GH-Pages and adding examples

.github/workflows/main.yml

@@ -0,0 +1,38 @@
+on:
+  push:
+    branches: main
+  pull_request:
+    branches: main
+name: Quarto Render and Deploy
+
+jobs:
+  build-deploy:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Set up Quarto
+        uses: quarto-dev/quarto-actions/setup@v2
+        with:
+          tinytex: true
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-renv@v2
+
+      # - uses: r-lib/actions/setup-r-dependencies@v2
+
+      - name: Render book to all format
+        run: |
+          quarto render
+      - name: deploy to GH pages
+        id: gh-pages-deploy
+        uses: peaceiris/actions-gh-pages@v4
+        if: github.ref == 'refs/heads/main'
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./docs

.gitignore

@@ -6,3 +6,7 @@
 *.DS_Store
 
 /.quarto/
+
+*_cache
+
+docs

_quarto.yml

@@ -74,7 +74,11 @@ book:
     - "class5.qmd"
     - "class6.qmd"
     - "class7.qmd"
-    - "class8.qmd"
+    - part: "class8.qmd"
+      chapters: 
+        - examples/example-temperatures.qmd
+        - examples/example-ebola.qmd
+        - examples/example-avida.qmd
 
 
 

deprecates/scripts/04_projects/class8_instructor-version.qmd

@@ -21,6 +21,9 @@ knitr::opts_chunk$set(echo=FALSE, digits = 3)
 
 ## Final class!
 
+\
+\
+
 ::: {.callout-note collapse="true"}
 ## Notes to instructors
 
@@ -163,6 +166,7 @@ knitr::kable(head(avida0))
 #### Column metadata
 
 | Column                      | Type      | Description                                                                       | Values                                                       |
+
 |------------------|------------------|-------------------|------------------|
 | `update`                    | integer   | Time elapsed                                                                      | Ranges 0-300                                                 |
 | `condition`                 | character | Testing conditions (single population or competition)                             | Based off csv: `wildtype-only`, `mutant-only`, `competition` |
@@ -234,6 +238,7 @@ knitr::kable(head(ebola0))
 #### Column metadata
 
 | Column                                                       | Type      | Description                     | Values     |
+
 |-------------------|------------------|------------------|------------------|
 | `Country`                                                    | character | Country of report               |            |
 | `Date`                                                       | character | Date of report                  | YYYY-MM-DD |
@@ -305,6 +310,7 @@ knitr::kable(head(temps0))
 #### Column metadata
 
 | Column        | Type      | Description                                                       | Values                                                                   |
+
 |------------------|------------------|------------------|-------------------|
 | `Subject.ID`  | character | Subject identifier where number (1-5) corresponds to neighborhood | 1=Coffelt, 2=Encanto-Palmcroft, 3=Garfield, 4=Thunderhill, 5=Power Ranch |
 | `period`      | character | 4 hour measurement period                                         | weekday, period                                                          |

deprecates/scripts/class8.html

@@ -20,6 +20,40 @@
   margin: 0 0.8em 0.2em -1em; /* quarto-specific, see https://github.com/quarto-dev/quarto-cli/issues/4556 */ 
   vertical-align: middle;
 }
+/* CSS for syntax highlighting */
+pre > code.sourceCode { white-space: pre; position: relative; }
+pre > code.sourceCode > span { line-height: 1.25; }
+pre > code.sourceCode > span:empty { height: 1.2em; }
+.sourceCode { overflow: visible; }
+code.sourceCode > span { color: inherit; text-decoration: inherit; }
+div.sourceCode { margin: 1em 0; }
+pre.sourceCode { margin: 0; }
+@media screen {
+div.sourceCode { overflow: auto; }
+}
+@media print {
+pre > code.sourceCode { white-space: pre-wrap; }
+pre > code.sourceCode > span { text-indent: -5em; padding-left: 5em; }
+}
+pre.numberSource code
+  { counter-reset: source-line 0; }
+pre.numberSource code > span
+  { position: relative; left: -4em; counter-increment: source-line; }
+pre.numberSource code > span > a:first-child::before
+  { content: counter(source-line);
+    position: relative; left: -1em; text-align: right; vertical-align: baseline;
+    border: none; display: inline-block;
+    -webkit-touch-callout: none; -webkit-user-select: none;
+    -khtml-user-select: none; -moz-user-select: none;
+    -ms-user-select: none; user-select: none;
+    padding: 0 4px; width: 4em;
+  }
+pre.numberSource { margin-left: 3em;  padding-left: 4px; }
+div.sourceCode
+  {   }
+@media screen {
+pre > code.sourceCode > span > a:first-child::before { text-decoration: underline; }
+}
 </style>
 
