1   1   1   1   0   1    1    1    1    0    0    1 #> 4_1    1   1   0   0   1   1   0   0   1    1    1    0    0    0    0 #> 4_2    1   0   1   0   1   1   0   0   0    1    0    1    1    1    0 #> 5_1    1   1   0   0   0   0   0   1   1    0    1    1    1    1    0 #> 5_2    1   0   1   0   1   1   0   1   0    0    1    1    1    1    1 #> 6_1    1   0   1   0   1   1   0   0   0    1    0    0    0    0    1 #> 6_2    0   0   1   0   0   1   0   0   1    0    0    1    0    0    1 #> 7_1    1   1   1   0   1   1   1   0   1    0    0    0    1    0    0 #> 7_2    0   1   0   1   1   0   0   0   1    0    1    1    1    0    1 #> 8_1    0   0   1   1   0   1   0   1   1    0    0    1    1    1    1 #> 8_2    0   1   0   0   0   1   1   1   1    1    1    0    1    0    1 #> 9_1    0   0   0   1   0   1   1   1   0    0    1    0    0    1    0 #> 9_2    1   0   1   0   0   1   1   0   0    1    0    0    1    1    1 #> 10_1   1   0   0   1   1   0   0   0   0    0    0    0    1    0    0 #> 10_2   0   1   1   0   0   0   1   1   1    0    1    0    0    1    1"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullSnpGeno.html","id":null,"dir":"Reference","previous_headings":"","what":"Pull SNP genotypes — pullSnpGeno","title":"Pull SNP genotypes — pullSnpGeno","text":"Retrieves SNP genotype data","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullSnpGeno.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pull SNP genotypes — pullSnpGeno","text":"","code":"pullSnpGeno(pop, snpChip = 1, chr = NULL, asRaw = FALSE, simParam = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullSnpGeno.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pull SNP genotypes — pullSnpGeno","text":"pop object Pop-class snpChip integer. Indicates SNP chip's genotypes retrieve. chr vector chromosomes retrieve. NULL, chromosome retrieved. asRaw return raw (byte) format simParam object SimParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullSnpGeno.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pull SNP genotypes — pullSnpGeno","text":"Returns matrix SNP genotypes.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullSnpGeno.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Pull SNP genotypes — pullSnpGeno","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=15)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitA(10) SP$addSnpChip(5)  #Create population pop = newPop(founderPop, simParam=SP) pullSnpGeno(pop, simParam=SP) #>    1_3 1_6 1_7 1_9 1_10 #> 1    2   0   0   2    0 #> 2    2   1   2   2    2 #> 3    1   0   0   2    1 #> 4    1   2   0   2    1 #> 5    0   1   2   1    1 #> 6    2   1   0   1    2 #> 7    1   1   0   0    0 #> 8    0   2   0   1    0 #> 9    2   1   2   0    1 #> 10   0   1   1   2    2"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullSnpHaplo.html","id":null,"dir":"Reference","previous_headings":"","what":"Pull SNP haplotypes — pullSnpHaplo","title":"Pull SNP haplotypes — pullSnpHaplo","text":"Retrieves SNP haplotype data","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullSnpHaplo.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pull SNP haplotypes — pullSnpHaplo","text":"","code":"pullSnpHaplo(   pop,   snpChip = 1,   haplo = \"all\",   chr = NULL,   asRaw = FALSE,   simParam = NULL )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullSnpHaplo.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pull SNP haplotypes — pullSnpHaplo","text":"pop object Pop-class snpChip integer. Indicates SNP chip's haplotypes retrieve. haplo either \"\" haplotypes integer single set haplotypes. Use value 1 female haplotypes value 2 male haplotypes diploids. chr vector chromosomes retrieve. NULL, chromosome retrieved. asRaw return raw (byte) format simParam object SimParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullSnpHaplo.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pull SNP haplotypes — pullSnpHaplo","text":"Returns matrix SNP haplotypes.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/pullSnpHaplo.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Pull SNP haplotypes — pullSnpHaplo","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=15)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitA(10) SP$addSnpChip(5)  #Create population pop = newPop(founderPop, simParam=SP) pullSnpHaplo(pop, simParam=SP) #>      1_1 1_2 1_4 1_7 1_10 #> 1_1    1   1   1   0    1 #> 1_2    0   0   0   0    1 #> 2_1    1   0   1   0    0 #> 2_2    1   1   0   0    1 #> 3_1    1   1   1   0    0 #> 3_2    0   1   0   1    0 #> 4_1    1   0   0   1    1 #> 4_2    0   1   0   1    0 #> 5_1    0   1   1   1    0 #> 5_2    0   1   1   0    1 #> 6_1    0   0   1   1    0 #> 6_2    1   0   1   0    1 #> 7_1    1   1   1   0    0 #> 7_2    0   1   0   0    0 #> 8_1    1   0   1   1    0 #> 8_2    1   1   1   1    1 #> 9_1    0   0   0   1    0 #> 9_2    1   1   0   0    1 #> 10_1   0   1   0   1    0 #> 10_2   1   0   0   1    1"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/quickHaplo.html","id":null,"dir":"Reference","previous_headings":"","what":"Quick founder haplotype simulation — quickHaplo","title":"Quick founder haplotype simulation — quickHaplo","text":"Rapidly simulates founder haplotypes randomly  sampling 0s 1s. equivalent loci  allele frequency 0.5 linkage equilibrium.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/quickHaplo.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Quick founder haplotype simulation — quickHaplo","text":"","code":"quickHaplo(nInd, nChr, segSites, genLen = 1, ploidy = 2L, inbred = FALSE)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/quickHaplo.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Quick founder haplotype simulation — quickHaplo","text":"nInd number individuals simulate nChr number chromosomes simulate segSites number segregating sites per chromosome genLen genetic length chromosomes ploidy ploidy level organism inbred founder individuals inbred","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/quickHaplo.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Quick founder haplotype simulation — quickHaplo","text":"object MapPop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/quickHaplo.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Quick founder haplotype simulation — quickHaplo","text":"","code":"# Creates a populations of 10 outbred individuals # Their genome consists of 1 chromosome and 100 segregating sites founderPop = quickHaplo(nInd=10,nChr=1,segSites=100)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/randCross.html","id":null,"dir":"Reference","previous_headings":"","what":"Make random crosses — randCross","title":"Make random crosses — randCross","text":"wrapper makeCross randomly selects parental combinations possible combinantions.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/randCross.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make random crosses — randCross","text":"","code":"randCross(   pop,   nCrosses,   nProgeny = 1,   balance = TRUE,   parents = NULL,   ignoreSexes = FALSE,   simParam = NULL )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/randCross.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make random crosses — randCross","text":"pop object Pop-class nCrosses total number crosses make nProgeny number progeny per cross balance using sexes, option balance number progeny per parent parents optional vector indices allowable parents ignoreSexes sexes ignored simParam object SimParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/randCross.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make random crosses — randCross","text":"Returns object Pop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/randCross.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Make random crosses — randCross","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L  #Create population pop = newPop(founderPop, simParam=SP)  #Make 10 crosses pop2 = randCross(pop, 10, simParam=SP)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/randCross2.html","id":null,"dir":"Reference","previous_headings":"","what":"Make random crosses — randCross2","title":"Make random crosses — randCross2","text":"wrapper makeCross2 randomly selects parental combinations possible combinantions two populations.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/randCross2.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make random crosses — randCross2","text":"","code":"randCross2(   females,   males,   nCrosses,   nProgeny = 1,   balance = TRUE,   femaleParents = NULL,   maleParents = NULL,   ignoreSexes = FALSE,   simParam = NULL )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/randCross2.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make random crosses — randCross2","text":"females object Pop-class female parents. males object Pop-class male parents. nCrosses total number crosses make nProgeny number progeny per cross balance option balance number progeny per parent femaleParents optional vector indices allowable female parents maleParents optional vector indices allowable male parents ignoreSexes sex ignored simParam object SimParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/randCross2.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make random crosses — randCross2","text":"Returns object Pop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/randCross2.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Make random crosses — randCross2","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L  #Create population pop = newPop(founderPop, simParam=SP)  #Make 10 crosses pop2 = randCross2(pop, pop, 10, simParam=SP)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/reduceGenome.html","id":null,"dir":"Reference","previous_headings":"","what":"Create individuals with reduced ploidy — reduceGenome","title":"Create individuals with reduced ploidy — reduceGenome","text":"Creates new individuals gametes. function  created model creation diploid potatoes  tetraploid potatoes. can used population  even ploidy level. newly created individuals half  ploidy level originals. reduction can occur  without genetic recombination.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/reduceGenome.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create individuals with reduced ploidy — reduceGenome","text":"","code":"reduceGenome(   pop,   nProgeny = 1,   useFemale = TRUE,   keepParents = TRUE,   simRecomb = TRUE,   simParam = NULL )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/reduceGenome.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create individuals with reduced ploidy — reduceGenome","text":"pop object 'Pop' superclass nProgeny total number progeny per individual useFemale female recombination rates used. keepParents previous parents used mother  father. simRecomb genetic recombination modeled. simParam object 'SimParam' class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/reduceGenome.