Deploying to gh-pages from @ 9f66216 🚀

core/core.html

@@ -273,7 +273,7 @@ <h1 class="title">Core: Supporting Information</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">13 September, 2024</p>
+      <p class="date">17 September, 2024</p>
     </div>
   </div>
 

core/week-1-old/overview.html

@@ -178,7 +178,7 @@ <h1 class="title">Overview</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">13 September, 2024</p>
+      <p class="date">17 September, 2024</p>
     </div>
   </div>
 

core/week-1-old/study_after_workshop.html

@@ -178,7 +178,7 @@ <h1 class="title">Independent Study to consolidate this week</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">13 September, 2024</p>
+      <p class="date">17 September, 2024</p>
     </div>
   </div>
 

core/week-1-old/study_before_workshop.html

@@ -171,7 +171,7 @@ <h1 class="title">Independent Study to prepare for workshop</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">13 September, 2024</p>
+      <p class="date">17 September, 2024</p>
     </div>
   </div>
 

core/week-1-old/workshop.html

@@ -232,7 +232,7 @@ <h1 class="title">Workshop</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">13 September, 2024</p>
+      <p class="date">17 September, 2024</p>
     </div>
   </div>
 

core/week-2-old/overview.html

@@ -169,7 +169,7 @@ <h1 class="title">Overview</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">13 September, 2024</p>
+      <p class="date">17 September, 2024</p>
     </div>
   </div>
 

core/week-2-old/study_after_workshop.html

@@ -169,7 +169,7 @@ <h1 class="title">Independent Study to consolidate this week</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">13 September, 2024</p>
+      <p class="date">17 September, 2024</p>
     </div>
   </div>
 

core/week-2-old/study_before_workshop.html

@@ -448,7 +448,7 @@
 </div>
 </div>
 
-  <p class="date">13 September, 2024</p>
+  <p class="date">17 September, 2024</p>
 </section><section id="overview" class="slide level2"><h2>Overview</h2>
 <ul>
 <li>RStudio Projects revisited

core/week-2-old/workshop.html

@@ -250,7 +250,7 @@ <h1 class="title">Workshop</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">13 September, 2024</p>
+      <p class="date">17 September, 2024</p>
     </div>
   </div>
 
