CSAFE-ISU · stephaniereinders · Aug 7, 2024 · Aug 7, 2024
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -13,3 +13,4 @@
 ^README\.Rmd$
 ^tools$
 ^scratch.R$
+^altdoc$
diff --git a/.gitignore b/.gitignore
@@ -12,4 +12,5 @@ revdep/
 inst/doc
 
 scratch*
-*.psd
+*.psd
+altdoc/freeze.rds
diff --git a/README.md b/README.md
@@ -1,4 +1,5 @@
 
+
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
 # handwriter
@@ -56,7 +57,7 @@ Use `processDocument()` to
 library(handwriter)
 phrase <- system.file("extdata", "phrase_example.png", package = "handwriter")
 doc <- processDocument(phrase)
-#> path in readPNGBinary: /private/var/folders/1z/jk9bqhdd06j1fxx0_xm2jj980000gn/T/RtmplsdN6z/temp_libpath947954bb6036/handwriter/extdata/phrase_example.png
+#> path in readPNGBinary: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/handwriter/extdata/phrase_example.png
 #> Starting Processing...
 #> Getting Nodes...
 #> Skeletonizing writing...
@@ -76,23 +77,23 @@ We can view the image:
 plotImage(doc)
 ```
 
-<img src="man/figures/README-image-1.png" width="100%" />
+<img src="man/figures/README-image-1.png" style="width:100.0%" />
 
 We can view the thinned image:
 
 ``` r
 plotImageThinned(doc)
 ```
 
-<img src="man/figures/README-thin-1.png" width="100%" />
+<img src="man/figures/README-thin-1.png" style="width:100.0%" />
 
 We can also view the nodes:
 
 ``` r
 plotNodes(doc)
 ```
 
-<img src="man/figures/README-nodes-1.png" width="100%" />
+<img src="man/figures/README-nodes-1.png" style="width:100.0%" />
 
 ## Perform Writership Analysis
 
@@ -194,7 +195,8 @@ template_data <- format_template_data(template = template)
 plot_cluster_fill_counts(template_data, facet = TRUE)
 ```
 
-<img src="man/figures/README-unnamed-chunk-4-1.png" width="100%" />
+<img src="man/figures/README-unnamed-chunk-4-1.png"
+style="width:100.0%" />
 
 ### STEP 3: Fit a Hierarchical Model
 
@@ -258,9 +260,11 @@ but the model data is already in the correct format.)
 plot_cluster_fill_counts(formatted_data=model, facet = TRUE)
 ```
 
-<img src="man/figures/README-unnamed-chunk-7-1.png" width="100%" /> The
-bars across the top of each graph show the Writer ID. Each graph has a
-line for each known handwriting sample from a given writer.
+<img src="man/figures/README-unnamed-chunk-7-1.png"
+style="width:100.0%" />
+
+The bars across the top of each graph show the Writer ID. Each graph has
+a line for each known handwriting sample from a given writer.
 
 #### Hierarchical Model Variables and Burn-in
 
@@ -297,7 +301,8 @@ View a trace plot of a variable.
 plot_trace(variable = "mu[1,1]", model = model)
 ```
 
-<img src="man/figures/README-unnamed-chunk-10-1.png" width="100%" />
+<img src="man/figures/README-unnamed-chunk-10-1.png"
+style="width:100.0%" />
 