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create individuals with reduced ploidy — reduceGenome","text":"Returns object Pop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/reduceGenome.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create individuals with reduced ploidy — reduceGenome","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=2, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L  #Create population pop = newPop(founderPop, simParam=SP)  #Create individuals with reduced ploidy pop2 = reduceGenome(pop, simParam=SP)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/resetPop.html","id":null,"dir":"Reference","previous_headings":"","what":"Reset population — resetPop","title":"Reset population — resetPop","text":"Recalculates population's genetic values resets phenotypes EBVs.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/resetPop.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Reset population — resetPop","text":"","code":"resetPop(pop, simParam = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/resetPop.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Reset population — resetPop","text":"pop object Pop-class simParam object SimParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/resetPop.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Reset population — resetPop","text":"object Pop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/resetPop.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Reset population — resetPop","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=2, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$addTraitA(10)  #Create population pop = newPop(founderPop, simParam=SP)  #Rescale to set mean to 1 SP$rescaleTraits(mean=1) pop = resetPop(pop, simParam=SP)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/runMacs.html","id":null,"dir":"Reference","previous_headings":"","what":"Create founder haplotypes using MaCS — runMacs","title":"Create founder haplotypes using MaCS — runMacs","text":"Uses MaCS software produce founder haplotypes  (Chen et al. 2009) .","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/runMacs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create founder haplotypes using MaCS — runMacs","text":"","code":"runMacs(   nInd,   nChr = 1,   segSites = NULL,   inbred = FALSE,   species = \"GENERIC\",   split = NULL,   ploidy = 2L,   manualCommand = NULL,   manualGenLen = NULL,   nThreads = NULL )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/runMacs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create founder haplotypes using MaCS — runMacs","text":"nInd number individuals simulate nChr number chromosomes simulate segSites number segregating sites keep per chromosome.  value NULL results sites retained. inbred founder individuals inbred species species history simulate. See details. split optional historic population split terms generations ago. ploidy ploidy level organism manualCommand user provided MaCS options. advanced users . manualGenLen user provided genetic length. must supplied using  manualCommand. using manualCommand, value replace predefined  genetic length species. However, genetic length used  AlphaSimR passed MaCS, MaCS still uses predefined genetic length.  advanced users . nThreads OpenMP available, allow simulating chromosomes parallel.  value NULL, number threads automatically detected.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/runMacs.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create founder haplotypes using MaCS — runMacs","text":"object MapPop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/runMacs.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Create founder haplotypes using MaCS — runMacs","text":"currently three species histories available: GENERIC, CATTLE, WHEAT, MAIZE. GENERIC history meant reasonable -purpose choice. runs quickly  models population effective populations size gone several historic  bottlenecks. species history used default arguments runMacs2  function, user examine function details species modeled. CATTLE history based real genome sequence data (MacLeod et al. 2013) . WHEAT (Gaynor et al. 2017)  MAIZE (Hickey et al. 2014)   histories included due use previous simulations. However,  noted neither faithfully simulates respective species. apparent  low number segregating sites simulated history relative real-world  analogs. Adjusting histories better represent real-world analogs result  drastic increase runtime.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/runMacs.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Create founder haplotypes using MaCS — runMacs","text":"Chen GK, Marjoram P, Wall JD (2009). “Fast Flexible Simulation DNA Sequence Data.” Genome Research, 19, 136-142. https://genome.cshlp.org/content/19/1/136. Gaynor RC, Gorjanc G, Bentley AR, Ober ES, Howell P, Jackson R, Mackay IJ, Hickey JM (2017). “Two-Part Strategy Using Genomic Selection Develop Inbred Lines.” Crop Science, 57(5), 2372--2386. ISSN 0011-183X, doi:10.2135/cropsci2016.09.0742 , https://acsess.onlinelibrary.wiley.com/doi/full/10.2135/cropsci2016.09.0742. Hickey JM, Dreisigacker S, Crossa J, Hearne S, Babu R, Prasanna BM, Grondona M, Zambelli , Windhausen VS, Mathews K, Gorjanc G (2014). “Evaluation Genomic Selection Training Population Designs Genotyping Strategies Plant Breeding Programs Using Simulation.” Crop Science, 54(4), 1476-1488. doi:10.2135/cropsci2013.03.0195 . MacLeod IM, Larkin DM, Lewin HA, Hayes BJ, Goddard (2013). “Inferring Demography Runs Homozygosity Whole-Genome Sequence, Correction Sequence Errors.” Molecular Biology Evolution, 30(9), 2209–2223. doi:10.1093/molbev/mst125 .","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/runMacs.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create founder haplotypes using MaCS — runMacs","text":"","code":"# Creates a populations of 10 outbred individuals # Their genome consists of 1 chromosome and 100 segregating sites if (FALSE) { founderPop = runMacs(nInd=10,nChr=1,segSites=100) }"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/runMacs2.html","id":null,"dir":"Reference","previous_headings":"","what":"Alternative wrapper for MaCS — runMacs2","title":"Alternative wrapper for MaCS — runMacs2","text":"wrapper function runMacs. wrapper designed  provide intuitive interface writing custom commands MaCS (Chen et al. 2009) . effectively automates creation  appropriate line manualCommand argument runMacs  using user supplied variables, allows subset functionality  offered argument. default arguments function chosen match  species=\"GENERIC\" runMacs.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/runMacs2.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Alternative wrapper for MaCS — runMacs2","text":"","code":"runMacs2(   nInd,   nChr = 1,   segSites = NULL,   Ne = 100,   bp = 1e+08,   genLen = 1,   mutRate = 2.5e-08,   histNe = c(500, 1500, 6000, 12000, 1e+05),   histGen = c(100, 1000, 10000, 1e+05, 1e+06),   inbred = FALSE,   split = NULL,   ploidy = 2L,   returnCommand = FALSE,   nThreads = NULL )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/runMacs2.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Alternative wrapper for MaCS — runMacs2","text":"nInd number individuals simulate nChr number chromosomes simulate segSites number segregating sites keep per chromosome Ne effective population size bp base pair length chromosome genLen genetic length chromosome Morgans mutRate per base pair mutation rate histNe effective population size previous  generations histGen number generations ago effective  population sizes given histNe inbred founder individuals inbred split optional historic population split terms generations ago ploidy ploidy level organism returnCommand command passed manualCommand  runMacs returned. TRUE, MaCS called  command returned instead. nThreads OpenMP available, allow simulating chromosomes parallel.  value NULL, number threads automatically detected.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/runMacs2.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Alternative wrapper for MaCS — runMacs2","text":"object MapPop-class  returnCommand true string giving MaCS command passed   manualCommand argument runMacs.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/runMacs2.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Alternative wrapper for MaCS — runMacs2","text":"Chen GK, Marjoram P, Wall JD (2009). “Fast Flexible Simulation DNA Sequence Data.” Genome Research, 19, 136-142. https://genome.cshlp.org/content/19/1/136.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/runMacs2.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Alternative wrapper for MaCS — runMacs2","text":"","code":"# Creates a populations of 10 outbred individuals # Their genome consists of 1 chromosome and 100 segregating sites # The command is equivalent to using species=\"GENERIC\" in runMacs if (FALSE) { founderPop = runMacs2(nInd=10,nChr=1,segSites=100) }"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/sampleHaplo.html","id":null,"dir":"Reference","previous_headings":"","what":"Sample haplotypes from a MapPop — sampleHaplo","title":"Sample haplotypes from a MapPop — sampleHaplo","text":"Creates new MapPop-class existing  MapPop-class randomly sampling haplotypes.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/sampleHaplo.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sample haplotypes from a MapPop — sampleHaplo","text":"","code":"sampleHaplo(mapPop, nInd, inbred = FALSE, ploidy = NULL, replace = TRUE)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/sampleHaplo.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sample haplotypes from a MapPop — sampleHaplo","text":"mapPop MapPop-class used  sample haplotypes nInd number individuals create inbred new individuals fully inbred ploidy new ploidy level organism. NULL,  ploidy level mapPop used. replace haplotypes sampled replacement","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/sampleHaplo.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Sample haplotypes from a MapPop — sampleHaplo","text":"object MapPop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/sampleHaplo.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Sample haplotypes from a MapPop — sampleHaplo","text":"","code":"founderPop = quickHaplo(nInd=2,nChr=1,segSites=11,inbred=TRUE) founderPop = sampleHaplo(mapPop=founderPop,nInd=20)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/selIndex.html","id":null,"dir":"Reference","previous_headings":"","what":"Selection index — selIndex","title":"Selection index — selIndex","text":"Calculates values selection index given trait values  weights. function intended used combination  selection functions working populations  selectInd.