@@ -338,52 +338,52 @@ <h1 class="title">Workshop</h1>
 <div class="sourceCode cell-code" id="cb9"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb9-1"><a href="#cb9-1" aria-hidden="true" tabindex="-1"></a><span class="fu">ls</span> <span class="at">-l</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 <div class="cell-output cell-output-stdout">
 <pre><code>total 128
-drwxr-xr-x 2 runner docker  4096 Sep 13 11:06 data
-drwxr-xr-x 2 runner docker  4096 Sep 13 11:06 images
--rw-r--r-- 1 runner docker  1597 Sep 13 11:06 overview.qmd
--rw-r--r-- 1 runner docker   184 Sep 13 11:06 study_after_workshop.qmd
--rw-r--r-- 1 runner docker  4807 Sep 13 11:06 study_before_workshop.ipynb
--rw-r--r-- 1 runner docker 13029 Sep 13 11:06 study_before_workshop.qmd
--rw-r--r-- 1 runner docker 58063 Sep 13 11:06 workshop.html
--rw-r--r-- 1 runner docker  8550 Sep 13 11:06 workshop.qmd
--rw-r--r-- 1 runner docker  8577 Sep 13 11:29 workshop.rmarkdown
-drwxr-xr-x 3 runner docker  4096 Sep 13 11:06 workshop_files</code></pre>
+drwxr-xr-x 2 runner docker  4096 Sep 17 16:24 data
+drwxr-xr-x 2 runner docker  4096 Sep 17 16:24 images
+-rw-r--r-- 1 runner docker  1597 Sep 17 16:24 overview.qmd
+-rw-r--r-- 1 runner docker   184 Sep 17 16:24 study_after_workshop.qmd
+-rw-r--r-- 1 runner docker  4807 Sep 17 16:24 study_before_workshop.ipynb
+-rw-r--r-- 1 runner docker 13029 Sep 17 16:24 study_before_workshop.qmd
+-rw-r--r-- 1 runner docker 58063 Sep 17 16:24 workshop.html
+-rw-r--r-- 1 runner docker  8550 Sep 17 16:24 workshop.qmd
+-rw-r--r-- 1 runner docker  8577 Sep 17 16:25 workshop.rmarkdown
+drwxr-xr-x 3 runner docker  4096 Sep 17 16:24 workshop_files</code></pre>
 </div>
 </div>
 <p>You can use more than one option at once. The <code>-h</code> option stands for “human readable” and makes the file sizes easier to understand for humans:</p>
 <div class="cell">
 <div class="sourceCode cell-code" id="cb11"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb11-1"><a href="#cb11-1" aria-hidden="true" tabindex="-1"></a><span class="fu">ls</span> <span class="at">-hl</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 <div class="cell-output cell-output-stdout">
 <pre><code>total 128K
-drwxr-xr-x 2 runner docker 4.0K Sep 13 11:06 data
-drwxr-xr-x 2 runner docker 4.0K Sep 13 11:06 images
--rw-r--r-- 1 runner docker 1.6K Sep 13 11:06 overview.qmd
--rw-r--r-- 1 runner docker  184 Sep 13 11:06 study_after_workshop.qmd
--rw-r--r-- 1 runner docker 4.7K Sep 13 11:06 study_before_workshop.ipynb
--rw-r--r-- 1 runner docker  13K Sep 13 11:06 study_before_workshop.qmd
--rw-r--r-- 1 runner docker  57K Sep 13 11:06 workshop.html
--rw-r--r-- 1 runner docker 8.4K Sep 13 11:06 workshop.qmd
--rw-r--r-- 1 runner docker 8.4K Sep 13 11:29 workshop.rmarkdown
-drwxr-xr-x 3 runner docker 4.0K Sep 13 11:06 workshop_files</code></pre>
+drwxr-xr-x 2 runner docker 4.0K Sep 17 16:24 data
+drwxr-xr-x 2 runner docker 4.0K Sep 17 16:24 images
+-rw-r--r-- 1 runner docker 1.6K Sep 17 16:24 overview.qmd
+-rw-r--r-- 1 runner docker  184 Sep 17 16:24 study_after_workshop.qmd
+-rw-r--r-- 1 runner docker 4.7K Sep 17 16:24 study_before_workshop.ipynb
+-rw-r--r-- 1 runner docker  13K Sep 17 16:24 study_before_workshop.qmd
+-rw-r--r-- 1 runner docker  57K Sep 17 16:24 workshop.html
+-rw-r--r-- 1 runner docker 8.4K Sep 17 16:24 workshop.qmd
+-rw-r--r-- 1 runner docker 8.4K Sep 17 16:25 workshop.rmarkdown
+drwxr-xr-x 3 runner docker 4.0K Sep 17 16:24 workshop_files</code></pre>
 </div>
 </div>
 <p>The <code>-a</code> option stands for “all” and shows us all the files, including hidden files.</p>
 <div class="cell">
 <div class="sourceCode cell-code" id="cb13"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb13-1"><a href="#cb13-1" aria-hidden="true" tabindex="-1"></a><span class="fu">ls</span> <span class="at">-alh</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 <div class="cell-output cell-output-stdout">
 <pre><code>total 136K
-drwxr-xr-x 5 runner docker 4.0K Sep 13 11:29 .
-drwxr-xr-x 7 runner docker 4.0K Sep 13 11:06 ..
-drwxr-xr-x 2 runner docker 4.0K Sep 13 11:06 data
-drwxr-xr-x 2 runner docker 4.0K Sep 13 11:06 images
--rw-r--r-- 1 runner docker 1.6K Sep 13 11:06 overview.qmd
--rw-r--r-- 1 runner docker  184 Sep 13 11:06 study_after_workshop.qmd
--rw-r--r-- 1 runner docker 4.7K Sep 13 11:06 study_before_workshop.ipynb
--rw-r--r-- 1 runner docker  13K Sep 13 11:06 study_before_workshop.qmd
--rw-r--r-- 1 runner docker  57K Sep 13 11:06 workshop.html
--rw-r--r-- 1 runner docker 8.4K Sep 13 11:06 workshop.qmd
--rw-r--r-- 1 runner docker 8.4K Sep 13 11:29 workshop.rmarkdown
-drwxr-xr-x 3 runner docker 4.0K Sep 13 11:06 workshop_files</code></pre>
+drwxr-xr-x 5 runner docker 4.0K Sep 17 16:25 .
+drwxr-xr-x 7 runner docker 4.0K Sep 17 16:24 ..
+drwxr-xr-x 2 runner docker 4.0K Sep 17 16:24 data
+drwxr-xr-x 2 runner docker 4.0K Sep 17 16:24 images
+-rw-r--r-- 1 runner docker 1.6K Sep 17 16:24 overview.qmd
+-rw-r--r-- 1 runner docker  184 Sep 17 16:24 study_after_workshop.qmd
+-rw-r--r-- 1 runner docker 4.7K Sep 17 16:24 study_before_workshop.ipynb
+-rw-r--r-- 1 runner docker  13K Sep 17 16:24 study_before_workshop.qmd
+-rw-r--r-- 1 runner docker  57K Sep 17 16:24 workshop.html
+-rw-r--r-- 1 runner docker 8.4K Sep 17 16:24 workshop.qmd
+-rw-r--r-- 1 runner docker 8.4K Sep 17 16:25 workshop.rmarkdown
+drwxr-xr-x 3 runner docker 4.0K Sep 17 16:24 workshop_files</code></pre>
 </div>
 </div>
 <p>You can move about with the <code>cd</code> command, which stands for “change directory”. You can use it to move into a directory by specifying the path to the directory:</p>