 If we need to, we can drop the beginning MCMC iterations for burn-in.
 For example, if we want to drop the first 25 iterations, we use
@@ -368,7 +373,8 @@ the cluster fill counts observed in each questioned document.
 plot_cluster_fill_counts(analysis, facet = TRUE)
 ```
 
-<img src="man/figures/README-unnamed-chunk-15-1.png" width="100%" />
+<img src="man/figures/README-unnamed-chunk-15-1.png"
+style="width:100.0%" />
 
 View the posterior probabilities of writership.
 

diff --git a/altdoc/.nojekyll b/altdoc/.nojekyll
diff --git a/altdoc/docsify.html b/altdoc/docsify.html
@@ -0,0 +1,45 @@
+<!-- index.html -->
+
+<!DOCTYPE html>
+<html>
+<head>
+  <meta http-equiv="X-UA-Compatible" content="IE=edge,chrome=1">
+  <meta name="viewport" content="width=device-width,initial-scale=1">
+  <meta charset="UTF-8">
+  <link rel="stylesheet" href="//cdn.jsdelivr.net/npm/docsify@4/themes/vue.css" />
+</head>
+<body>
+  <div id="app"></div>
+  <script>
+    window.$docsify = {
+      name: '$ALTDOC_PACKAGE_NAME',
+      repo: '$ALTDOC_PACKAGE_URL_GITHUB',
+      loadSidebar: true,
+      subMaxLevel: 2,
+      search: {
+        placeholder: 'Search',
+        depth: 3,
+      },
+      auto2top: true,
+      copyCode: {
+        buttonText : 'Copy',
+        errorText  : 'Error',
+        successText: 'Copied'
+      },
+      plugins: [
+        function(hook) {
+          var footer = ["<a href='$ALTDOC_PACKAGE_URL'> <code> $ALTDOC_PACKAGE_NAME </code> v. $ALTDOC_PACKAGE_VERSION </a> | Documentation made with <a href='https://altdoc.etiennebacher.com/'> <code> altdoc </code> v. $ALTDOC_VERSION</a>"].join('');
+
+          hook.afterEach(function(html) {
+            return html + footer;
+          });
+        }
+      ]
+    }
+  </script>
+  <script src="//cdn.jsdelivr.net/npm/docsify@4"></script>
+  <script src="//cdn.jsdelivr.net/npm/docsify-copy-code"></script>
+  <script src="//cdn.jsdelivr.net/npm/prismjs@1.24.1/components/prism-r.js"></script>
+  <script src="//unpkg.com/docsify/lib/plugins/search.min.js"></script>
+</body>
+</html>
diff --git a/altdoc/docsify.md b/altdoc/docsify.md
@@ -0,0 +1,9 @@
+* [Home](/)
+* Articles: $ALTDOC_VIGNETTE_BLOCK
+* Reference: $ALTDOC_MAN_BLOCK
+* [News]($ALTDOC_NEWS)
+* [Changelog]($ALTDOC_CHANGELOG)
+* [Code of Conduct]($ALTDOC_CODE_OF_CONDUCT)
+* [License]($ALTDOC_LICENSE)
+* [Licence]($ALTDOC_LICENCE)
+* [Citation]($ALTDOC_CITATION)
diff --git a/altdoc/preamble_man_qmd.yml b/altdoc/preamble_man_qmd.yml
@@ -0,0 +1,6 @@
+---
+format:
+  md:
+    prefer-html: true
+---
+
diff --git a/altdoc/preamble_vignettes_qmd.yml b/altdoc/preamble_vignettes_qmd.yml
@@ -0,0 +1,6 @@
+---
+format:
+  md:
+    prefer_html: true
+default-image-extension: ""
+---
diff --git a/altdoc/preamble_vignettes_rmd.yml b/altdoc/preamble_vignettes_rmd.yml
@@ -0,0 +1,4 @@
+---
+always_allow_html: yes
+---
+
diff --git a/docs/.nojekyll b/docs/.nojekyll
diff --git a/docs/CITATION.md b/docs/CITATION.md
@@ -0,0 +1,22 @@
+# Citation
+
+```verbatim
+To cite package ‘handwriter’ in publications use:
+
+  Iowa State University of Science and Technology on behalf of its
+  Center for Statistics and Applications in Forensic Evidence, Berry
+  N, Reinders S, Taylor J (2024). _handwriter: Handwriting Analysis in
+  R_. R package version 3.1.1.9000, commit
+  2ca3187a3e750fed34d373eae7dd587483c96b75,
+  <https://github.com/CSAFE-ISU/handwriter>.
+
+A BibTeX entry for LaTeX users is
+
+  @Manual{,
+    title = {handwriter: Handwriting Analysis in R},
+    author = {{Iowa State University of Science and Technology on behalf of its Center for Statistics and Applications in Forensic Evidence} and Nick Berry and Stephanie Reinders and James Taylor},
+    year = {2024},
+    note = {R package version 3.1.1.9000, commit 2ca3187a3e750fed34d373eae7dd587483c96b75},
+    url = {https://github.com/CSAFE-ISU/handwriter},
+  }
+```