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/selIndex.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Selection index — selIndex","text":"","code":"selIndex(Y, b, scale = FALSE)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/selIndex.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Selection index — selIndex","text":"Y matrix trait values b vector weights scale Y scaled centered","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/selIndex.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Selection index — selIndex","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L #Model two genetically correlated traits G = 1.5*diag(2)-0.5 #Genetic correlation matrix SP$addTraitA(10, mean=c(0,0), var=c(1,1), corA=G) SP$setVarE(h2=c(0.5,0.5))  #Create population pop = newPop(founderPop, simParam=SP)  #Calculate Smith-Hazel weights econWt = c(1, 1) b = smithHazel(econWt, varG(pop), varP(pop))  #Selection 2 best individuals using Smith-Hazel index #selIndex is used as a trait pop2 = selectInd(pop, nInd=2, trait=selIndex,                   simParam=SP, b=b)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/selInt.html","id":null,"dir":"Reference","previous_headings":"","what":"Selection intensity — selInt","title":"Selection intensity — selInt","text":"Calculates standardized selection intensity","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/selInt.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Selection intensity — selInt","text":"","code":"selInt(p)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/selInt.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Selection intensity — selInt","text":"p proportion individuals selected","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/selInt.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Selection intensity — selInt","text":"","code":"selInt(0.1) #> [1] 1.754983"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/selectCross.html","id":null,"dir":"Reference","previous_headings":"","what":"Select and randomly cross — selectCross","title":"Select and randomly cross — selectCross","text":"wrapper combines functionalities randCross selectInd. purpose wrapper combine selection crossing one function call minimized amount intermediate populations created. reduces RAM usage simplifies code writing. Note wrapper provide full functionality either function.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/selectCross.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Select and randomly cross — selectCross","text":"","code":"selectCross(   pop,   nInd = NULL,   nFemale = NULL,   nMale = NULL,   nCrosses,   nProgeny = 1,   trait = 1,   use = \"pheno\",   selectTop = TRUE,   simParam = NULL,   ...,   balance = TRUE )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/selectCross.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Select and randomly cross — selectCross","text":"pop object Pop-class nInd number individuals select. individuals selected without regards sex supercedes values nFemale nMale. Thus simulation uses sexes, likely better leave value NULL use nFemale nMale instead. nFemale number females select. value ignored nInd set. nMale number males select. value ignored nInd set. nCrosses total number crosses make nProgeny number progeny per cross trait trait selection. Either number indicating single trait function returning vector length nInd. use select genetic values \"gv\", estimated breeding values \"ebv\", breeding values \"bv\", phenotypes \"pheno\", randomly \"rand\" selectTop selects highest values true. Selects lowest values false. simParam object SimParam ... additional arguments using function trait balance using sexes, option balance number progeny per parent. argument occurs ..., argument name must matched exactly.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/selectCross.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Select and randomly cross — selectCross","text":"Returns object Pop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/selectCross.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Select and randomly cross — selectCross","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitA(10) SP$setVarE(h2=0.5)  #Create population pop = newPop(founderPop, simParam=SP)  #Select 4 individuals and make 8 crosses pop2 = selectCross(pop, nInd=4, nCrosses=8, simParam=SP)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/selectFam.html","id":null,"dir":"Reference","previous_headings":"","what":"Select families — selectFam","title":"Select families — selectFam","text":"Selects subset full-sib families population.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/selectFam.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Select families — selectFam","text":"","code":"selectFam(   pop,   nFam,   trait = 1,   use = \"pheno\",   sex = \"B\",   famType = \"B\",   selectTop = TRUE,   returnPop = TRUE,   candidates = NULL,   simParam = NULL,   ... )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/selectFam.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Select families — selectFam","text":"pop object Pop-class, HybridPop-class MultiPop-class nFam number families select trait trait selection. Either number indicating single trait function returning vector length nInd. function must work vector matrix use values. See examples selectInd selIndex. use select genetic values \"gv\", estimated breeding values \"ebv\", breeding values \"bv\", phenotypes \"pheno\", randomly \"rand\" sex sex select. Use \"B\" , \"F\" females \"M\" males. simulation using sexes, argument ignored. famType type family select. Use \"B\" full-sib families, \"F\" half-sib families female side \"M\" half-sib families male side. selectTop selects highest values true. Selects lowest values false. returnPop results returned Pop-class. FALSE, index selected individuals returned. candidates optional vector eligible selection candidates. simParam object SimParam ... additional arguments using function trait","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/selectFam.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Select families — selectFam","text":"Returns object Pop-class, HybridPop-class MultiPop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/selectFam.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Select families — selectFam","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitA(10) SP$setVarE(h2=0.5)  #Create population pop = newPop(founderPop, simParam=SP)  #Create 3 biparental families with 10 progeny pop2 = randCross(pop, nCrosses=3, nProgeny=10, simParam=SP)  #Select best 2 families pop3 = selectFam(pop2, 2, simParam=SP)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/selectInd.html","id":null,"dir":"Reference","previous_headings":"","what":"Select individuals — selectInd","title":"Select individuals — selectInd","text":"Selects subset nInd individuals population.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/selectInd.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Select individuals — selectInd","text":"","code":"selectInd(   pop,   nInd,   trait = 1,   use = \"pheno\",   sex = \"B\",   selectTop = TRUE,   returnPop = TRUE,   candidates = NULL,   simParam = NULL,   ... )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/selectInd.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Select individuals — selectInd","text":"pop object Pop-class, HybridPop-class MultiPop-class nInd number individuals select trait trait selection. Either number indicating single trait function returning vector length nInd. function must work vector matrix use values. See examples selIndex. use select genetic values \"gv\", estimated breeding values \"ebv\", breeding values \"bv\", phenotypes \"pheno\", randomly \"rand\" sex sex select. Use \"B\" , \"F\" females \"M\" males. simulation using sexes, argument ignored. selectTop selects highest values true. Selects lowest values false. returnPop results returned Pop-class. FALSE, index selected individuals returned. candidates optional vector eligible selection candidates. simParam object SimParam ... additional arguments using function trait","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/selectInd.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Select individuals — selectInd","text":"Returns object Pop-class, HybridPop-class MultiPop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/selectInd.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Select individuals — selectInd","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitA(10) SP$setVarE(h2=0.5)  #Create population pop = newPop(founderPop, simParam=SP)  #Select top 5 (directional selection) pop2 = selectInd(pop, 5, simParam=SP) hist(pop@pheno); abline(v = pop@pheno, lwd = 2) abline(v = pop2@pheno, col = \"red\", lwd = 2)   #Select 5 most deviating from an optima (disruptive selection) squaredDeviation = function(x, optima = 0) (x - optima)^2 pop3 = selectInd(pop, 5, simParam=SP, trait = squaredDeviation, selectTop = TRUE) hist(pop@pheno); abline(v = pop@pheno, lwd = 2) abline(v = pop3@pheno, col = \"red\", lwd = 2)   #Select 5 least deviating from an optima (stabilising selection) pop4 = selectInd(pop, 5, simParam=SP, trait = squaredDeviation, selectTop = FALSE) hist(pop@pheno); abline(v = pop@pheno, lwd = 2) abline(v = pop4@pheno, col = \"red\", lwd = 2)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/selectOP.html","id":null,"dir":"Reference","previous_headings":"","what":"Select open pollinating plants — selectOP","title":"Select open pollinating plants — selectOP","text":"function models selection open pollinating plant population. allows varying percentage selfing. function also provides option modeling selection occuring pollination.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/selectOP.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Select open pollinating plants — selectOP","text":"","code":"selectOP(   pop,   nInd,   nSeeds,   probSelf = 0,   pollenControl = FALSE,   trait = 1,   use = \"pheno\",   selectTop = TRUE,   candidates = NULL,   simParam = NULL,   ... )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/selectOP.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Select open pollinating plants — selectOP","text":"pop object Pop-class MultiPop-class nInd number plants select nSeeds number seeds per plant probSelf percentage seeds expected selfing. Value ranges 0 1. pollenControl plants selected pollination trait trait selection. Either number indicating single trait function returning vector length nInd. function must work vector matrix use values. See examples selectInd selIndex. use select genetic values \"gv\", estimated breeding values \"ebv\", breeding values \"bv\", phenotypes \"pheno\", randomly \"rand\" selectTop selects highest values true. Selects lowest values false. candidates optional vector eligible selection candidates. simParam object SimParam ... additional arguments using function trait","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/selectOP.