core/week-2/overview.html

@@ -271,7 +271,7 @@ <h1 class="title">Overview</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">13 September, 2024</p>
+      <p class="date">17 September, 2024</p>
     </div>
   </div>
 

core/week-2/study_after_workshop.html

@@ -264,7 +264,7 @@ <h1 class="title">Independent Study to consolidate this week</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">13 September, 2024</p>
+      <p class="date">17 September, 2024</p>
     </div>
   </div>
 

core/week-2/study_before_workshop.html

@@ -264,7 +264,7 @@ <h1 class="title">Independent Study to prepare for workshop</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">13 September, 2024</p>
+      <p class="date">17 September, 2024</p>
     </div>
   </div>
 

core/week-2/workshop.html

@@ -448,7 +448,7 @@
 </div>
 </div>
 
-  <p class="date">13 September, 2024</p>
+  <p class="date">17 September, 2024</p>
 </section><section><section id="introduction" class="title-slide slide level1 center"><h1>Introduction</h1>
 
 </section><section id="session-overview" class="slide level2"><h2>Session overview</h2>
@@ -878,7 +878,7 @@
 <li>Excuse Me, Do You Have a Moment to Talk About Version Control? <span class="citation" data-cites="bryan2018">(<a href="#/references" role="doc-biblioref" onclick="">Bryan 2018</a>)</span>
 </li>
 </ul>
-<p>Pages made with R <span class="citation" data-cites="R-core">(<a href="#/references" role="doc-biblioref" onclick="">R Core Team 2024</a>)</span> and Quarto <span class="citation" data-cites="allaire2022">(<a href="#/references" role="doc-biblioref" onclick=""><strong>allaire2022?</strong></a>)</span></p>
+<p>Pages made with R <span class="citation" data-cites="R-core">(<a href="#/references" role="doc-biblioref" onclick="">R Core Team 2024</a>)</span>, Quarto <span class="citation" data-cites="Allaire_Quarto_2024">(<a href="#/references" role="doc-biblioref" onclick="">Allaire et al. 2024</a>)</span>, <code>knitr</code> [<span class="citation" data-cites="knitr1">Xie (<a href="#/references" role="doc-biblioref" onclick="">2024</a>)</span>; knitr2; knitr3], <code>kableExtra</code> <span class="citation" data-cites="kableExtra">(<a href="#/references" role="doc-biblioref" onclick="">Zhu 2021</a>)</span></p>
 </section><section id="references" class="slide level2 smaller scrollable"><h2>References</h2>
 
 <div class="quarto-auto-generated-content">
@@ -887,6 +887,9 @@
 </div>
 </div>
 <div id="refs" class="references csl-bib-body hanging-indent" data-entry-spacing="0" role="list">
+<div id="ref-Allaire_Quarto_2024" class="csl-entry" role="listitem">
+Allaire, J. J., Charles Teague, Carlos Scheidegger, Yihui Xie, and Christophe Dervieux. 2024. <span>“<span>Quarto</span>.”</span> <a href="https://doi.org/10.5281/zenodo.5960048">https://doi.org/10.5281/zenodo.5960048</a>.
+</div>
 <div id="ref-baggerly2009" class="csl-entry" role="listitem">
 Baggerly, Keith A, and Kevin R Coombes. 2009. <span>“DERIVING CHEMOSENSITIVITY FROM CELL LINES: FORENSIC BIOINFORMATICS AND REPRODUCIBLE RESEARCH IN HIGH-THROUGHPUT BIOLOGY.”</span> <em>Ann. Appl. Stat.</em> 3 (4): 1309–34. <a href="https://doi.org/10.2307/27801549">https://doi.org/10.2307/27801549</a>.
 </div>
@@ -914,6 +917,12 @@
 <div id="ref-wilson2017" class="csl-entry" role="listitem">
 Wilson, Greg, Jennifer Bryan, Karen Cranston, Justin Kitzes, Lex Nederbragt, and Tracy K Teal. 2017. <span>“Good Enough Practices in Scientific Computing.”</span> <em>PLoS Comput. Biol.</em> 13 (6): e1005510. <a href="https://doi.org/10.1371/journal.pcbi.1005510">https://doi.org/10.1371/journal.pcbi.1005510</a>.
 </div>
+<div id="ref-knitr1" class="csl-entry" role="listitem">
+Xie, Yihui. 2024. <em>Knitr: A General-Purpose Package for Dynamic Report Generation in r</em>. <a href="https://yihui.org/knitr/">https://yihui.org/knitr/</a>.
+</div>
+<div id="ref-kableExtra" class="csl-entry" role="listitem">
+Zhu, Hao. 2021. <span>“kableExtra: Construct Complex Table with ’Kable’ and Pipe Syntax.”</span> <a href="https://CRAN.R-project.org/package=kableExtra">https://CRAN.R-project.org/package=kableExtra</a>.
+</div>
 </div>
 </section></section>
 </div>

