Rebuild doc.

pbastide · May 1, 2017 · 387b475 · 387b475
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diff --git a/README.md b/README.md
@@ -8,7 +8,7 @@ PhylogeneticEM
 Implementation of the EM algorithm for the detection of shifts in a phylogeny.
 
 ## Installation
-Stable version (1.0.0) on the [CRAN](https://cran.rstudio.com/web/packages/PhylogeneticEM/).
+Stable version on the [CRAN](https://cran.rstudio.com/web/packages/PhylogeneticEM/).
 
 To get the latest (and possibly unstable) version, you can use the [`devtools`](https://github.com/hadley/devtools) package:
 ```R

diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/articles/tutorial.html b/docs/articles/tutorial.html
diff --git a/docs/articles/tutorial_files/figure-html/unnamed-chunk-2-1.png b/docs/articles/tutorial_files/figure-html/unnamed-chunk-2-1.png
diff --git a/docs/articles/tutorial_files/figure-html/unnamed-chunk-4-1.png b/docs/articles/tutorial_files/figure-html/unnamed-chunk-4-1.png
diff --git a/docs/articles/tutorial_files/figure-html/unnamed-chunk-6-1.png b/docs/articles/tutorial_files/figure-html/unnamed-chunk-6-1.png
diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/news/index.html b/docs/news/index.html
diff --git a/docs/pkgdown.css b/docs/pkgdown.css
@@ -36,11 +36,8 @@ img.icon {
 
 /* Section anchors ---------------------------------*/
 
-.hasAnchor {
-  margin-left: -30px;
-}
-
 a.anchor {
+  margin-left: -30px;
   display:inline-block;
   width: 30px;
   height: 30px;
@@ -56,13 +53,31 @@ a.anchor {
   visibility: visible;
 }
 
+@media (max-width: 767px) {
+  .hasAnchor:hover a.anchor {
+    visibility: hidden;
+  }
+}
+
+
 /* Fixes for fixed navbar --------------------------*/
 
 .contents h1, .contents h2, .contents h3, .contents h4 {
   padding-top: 60px;
   margin-top: -60px;
 }
 
+/* Static header placement on mobile devices */
+@media (max-width: 767px) {
+  .navbar-fixed-top {
+    position: absolute;
+  }
+  .navbar {
+    padding: 0;
+  }
+}
+
+
 /* Sidebar --------------------------*/
 
 #sidebar {
@@ -107,31 +122,33 @@ table {
 
 /* Syntax highlighting ---------------------------------------------------- */
 
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-  color: #333;
+pre {
+  word-wrap: normal;
+  word-break: normal;
+  border: 1px solid #eee;
 }
-code a {
-  color: #375f84;
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-
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-.formalargs {color: #264D66;}
-.eqformalargs {color:#264D66;}
-.slot {font-style:italic;}
-.symbol {color:black ;}
-.prompt {color:black ;}
+pre, code {
+  background-color: #f8f8f8;
+  color: #333;
+}
 
 pre img {
   background-color: #fff;
   display: block;
 }
+
+code a, pre a {
+  color: #375f84;
+}
+
+.fl      {color: #1514b5;}
+.fu      {color: #000000;} /* function */
+.ch,.st  {color: #036a07;} /* string */
+.kw      {color: #264D66;} /* keyword */
+.co      {color: #888888;} /* comment */
+
+.message { color: black;   font-weight: bolder;}
+.error   { color: orange;  font-weight: bolder;}
+.warning { color: #6A0366; font-weight: bolder;}
+
diff --git a/docs/reference/PhyloEM.html b/docs/reference/PhyloEM.html
diff --git a/docs/reference/add_complementary.html b/docs/reference/add_complementary.html
diff --git a/docs/reference/allocate_regimes_from_shifts.html b/docs/reference/allocate_regimes_from_shifts.html
diff --git a/docs/reference/allocate_shifts_from_regimes.html b/docs/reference/allocate_shifts_from_regimes.html
diff --git a/docs/reference/allocate_subset_node.simulate.html b/docs/reference/allocate_subset_node.simulate.html