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Select open pollinating plants — selectOP","text":"Returns object Pop-class MultiPop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/selectOP.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Select open pollinating plants — selectOP","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitA(10) SP$setVarE(h2=0.5)  #Create population pop = newPop(founderPop, simParam=SP)  #Create new population by selecting the best 3 plant #Assuming 50% selfing in plants and 10 seeds per plant pop2 = selectOP(pop, nInd=3, nSeeds=10, probSelf=0.5, simParam=SP)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/selectWithinFam.html","id":null,"dir":"Reference","previous_headings":"","what":"Select individuals within families — selectWithinFam","title":"Select individuals within families — selectWithinFam","text":"Selects subset nInd individuals full-sib family within population. return individuals full-sib family less equal nInd individuals.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/selectWithinFam.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Select individuals within families — selectWithinFam","text":"","code":"selectWithinFam(   pop,   nInd,   trait = 1,   use = \"pheno\",   sex = \"B\",   famType = \"B\",   selectTop = TRUE,   returnPop = TRUE,   candidates = NULL,   simParam = NULL,   ... )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/selectWithinFam.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Select individuals within families — selectWithinFam","text":"pop object Pop-class, HybridPop-class MultiPop-class nInd number individuals select within family trait trait selection. Either number indicating single trait function returning vector length nInd. function must work vector matrix use values. See examples selectInd selIndex. use select genetic values \"gv\", estimated breeding values \"ebv\", breeding values \"bv\", phenotypes \"pheno\", randomly \"rand\" sex sex select. Use \"B\" , \"F\" females \"M\" males. simulation using sexes, argument ignored. famType type family select. Use \"B\" full-sib families, \"F\" half-sib families female side \"M\" half-sib families male side. selectTop selects highest values true. Selects lowest values false. returnPop results returned Pop-class. FALSE, index selected individuals returned. candidates optional vector eligible selection candidates. simParam object SimParam ... additional arguments using function trait","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/selectWithinFam.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Select individuals within families — selectWithinFam","text":"Returns object Pop-class, HybridPop-class MultiPop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/selectWithinFam.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Select individuals within families — selectWithinFam","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitA(10) SP$setVarE(h2=0.5)  #Create population pop = newPop(founderPop, simParam=SP)  #Create 3 biparental families with 10 progeny pop2 = randCross(pop, nCrosses=3, nProgeny=10, simParam=SP)  #Select best individual per family pop3 = selectWithinFam(pop2, 1, simParam=SP)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/self.html","id":null,"dir":"Reference","previous_headings":"","what":"Self individuals — self","title":"Self individuals — self","text":"Creates selfed progeny individual population. works sexes \"\".","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/self.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Self individuals — self","text":"","code":"self(pop, nProgeny = 1, parents = NULL, keepParents = TRUE, simParam = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/self.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Self individuals — self","text":"pop object Pop-class nProgeny total number selfed progeny per individual parents optional vector indices allowable parents keepParents previous parents used mother father. simParam object SimParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/self.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Self individuals — self","text":"Returns object Pop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/self.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Self individuals — self","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=2, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L  #Create population pop = newPop(founderPop, simParam=SP)  #Self pollinate each individual pop2 = self(pop, simParam=SP)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/setEBV.html","id":null,"dir":"Reference","previous_headings":"","what":"Set EBV — setEBV","title":"Set EBV — setEBV","text":"Adds genomic estimated values populations's EBV  slot using output genomic selection functions.  genomic estimated values can either estimated  breeding values, estimated genetic values,  estimated general combining values.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/setEBV.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set EBV — setEBV","text":"","code":"setEBV(   pop,   solution,   value = \"gv\",   targetPop = NULL,   append = FALSE,   simParam = NULL )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/setEBV.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set EBV — setEBV","text":"pop object Pop-class solution object RRsol-class value genomic value estimated. Can  either \"gv\", \"bv\", \"female\", \"male\". targetPop optional target population can  used value \"bv\", \"female\", \"male\".  supplied, allele frequency targetPop used  set values. append estimated values appended  existing data EBV slot. TRUE, new column  added. FALSE, existing data replaced  new estimates. simParam object SimParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/setEBV.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set EBV — setEBV","text":"Returns object Pop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/setEBV.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set EBV — setEBV","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=20)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitA(10) SP$setVarE(h2=0.5) SP$addSnpChip(10)  #Create population pop = newPop(founderPop, simParam=SP)  #Run GS model and set EBV ans = RRBLUP(pop, simParam=SP) pop = setEBV(pop, ans, simParam=SP)  #Evaluate accuracy cor(gv(pop), ebv(pop)) #>        est_GV_Trait1 #> Trait1     0.6280871"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/setMarkerHaplo.html","id":null,"dir":"Reference","previous_headings":"","what":"Set marker haplotypes — setMarkerHaplo","title":"Set marker haplotypes — setMarkerHaplo","text":"Manually sets haplotypes population  individuals one loci.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/setMarkerHaplo.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set marker haplotypes — setMarkerHaplo","text":"","code":"setMarkerHaplo(pop, haplo, simParam = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/setMarkerHaplo.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set marker haplotypes — setMarkerHaplo","text":"pop object RawPop-class MapPop-class haplo matrix haplotypes, see details simParam object SimParam,  used pop MapPop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/setMarkerHaplo.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set marker haplotypes — setMarkerHaplo","text":"object class \"pop\" input","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/setMarkerHaplo.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Set marker haplotypes — setMarkerHaplo","text":"format haplotype matrix match  format output pullMarkerHaplo option haplo=\"\". Thus, recommended  function first used extract haplotypes  desired changes made output pullMarkerHaplo  passing matrix setMarkerHaplo. changes made QTL  may potentially result changes individuals genetic  value. changes reflected gv /gxe slot.  slots remain unchanged, ebv pheno slots  reflect new genotypes.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/setMarkerHaplo.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set marker haplotypes — setMarkerHaplo","text":"","code":"# Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=15)  # Extract haplotypes for marker \"1_1\" H = pullMarkerHaplo(founderPop, markers=\"1_1\")  # Set the first haplotype to 1 H[1,1] = 1L  # Set marker haplotypes founderPop = setMarkerHaplo(founderPop, haplo=H)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/setMisc.html","id":null,"dir":"Reference","previous_headings":"","what":"Set miscelaneous information in a population — setMisc","title":"Set miscelaneous information in a population — setMisc","text":"Set miscelaneous information population","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/setMisc.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set miscelaneous information in a population — setMisc","text":"","code":"setMisc(x, node = NULL, value = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/setMisc.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set miscelaneous information in a population — setMisc","text":"x Pop-class node character, name node set within x@misc slot value, value saved x@misc[[*]][[node]]; length value equal nInd(x); length 1, repeated using rep (see examples)","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/setMisc.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set miscelaneous information in a population — setMisc","text":"Pop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/setMisc.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Set miscelaneous information in a population — setMisc","text":"NULL value ignored","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/setPheno.html","id":null,"dir":"Reference","previous_headings":"","what":"Set phenotypes — setPheno","title":"Set phenotypes — setPheno","text":"Sets phenotypes traits adding random error multivariate normal distribution.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/setPheno.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set phenotypes — setPheno","text":"","code":"setPheno(   pop,   h2 = NULL,   H2 = NULL,   varE = NULL,   corE = NULL,   reps = 1,   fixEff = 1L,   p = NULL,   onlyPheno = FALSE,   traits = NULL,   simParam = NULL )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/setPheno.