 
@@ -47,6 +81,7 @@ <h2 id="toc-title">Table of contents</h2>
   <ul>
   <li><a href="#final-class" id="toc-final-class" class="nav-link active" data-scroll-target="#final-class">Final class!</a></li>
   <li><a href="#datasets" id="toc-datasets" class="nav-link" data-scroll-target="#datasets">Datasets</a>
+
   <ul class="collapse">
   <li><a href="#avida-digital-evolution-dataset" id="toc-avida-digital-evolution-dataset" class="nav-link" data-scroll-target="#avida-digital-evolution-dataset">Avida digital evolution dataset</a></li>
   <li><a href="#western-africa-ebola-public-health-dataset" id="toc-western-africa-ebola-public-health-dataset" class="nav-link" data-scroll-target="#western-africa-ebola-public-health-dataset">Western Africa Ebola public health dataset</a></li>
@@ -106,6 +141,7 @@ <h2 class="anchored" data-anchor-id="final-class">Final class!</h2>
 <li><p>Make your code reproducible by using GitHub.</p></li>
 </ol>
 </blockquote>
+
 <p>To help with your analyses, we have included a <strong>project template</strong> document outlining these steps that you are welcome to use in <code>data/project-day-2-files/example-analyses</code>; the location of additional files are specified below.</p>
 </section>
 <section id="datasets" class="level2">
@@ -183,6 +219,7 @@ <h3 class="anchored" data-anchor-id="avida-digital-evolution-dataset">Avida digi
 <div id="tabset-1-1" class="tab-pane active" role="tabpanel" aria-labelledby="tabset-1-1-tab">
 <p>Data for <code>avida_wildtype.csv</code> shown only:</p>
 <div class="cell">
+<div class="sourceCode cell-code" id="cb1"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a>knitr<span class="sc">::</span><span class="fu">kable</span>(<span class="fu">head</span>(avida0))</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 <div class="cell-output-display">
 <table class="caption-top table table-sm table-striped small">
 <colgroup>
@@ -454,6 +491,7 @@ <h3 class="anchored" data-anchor-id="western-africa-ebola-public-health-dataset"
 <div class="tab-content">
 <div id="tabset-3-1" class="tab-pane active" role="tabpanel" aria-labelledby="tabset-3-1-tab">
 <div class="cell">
+<div class="sourceCode cell-code" id="cb2"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a>knitr<span class="sc">::</span><span class="fu">kable</span>(<span class="fu">head</span>(ebola0))</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 <div class="cell-output-display">
 <table class="caption-top table table-sm table-striped small">
 <colgroup>
@@ -634,6 +672,7 @@ <h3 class="anchored" data-anchor-id="heat-exposure-in-phoenix-arizona-ecological
 <div class="tab-content">
 <div id="tabset-5-1" class="tab-pane active" role="tabpanel" aria-labelledby="tabset-5-1-tab">
 <div class="cell">
+<div class="sourceCode cell-code" id="cb3"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a>knitr<span class="sc">::</span><span class="fu">kable</span>(<span class="fu">head</span>(temps0))</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 <div class="cell-output-display">
 <table class="caption-top table table-sm table-striped small">
 <thead>