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set phenotypes — setPheno","text":"pop object Pop-class HybridPop-class h2 vector desired narrow-sense heritabilities trait. See details. H2 vector desired broad-sense heritabilities trait. See details. varE error (co)variances traits. See details. corE optional matrix correlations errors. See details. reps number replications phenotype. See details. fixEff fixed effect assign population. Used genomic selection models . p p-value environmental covariate used GxE traits. NULL, value sampled random. onlyPheno phenotype returned, see return traits integer vector indicate traits set. NULL, traits set. simParam object SimParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/setPheno.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set phenotypes — setPheno","text":"Returns object Pop-class HybridPop-class onlyPheno=FALSE, onlyPheno=TRUE matrix returned","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/setPheno.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Set phenotypes — setPheno","text":"three arguments setting error variance phenotype: h2, H2, varE. user use one arguments. user supplies values one, one used according order listed . h2 argument allows user specify error variance according narrow-sense heritability. calculation uses additive genetic variance total genetic variance founder population. Thus, heritability relates founder population current population. H2 argument allows user specify error variance according broad-sense heritability. calculation uses total genetic variance founder population. Thus, heritability relates founder population current population. varE argument allows user specify error variance directly. user may supply vector describing error variance trait supply matrix specify covariance errors. corE argument allows user specify correlations error covariance matrix. correlations supplied addition h2, H2, varE arguments. correlations used construct covariance matrix vector variances. user supplied covariance matrix varE, correlations supercede values provided matrix. reps parameter convenient representation replicated data. intended represent replicated yield trials plant breeding programs. case, varE set plot error reps set number plots per entry. resulting phenotype represents entry-means.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/setPheno.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set phenotypes — setPheno","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitA(10)  #Create population pop = newPop(founderPop, simParam=SP)  #Add phenotype with error variance of 1 pop = setPheno(pop, varE=1) #> Error in get(\"SP\", envir = .GlobalEnv): object 'SP' not found"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/setPhenoGCA.html","id":null,"dir":"Reference","previous_headings":"","what":"Set GCA as phenotype — setPhenoGCA","title":"Set GCA as phenotype — setPhenoGCA","text":"Calculates general combining ability set testers returns values phenotypes population.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/setPhenoGCA.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set GCA as phenotype — setPhenoGCA","text":"","code":"setPhenoGCA(   pop,   testers,   use = \"pheno\",   h2 = NULL,   H2 = NULL,   varE = NULL,   corE = NULL,   reps = 1,   fixEff = 1L,   p = NULL,   inbred = FALSE,   onlyPheno = FALSE,   simParam = NULL )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/setPhenoGCA.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set GCA as phenotype — setPhenoGCA","text":"pop object Pop-class testers object Pop-class use true genetic value (gv) phenotypes (pheno, default) h2 vector desired narrow-sense heritabilities trait. See details setPheno. H2 vector desired broad-sense heritabilities trait. See details setPheno. varE error (co)variances traits. See details setPheno. corE optional matrix correlations errors. See details setPheno. reps number replications phenotype. See details setPheno. fixEff fixed effect assign population. Used genomic selection models . p p-value environmental covariate used GxE traits. NULL, value sampled random. inbred pop testers fully inbred. fully inbred created newPop using inbred founders makeDH function onlyPheno phenotype returned, see return simParam object SimParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/setPhenoGCA.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set GCA as phenotype — setPhenoGCA","text":"Returns object Pop-class matrix onlyPheno=TRUE","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/setPhenoGCA.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set GCA as phenotype — setPhenoGCA","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10, inbred=TRUE)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitA(10)  #Create population pop = newPop(founderPop, simParam=SP)  #Set phenotype to average per pop2 = setPhenoGCA(pop, pop, use=\"gv\", inbred=TRUE, simParam=SP)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/setPhenoProgTest.html","id":null,"dir":"Reference","previous_headings":"","what":"Set progeny test as phenotype — setPhenoProgTest","title":"Set progeny test as phenotype — setPhenoProgTest","text":"Models progeny test individuals 'pop'. Returns 'pop' phenotype representing average performance progeny. phenotype generated mating individuals 'pop' randomly chosen individuals testPop number times equal 'nMatePerInd'.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/setPhenoProgTest.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set progeny test as phenotype — setPhenoProgTest","text":"","code":"setPhenoProgTest(   pop,   testPop,   nMatePerInd = 1L,   use = \"pheno\",   h2 = NULL,   H2 = NULL,   varE = NULL,   corE = NULL,   reps = 1,   fixEff = 1L,   p = NULL,   onlyPheno = FALSE,   simParam = NULL )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/setPhenoProgTest.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set progeny test as phenotype — setPhenoProgTest","text":"pop object Pop-class testPop object Pop-class nMatePerInd number times individual 'pop' mated individual testPop use true genetic value (gv) phenotypes (pheno, default) h2 vector desired narrow-sense heritabilities trait. See details setPheno. H2 vector desired broad-sense heritabilities trait. See details setPheno. varE error (co)variances traits. See details setPheno. corE optional matrix correlations errors. See details setPheno. reps number replications phenotype. See details setPheno. fixEff fixed effect assign population. Used genomic selection models . p p-value environmental covariate used GxE traits. NULL, value sampled random. onlyPheno phenotype returned, see return simParam object SimParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/setPhenoProgTest.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set progeny test as phenotype — setPhenoProgTest","text":"Returns object Pop-class matrix onlyPheno=TRUE","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/setPhenoProgTest.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Set progeny test as phenotype — setPhenoProgTest","text":"reps parameter convenient representation replicated data. intended representation replicated yield trials plant breeding programs. case, varE set plot error reps set number plots per entry. resulting phenotype reflect mean replications.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/setPhenoProgTest.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set progeny test as phenotype — setPhenoProgTest","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10, inbred=TRUE)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitA(10)  #Create two populations of 5 individuals pop1 = newPop(founderPop[1:5], simParam=SP) pop2 = newPop(founderPop[6:10], simParam=SP)  #Set phenotype according to a progeny test pop3 = setPhenoProgTest(pop1, pop2, use=\"gv\", simParam=SP)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/smithHazel.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate Smith-Hazel weights — smithHazel","title":"Calculate Smith-Hazel weights — smithHazel","text":"Calculates weights Smith-Hazel index given economice weights  phenotypic genotypic variance-covariance matrices.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/smithHazel.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate Smith-Hazel weights — smithHazel","text":"","code":"smithHazel(econWt, varG, varP)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/smithHazel.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate Smith-Hazel weights — smithHazel","text":"econWt vector economic weights varG genetic variance-covariance matrix varP phenotypic variance-covariance matrix","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/smithHazel.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate Smith-Hazel weights — smithHazel","text":"vector weight calculating index values","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/smithHazel.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate Smith-Hazel weights — smithHazel","text":"","code":"G = 1.5*diag(2)-0.5 E = diag(2) P = G+E wt = c(1,1) smithHazel(wt, G, P) #>           [,1] #> [1,] 0.3333333 #> [2,] 0.3333333"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/solveMKM.html","id":null,"dir":"Reference","previous_headings":"","what":"Solve Multikernel Model — solveMKM","title":"Solve Multikernel Model — solveMKM","text":"Solves univariate mixed model multiple random effects.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/solveMKM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Solve Multikernel Model — solveMKM","text":"","code":"solveMKM(y, X, Zlist, Klist, maxIter = 40L, tol = 1e-04)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/solveMKM.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Solve Multikernel Model — solveMKM","text":"y matrix n rows 1 column X matrix n rows x columns Zlist list Z matrices Klist list K matrices maxIter maximum number iteration tol tolerance convergence","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/solveMVM.html","id":null,"dir":"Reference","previous_headings":"","what":"Solve Multivariate Model — solveMVM","title":"Solve Multivariate Model — solveMVM","text":"Solves multivariate mixed model form \\(Y=X\\beta+Zu+e\\)","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/solveMVM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Solve Multivariate Model — solveMVM","text":"","code":"solveMVM(Y, X, Z, K, tol = 1e-06, maxIter = 1000L)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/solveMVM.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Solve Multivariate Model — solveMVM","text":"Y matrix n rows q columns X matrix n rows x columns Z matrix n rows m columns K matrix m rows m columns tol tolerance convergence maxIter maximum number iteration","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/solveRRBLUP.html","id":null,"dir":"Reference","previous_headings":"","what":"Solve RR-BLUP — solveRRBLUP","title":"Solve RR-BLUP — solveRRBLUP","text":"Solves univariate mixed model form \\(y=X\\beta+Mu+e\\)","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/solveRRBLUP.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Solve RR-BLUP — solveRRBLUP","text":"","code":"solveRRBLUP(y, X, M)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/solveRRBLUP.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Solve RR-BLUP — solveRRBLUP","text":"y matrix n rows 1 column X matrix n rows x columns M matrix n rows m columns","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/solveRRBLUPMK.html","id":null,"dir":"Reference","previous_headings":"","what":"Solve Multikernel RR-BLUP — solveRRBLUPMK","title":"Solve Multikernel RR-BLUP — solveRRBLUPMK","text":"Solves univariate mixed model multiple random effects.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/solveRRBLUPMK.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Solve Multikernel RR-BLUP — solveRRBLUPMK","text":"","code":"solveRRBLUPMK(y, X, Mlist, maxIter = 40L)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/solveRRBLUPMK.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Solve Multikernel RR-BLUP — solveRRBLUPMK","text":"y matrix n rows 1 column X matrix n rows x columns Mlist list M matrices maxIter maximum number iteration","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/solveRRBLUPMV.html","id":null,"dir":"Reference","previous_headings":"","what":"Solve Multivariate RR-BLUP — solveRRBLUPMV","title":"Solve Multivariate RR-BLUP — solveRRBLUPMV","text":"Solves multivariate mixed model form \\(Y=X\\beta+Mu+e\\)","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/solveRRBLUPMV.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Solve Multivariate RR-BLUP — solveRRBLUPMV","text":"","code":"solveRRBLUPMV(Y, X, M, maxIter = 1000L, tol = 1e-06)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/solveRRBLUPMV.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Solve Multivariate RR-BLUP — solveRRBLUPMV","text":"Y matrix n rows q columns X matrix n rows x columns M matrix n rows m columns maxIter maximum number iteration tol tolerance convergence","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/solveRRBLUP_EM.html","id":null,"dir":"Reference","previous_headings":"","what":"Solve RR-BLUP with EM — solveRRBLUP_EM","title":"Solve RR-BLUP with EM — solveRRBLUP_EM","text":"Solves univariate mixed model form \\(y=X\\beta+Mu+e\\) using Expectation-Maximization algorithm.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/solveRRBLUP_EM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Solve RR-BLUP with EM — solveRRBLUP_EM","text":"","code":"solveRRBLUP_EM(Y, X, M, Vu, Ve, tol, maxIter, useEM)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/solveRRBLUP_EM.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Solve RR-BLUP with EM — solveRRBLUP_EM","text":"Y matrix n rows 1 column X matrix n rows x columns M matrix n rows m columns Vu initial guess variance marker effects Ve initial guess error variance tol tolerance declaring convergence maxIter maximum iteration attempting convergence useEM EM algorithm used. false, estimation variance components performed. initial values treated true.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/solveRRBLUP_EM2.html","id":null,"dir":"Reference","previous_headings":"","what":"Solve RR-BLUP with EM and 2 random effects — solveRRBLUP_EM2","title":"Solve RR-BLUP with EM and 2 random effects — solveRRBLUP_EM2","text":"Solves univariate mixed model form \\(y=X\\beta+M_1u_1+M_2u_2+e\\) using Expectation-Maximization algorithm.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/solveRRBLUP_EM2.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Solve RR-BLUP with EM and 2 random effects — solveRRBLUP_EM2","text":"","code":"solveRRBLUP_EM2(Y, X, M1, M2, Vu1, Vu2, Ve, tol, maxIter, useEM)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/solveRRBLUP_EM2.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Solve RR-BLUP with EM and 2 random effects — solveRRBLUP_EM2","text":"Y matrix n rows 1 column X matrix n rows x columns M1 matrix n rows m1 columns M2 matrix n rows m2 columns Vu1 initial guess variance first marker effects Vu2 initial guess variance second marker effects Ve initial guess error variance tol tolerance declaring convergence maxIter maximum iteration attempting convergence useEM EM algorithm used. false, estimation variance components performed. initial values treated true.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/solveRRBLUP_EM3.html","id":null,"dir":"Reference","previous_headings":"","what":"Solve RR-BLUP with EM and 3 random effects — solveRRBLUP_EM3","title":"Solve RR-BLUP with EM and 3 random effects — solveRRBLUP_EM3","text":"Solves univariate mixed model form \\(y=X\\beta+M_1u_1+M_2u_2+M_3u_3+e\\) using Expectation-Maximization algorithm.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/solveRRBLUP_EM3.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Solve RR-BLUP with EM and 3 random effects — solveRRBLUP_EM3","text":"","code":"solveRRBLUP_EM3(Y, X, M1, M2, M3, Vu1, Vu2, Vu3, Ve, tol, maxIter, useEM)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/solveRRBLUP_EM3.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Solve RR-BLUP with EM and 3 random effects — solveRRBLUP_EM3","text":"Y matrix n rows 1 column X matrix n rows x columns M1 matrix n rows m1 columns M2 matrix n rows m2 columns M3 matrix n rows m3 columns Vu1 initial guess variance first marker effects Vu2 initial guess variance second marker effects Vu3 initial guess variance second marker effects Ve initial guess error variance tol tolerance declaring convergence maxIter maximum iteration attempting convergence useEM EM algorithm used. false, estimation variance components performed. initial values treated true.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/solveUVM.html","id":null,"dir":"Reference","previous_headings":"","what":"Solve Univariate Model — solveUVM","title":"Solve Univariate Model — solveUVM","text":"Solves univariate mixed model form \\(y=X\\beta+Zu+e\\)","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/solveUVM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Solve Univariate Model — solveUVM","text":"","code":"solveUVM(y, X, Z, K)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/solveUVM.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Solve Univariate Model — solveUVM","text":"y matrix n rows 1 column X matrix n rows x columns Z matrix n rows m columns K matrix m rows m columns","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/transMat.html","id":null,"dir":"Reference","previous_headings":"","what":"Linear transformation matrix — transMat","title":"Linear transformation matrix — transMat","text":"Creates m m linear transformation matrix  can applied n m uncorrelated deviates  sampled standard normal distribution produce correlated deviates arbitrary correlation  R. R positive semi-definite, function  returns smoothing returns warning (see details).","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/transMat.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Linear transformation matrix — transMat","text":"","code":"transMat(R)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/transMat.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Linear transformation matrix — transMat","text":"R correlation matrix","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/transMat.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Linear transformation matrix — transMat","text":"eigendecomposition applied correlation  matrix used test positive semi-definite.  matrix positive semi-definite,  valid correlation matrix. case, smoothing  applied matrix (described 'cor.smooth'  'psych' library) obtain valid correlation matrix.  resulting deviates thus exactly match  desired correlation, hopefully close  input matrix far removed valid  correlation matrix.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/transMat.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Linear transformation matrix — transMat","text":"","code":"# Create an 2x2 correlation matrix R = 0.5*diag(2) + 0.5  # Sample 1000 uncorrelated deviates from a  # bivariate standard normal distribution X = matrix(rnorm(2*1000), ncol=2)  # Compute the transformation matrix T = transMat(R)  # Apply the transformation to the deviates Y = X%*%T  # Measure the sample correlation cor(Y) #>           [,1]      [,2] #> [1,] 1.0000000 0.5236831 #> [2,] 0.5236831 1.0000000"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/usefulness.html","id":null,"dir":"Reference","previous_headings":"","what":"Usefulness criterion — usefulness","title":"Usefulness criterion — usefulness","text":"Calculates usefulness criterion","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/usefulness.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Usefulness criterion — usefulness","text":"","code":"usefulness(   pop,   trait = 1,   use = \"gv\",   p = 0.1,   selectTop = TRUE,   simParam = NULL,   ... )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/usefulness.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Usefulness criterion — usefulness","text":"pop object Pop-class  HybridPop-class trait trait selection. Either number indicating  single trait function returning vector length nInd. use select genetic values (gv, default), estimated breeding values (ebv), breeding values (bv),  phenotypes (pheno) p proportion individuals selected selectTop selects highest values true.  Selects lowest values false. simParam object SimParam ... additional arguments using function  trait","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/usefulness.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Usefulness criterion — usefulness","text":"Returns numeric value","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/usefulness.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Usefulness criterion — usefulness","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=2, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$nThreads = 1L SP$addTraitA(10)  #Create population pop = newPop(founderPop, simParam=SP)  #Determine usefulness of population  usefulness(pop, simParam=SP) #> [1] 1  #Should be equivalent to GV of best individual max(gv(pop)) #> [1] 1"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/varA.html","id":null,"dir":"Reference","previous_headings":"","what":"Additive variance — varA","title":"Additive variance — varA","text":"Returns additive variance traits","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/varA.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Additive variance — varA","text":"","code":"varA(pop, simParam = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/varA.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Additive variance — varA","text":"pop object Pop-class simParam object SimParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/varA.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Additive variance — varA","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$addTraitAD(10, meanDD=0.5) SP$setVarE(h2=0.5) SP$nThreads = 1L  #Create population pop = newPop(founderPop, simParam=SP) varA(pop, simParam=SP) #>        Trait1 #> Trait1      1"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/varAA.html","id":null,"dir":"Reference","previous_headings":"","what":"Additive-by-additive epistatic variance — varAA","title":"Additive-by-additive epistatic variance — varAA","text":"Returns additive--additive epistatic variance traits","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/varAA.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Additive-by-additive epistatic variance — varAA","text":"","code":"varAA(pop, simParam = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/varAA.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Additive-by-additive epistatic variance — varAA","text":"pop object Pop-class simParam object SimParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/varAA.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Additive-by-additive epistatic variance — varAA","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$addTraitAD(10, meanDD=0.5) SP$setVarE(h2=0.5) SP$nThreads = 1L  #Create population pop = newPop(founderPop, simParam=SP) varAA(pop, simParam=SP) #>        Trait1 #> Trait1      0"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/varD.html","id":null,"dir":"Reference","previous_headings":"","what":"Dominance variance — varD","title":"Dominance variance — varD","text":"Returns dominance variance traits","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/varD.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Dominance variance — varD","text":"","code":"varD(pop, simParam = NULL)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/varD.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Dominance variance — varD","text":"pop object Pop-class simParam object SimParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/varD.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Dominance variance — varD","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$addTraitAD(10, meanDD=0.5) SP$setVarE(h2=0.5) SP$nThreads = 1L  #Create population pop = newPop(founderPop, simParam=SP) varD(pop, simParam=SP) #>            Trait1 #> Trait1 0.07623885"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/varG.html","id":null,"dir":"Reference","previous_headings":"","what":"Total genetic variance — varG","title":"Total genetic variance — varG","text":"Returns total genetic variance traits","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/varG.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Total genetic variance — varG","text":"","code":"varG(pop)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/varG.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Total genetic variance — varG","text":"pop object Pop-class HybridPop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/varG.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Total genetic variance — varG","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$addTraitA(10) SP$setVarE(h2=0.5) SP$nThreads = 1L  #Create population pop = newPop(founderPop, simParam=SP) varG(pop) #>        Trait1 #> Trait1      1"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/varP.html","id":null,"dir":"Reference","previous_headings":"","what":"Phenotypic variance — varP","title":"Phenotypic variance — varP","text":"Returns phenotypic variance traits","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/varP.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Phenotypic variance — varP","text":"","code":"varP(pop)"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/varP.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Phenotypic variance — varP","text":"pop object Pop-class HybridPop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/varP.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Phenotypic variance — varP","text":"","code":"#Create founder haplotypes founderPop = quickHaplo(nInd=10, nChr=1, segSites=10)  #Set simulation parameters SP = SimParam$new(founderPop) SP$addTraitA(10) SP$setVarE(h2=0.5) SP$nThreads = 1L  #Create population pop = newPop(founderPop, simParam=SP) varP(pop) #>          Trait1 #> Trait1 2.106527"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/writePlink.html","id":null,"dir":"Reference","previous_headings":"","what":"Writes a Pop-class as PLINK files — writePlink","title":"Writes a Pop-class as PLINK files — writePlink","text":"Writes Pop-class PLINK PED MAP files. arguments  function chosen consistency  RRBLUP2. base pair coordinate locus position stored AlphaSimR actual base pair  position. AlphaSimR track base pair  positions, relative positions loci used  simulation.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/writePlink.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Writes a Pop-class as PLINK files — writePlink","text":"","code":"writePlink(   pop,   baseName,   traits = 1,   use = \"pheno\",   snpChip = 1,   useQtl = FALSE,   simParam = NULL,   ... )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/writePlink.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Writes a Pop-class as PLINK files — writePlink","text":"pop object Pop-class baseName basename PED MAP files. traits integer indicating trait write, trait name, function traits returning single value. use use PLINK's phenotype field. Either phenotypes \"pheno\",  genetic values \"gv\", estimated breeding values \"ebv\", breeding values \"bv\",  random values \"rand\". snpChip integer indicating SNP chip genotype  use useQtl QTL genotypes used instead SNP chip.  TRUE, snpChip specifies trait's QTL use, thus  QTL may match QTL underlying phenotype supplied traits. simParam object SimParam ... additional arguments using function  traits","code":""},{"path":[]},{"path":"https://gaynorr.github.io/AlphaSimR/reference/writeRecords.html","id":null,"dir":"Reference","previous_headings":"","what":"Write data records — writeRecords","title":"Write data records — writeRecords","text":"Saves population's phenotypic marker data directory.","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/reference/writeRecords.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Write data records — writeRecords","text":"","code":"writeRecords(   pop,   dir,   snpChip = 1,   useQtl = FALSE,   includeHaplo = FALSE,   append = TRUE,   simParam = NULL )"},{"path":"https://gaynorr.github.io/AlphaSimR/reference/writeRecords.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Write data records — writeRecords","text":"pop object Pop-class dir path directory saving output snpChip SNP chip genotype save. useQtl=TRUE, value indicate trait's QTL genotype save. value 0 skip writing snpChip. useQtl QTL genotype written instead SNP chip genotypes. includeHaplo markers separated female male haplotypes. append true, new records added existing records. false, existing records deleted writing new records. Note delete files 'dir' directory. simParam object SimParam","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-153","dir":"Changelog","previous_headings":"","what":"AlphaSimR 1.5.3","title":"AlphaSimR 1.5.3","text":"*fixed bug SimParam$restrSegSites excluding sites end chromosome","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-152","dir":"Changelog","previous_headings":"","what":"AlphaSimR 1.5.2","title":"AlphaSimR 1.5.2","text":"CRAN release: 2023-11-01 *fix SimParam examples CRAN","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-151","dir":"Changelog","previous_headings":"","what":"AlphaSimR 1.5.1","title":"AlphaSimR 1.5.1","text":"*deleted bad example code setMisc *changed examples use single thread CRAN testing change shown documentation","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-150","dir":"Changelog","previous_headings":"","what":"AlphaSimR 1.5.0","title":"AlphaSimR 1.5.0","text":"*renamed MegaPop MultiPop *fixed bug writePlink correctly export map positions cM *fixed bug writeRecords due removed reps slot pops *added altAddTraitAD specifying traits dominance effects using dominance variance inbreeding depression *add miscPop slot class Pop","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-142","dir":"Changelog","previous_headings":"","what":"AlphaSimR 1.4.2","title":"AlphaSimR 1.4.2","text":"CRAN release: 2023-03-27 *updated MaCS citation https site","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-141","dir":"Changelog","previous_headings":"","what":"AlphaSimR 1.4.1","title":"AlphaSimR 1.4.1","text":"*Changed citation use bibentry instead citEntry","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-140","dir":"Changelog","previous_headings":"","what":"AlphaSimR 1.4.0","title":"AlphaSimR 1.4.0","text":"*fixed bug IBD tracking *add setFounderHap SimParam applying custom haplotypes founders *added addSnpChipByName SimParam defining SNP chips marker names","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-134","dir":"Changelog","previous_headings":"","what":"AlphaSimR 1.3.4","title":"AlphaSimR 1.3.4","text":"CRAN release: 2022-12-09 *changed C++ using sprintf use snprintf","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-133","dir":"Changelog","previous_headings":"","what":"AlphaSimR 1.3.3","title":"AlphaSimR 1.3.3","text":"*fixed bug calculation genic variance *fixed importHaplo passing ploidy newMapPop *fixed bug correlated error variances","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-132","dir":"Changelog","previous_headings":"","what":"AlphaSimR 1.3.2","title":"AlphaSimR 1.3.2","text":"CRAN release: 2022-11-02 *fixed column name bug multiple traits setEBV *fixed CTD caused runMacs many segSites requested *fixed missing names GV using resetPop *fixed bug importTrait *popVar now deals matrices 1 row","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-131","dir":"Changelog","previous_headings":"","what":"AlphaSimR 1.3.1","title":"AlphaSimR 1.3.1","text":"CRAN release: 2022-08-25 *updated link Gaynor, 2017","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-130","dir":"Changelog","previous_headings":"","what":"AlphaSimR 1.3.0","title":"AlphaSimR 1.3.0","text":"*added ability exclude loci name SimParam$restrSegSites *pullMarkerGeno pullMarkerHaplo now work MapPop class *added setMarkerHaplo manually change genotypes Pop MapPop *added addSegSite manually adding segregating sites MapPop class *simParam$setCorE deprecated favor corE argument simParam$setVarE *setPheno now takes corE argument *setPheno now allows user set phenotypes subset traits *add newEmptyPop create populations zero individuals *removed reps slot populations heterogeneous residual variance GS models *added h2, H2, corE setPhenoGCA setPhenoProgTest *“EUROPEAN” species history removed runMacs due lengthy runtime","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-122","dir":"Changelog","previous_headings":"","what":"AlphaSimR 1.2.2","title":"AlphaSimR 1.2.2","text":"*added getPed quick extract population’s pedigree *added getGenMap pull genetic map data.frame format","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-121","dir":"Changelog","previous_headings":"","what":"AlphaSimR 1.2.1","title":"AlphaSimR 1.2.1","text":"CRAN release: 2022-07-05 *fixed bugs relating importData functions *fixed writePlink errors longer requires equal length chromosomes","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-120","dir":"Changelog","previous_headings":"","what":"AlphaSimR 1.2.0","title":"AlphaSimR 1.2.0","text":"*added importGenMap format genetic maps AlphaSimR *added importInbredGeno importHaplo make easier create simulation external data *added importSnpChip, importTrait SimParam make easier manually define traits *added pullMarkerGeno pullMarkerHaplo make easier extract genotypes haplotypes specific loci without defining trait SNP chip *reduceGenome, mergeGenome doubleGenome really now work pedigree recombination tracking","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-112","dir":"Changelog","previous_headings":"","what":"AlphaSimR 1.1.2","title":"AlphaSimR 1.1.2","text":"CRAN release: 2022-02-17 *added missing #ifdef _OPENMP OCS.cpp","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-111","dir":"Changelog","previous_headings":"","what":"AlphaSimR 1.1.1","title":"AlphaSimR 1.1.1","text":"*removed use PI variable C++ code due compiler specific","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-110","dir":"Changelog","previous_headings":"","what":"AlphaSimR 1.1.0","title":"AlphaSimR 1.1.0","text":"*added snpChip argument pullIbdHaplo backwards compatibility *exposed internal mixed model solvers *selection functions now return warning enough individuals *fixed error pullIbdHaplo chr isn’t NULL *fixed error assigning 1 QTL /SNP *changed geno slot matrix list support future RcppArmadillo changes *doubleGenome reduceGenome now work IBD tracking","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-104","dir":"Changelog","previous_headings":"","what":"AlphaSimR 1.0.4","title":"AlphaSimR 1.0.4","text":"CRAN release: 2021-09-08 *fixed errors implementation Gamma Sprinkling model","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-103","dir":"Changelog","previous_headings":"","what":"AlphaSimR 1.0.3","title":"AlphaSimR 1.0.3","text":"CRAN release: 2021-07-29 *fixed formatting error genetic maps created runMacs broke genotype extraction functions","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-102","dir":"Changelog","previous_headings":"","what":"AlphaSimR 1.0.2","title":"AlphaSimR 1.0.2","text":"CRAN release: 2021-07-28 *added h2 H2 setPhenoGCA *pullGeno pullHaplo functions now report marker names genetic map","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-101","dir":"Changelog","previous_headings":"","what":"AlphaSimR 1.0.1","title":"AlphaSimR 1.0.1","text":"CRAN release: 2021-05-14 *removed lazyData field DESCRIPTION","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-100","dir":"Changelog","previous_headings":"","what":"AlphaSimR 1.0.0","title":"AlphaSimR 1.0.0","text":"*AlphaSimR manuscript published G3 (citation added) *changed Gamma Sprinkling model crossovers, default still Gamma model *change default interference parameter (v) 2.6 consistent Kosambi mapping function (1, consistent Haldane mapping function) *new internal id (iid) allows user freely change id slot populations *runMacs2 now adjusts Ne autopolyploids *parent populations now passed finalizePop *check added throws error use discontinued “gender” argument detected *added experimental MegaPop-class","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-0130","dir":"Changelog","previous_headings":"","what":"AlphaSimR 0.13.0","title":"AlphaSimR 0.13.0","text":"CRAN release: 2020-10-11 *references gender changed appropriate terms sex sexes *added misc slot populations *added finalizePop SimParam *added physical positions getSnpMap getQtlMap *can now use h2 H2 specify error variance setPheno *SimParam$setVarE now accepts matrix varE *fixed bug editGenome making multiple edits *adding merging centromere vector cChr","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-0122","dir":"Changelog","previous_headings":"","what":"AlphaSimR 0.12.2","title":"AlphaSimR 0.12.2","text":"CRAN release: 2020-05-19 *GxE traits now default random sampling p-values *fixed bug restrSegSites","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-0121","dir":"Changelog","previous_headings":"","what":"AlphaSimR 0.12.1","title":"AlphaSimR 0.12.1","text":"CRAN release: 2020-03-30 *fixed bug selection segSites","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-0120","dir":"Changelog","previous_headings":"","what":"AlphaSimR 0.12.0","title":"AlphaSimR 0.12.0","text":"*changed output genParam match Bulmer, 1976 *nProgeny added makeCross makeCross2 *SimParam documentation now ?SimParam *non-overlapping QTL SNP now default *new interface restrSegSites SimParam *fixed subset id populations *fixed major bug newMapPop","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-0111","dir":"Changelog","previous_headings":"","what":"AlphaSimR 0.11.1","title":"AlphaSimR 0.11.1","text":"CRAN release: 2020-01-13 *switched circular design balance option randCross randCross2 *added reduceGenome doubleGenome changing ploidy levels *added minSnpFreq SimParam_addSnpChip reference population *c function now merges individuals MapPop objects (chromosomes ) *cChr function new merges chromosomes MapPop objects *fixed broken SimParam_addStructuredSnpChip *removed broken pullMultipleSnpGeno pullMultipleSnpHaplo *fixed broken writePlink","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-0110","dir":"Changelog","previous_headings":"","what":"AlphaSimR 0.11.0","title":"AlphaSimR 0.11.0","text":"CRAN release: 2019-10-11 *rework setEBV (breaks scripts) *genotype data now stored bits (bytes) *implemented gamma model crossover interference *added mutate function model random mutations *added vignette explaining biological model traits *GS models now handle polyploids *heterogenous error variance now optional GS models (default homogeneous error) *improved gene drop functionality pedigreeCross *added keepParents option makeDH self (indirectly extends selectFam selectWithinFam) *added RRBLUP_SCA2 *set methods “show” function applied populations *fixed bug returning first individual selecting 0 *fixed error recombination track using makeDH *fixed error causing epistatic effects mask GxE effects *fixed error pullSegSiteGeno pullSegSiteHaplo variable number sites per chromosome","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-0100","dir":"Changelog","previous_headings":"","what":"AlphaSimR 0.10.0","title":"AlphaSimR 0.10.0","text":"CRAN release: 2019-03-15 *added traits epistasis *Max number threads automatically detected *added RRBLUP_D2 *added version tracking SimParam *removed trackHaploPop (super-ceded pullIbdHaplo) *added fastRRBLUP *fixed faulty double crossover logic *fixed broken writePlink *fixed broken pullIbdHaplo *mergePops longer assumes diploidy","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-090","dir":"Changelog","previous_headings":"","what":"AlphaSimR 0.9.0","title":"AlphaSimR 0.9.0","text":"CRAN release: 2019-02-07 *added support autopolyploids *added RRBLUP_GCA2 *randCross2 can now “balance” crossing using gender *fixed recombination tracking bug createDH2 *removed bug setEBV append=TRUE","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-082","dir":"Changelog","previous_headings":"","what":"AlphaSimR 0.8.2","title":"AlphaSimR 0.8.2","text":"CRAN release: 2018-10-15 *fixed ambiguous overloading optimize.cpp","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-081","dir":"Changelog","previous_headings":"","what":"AlphaSimR 0.8.1","title":"AlphaSimR 0.8.1","text":"CRAN release: 2018-10-12 *setPheno (setPhenoGCA) passes number reps populations *fixed bug editGenomeTopQtl *fixed bug RRBLUP_D *fixed bug resetPop *fixed bug SimParam_rescaleTraits *removed unimplemented SimParam_restrSnpSites SimParam_restrQtlSites *add error message traits calcGCA","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-080","dir":"Changelog","previous_headings":"","what":"AlphaSimR 0.8.0","title":"AlphaSimR 0.8.0","text":"*added GxE traits zero environmental variance *faster trait scaling *faster calculation genetic values *dsyevr now called via arma_fortran *added OpenMP support *parallelized cross2 *parallelized runMacs *parallelized calculation genetic values *variance calculations now account inbreeding *fixes male selection selectOP","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-071","dir":"Changelog","previous_headings":"","what":"AlphaSimR 0.7.1","title":"AlphaSimR 0.7.1","text":"*add fixEff setPhenoGCA","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-070","dir":"Changelog","previous_headings":"","what":"AlphaSimR 0.7.0","title":"AlphaSimR 0.7.0","text":"*added default runMacs option return segSites *added ability specify separate male female genetic maps *pullGeno pullHaplo functions can now specify chromosomes *added RRBLUP2 special GS cases *improved speed replacing Rcpp random number generators *changed available MaCS species *GS functions now use populations directly *added pullIbdHaplo *added writePlink *fixed population sub-setting checks prevent invalid selections *fixed slow calcGCA *fixed error addTraitAG preventing multiple traits *fixed bug mergePops merging ebv *fixed bug setVarE using H2 multiple traits","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-061","dir":"Changelog","previous_headings":"","what":"AlphaSimR 0.6.1","title":"AlphaSimR 0.6.1","text":"*selectFam now handles half-sib families *selectWithinFam now handles half-sib families *Removed restriction varE=NULL setPhenoGCA","code":""},{"path":"https://gaynorr.github.io/AlphaSimR/news/index.html","id":"alphasimr-060","dir":"Changelog","previous_headings":"","what":"AlphaSimR 0.6.0","title":"AlphaSimR 0.6.0","text":"*Added NEWS file *Added selectOP model selection open pollinating plants *Added runMacs2 wrapper runMacs *Fixed error using H2 SimParam_setVarE","code":""}]