core/week-6-old/overview.html

@@ -177,7 +177,7 @@ <h1 class="title">Overview</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">13 September, 2024</p>
+      <p class="date">17 September, 2024</p>
     </div>
   </div>
 

core/week-6-old/study_after_workshop.html

@@ -171,7 +171,7 @@ <h1 class="title">Independent Study to consolidate this week</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">13 September, 2024</p>
+      <p class="date">17 September, 2024</p>
     </div>
   </div>
 

core/week-6-old/study_before_workshop.html

@@ -171,7 +171,7 @@ <h1 class="title">Independent Study to prepare for workshop</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">13 September, 2024</p>
+      <p class="date">17 September, 2024</p>
     </div>
   </div>
 

core/week-6-old/workshop.html

@@ -207,7 +207,7 @@ <h1 class="title">Workshop</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">13 September, 2024</p>
+      <p class="date">17 September, 2024</p>
     </div>
   </div>
 

core/week-6/overview.html

@@ -271,7 +271,7 @@ <h1 class="title">Overview</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">13 September, 2024</p>
+      <p class="date">17 September, 2024</p>
     </div>
   </div>
 

core/week-6/study_after_workshop.html

@@ -271,7 +271,7 @@ <h1 class="title">Independent Study to consolidate this week</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">13 September, 2024</p>
+      <p class="date">17 September, 2024</p>
     </div>
   </div>
 

core/week-6/study_before_workshop.html

@@ -264,7 +264,7 @@ <h1 class="title">Independent Study to prepare for workshop</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">13 September, 2024</p>
+      <p class="date">17 September, 2024</p>
     </div>
   </div>
 

core/week-6/workshop.html

@@ -325,7 +325,7 @@ <h1 class="title">Workshop</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">13 September, 2024</p>
+      <p class="date">17 September, 2024</p>
     </div>
   </div>
 
@@ -557,7 +557,7 @@ <h1>🥳 Well Done! 🎉</h1>
 <section id="independent-study-following-the-workshop" class="level1">
 <h1>Independent study following the workshop</h1>
 <p><a href="../../core/week-6/study_after_workshop.html">Consolidate</a></p>
-<p>Pages made with R <span class="citation" data-cites="R-core">(<a href="#ref-R-core" role="doc-biblioref">R Core Team 2024</a>)</span>, Quarto <span class="citation" data-cites="allaire2022">(<a href="#ref-allaire2022" role="doc-biblioref"><strong>allaire2022?</strong></a>)</span>, <code>knitr</code> <span class="citation" data-cites="knitr">(<a href="#ref-knitr" role="doc-biblioref"><strong>knitr?</strong></a>)</span>, <code>kableExtra</code> <span class="citation" data-cites="kableExtra">(<a href="#ref-kableExtra" role="doc-biblioref">Zhu 2021</a>)</span></p>
+<p>Pages made with R <span class="citation" data-cites="R-core">(<a href="#ref-R-core" role="doc-biblioref">R Core Team 2024</a>)</span>, Quarto <span class="citation" data-cites="Allaire_Quarto_2024">(<a href="#ref-Allaire_Quarto_2024" role="doc-biblioref">Allaire et al. 2024</a>)</span>, <code>knitr</code> [<span class="citation" data-cites="knitr1">Xie (<a href="#ref-knitr1" role="doc-biblioref">2024</a>)</span>; knitr2; knitr3], <code>kableExtra</code> <span class="citation" data-cites="kableExtra">(<a href="#ref-kableExtra" role="doc-biblioref">Zhu 2021</a>)</span></p>
 </section>
 <section id="references" class="level1">
 
@@ -567,6 +567,9 @@ <h1>Independent study following the workshop</h1>
 </section>
 
 <div id="quarto-appendix" class="default"><section class="quarto-appendix-contents" role="doc-bibliography" id="quarto-bibliography"><h2 class="anchored quarto-appendix-heading">References</h2><div id="refs" class="references csl-bib-body hanging-indent" data-entry-spacing="0" role="list">
+<div id="ref-Allaire_Quarto_2024" class="csl-entry" role="listitem">
+Allaire, J. J., Charles Teague, Carlos Scheidegger, Yihui Xie, and Christophe Dervieux. 2024. <span>“<span>Quarto</span>.”</span> <a href="https://doi.org/10.5281/zenodo.5960048">https://doi.org/10.5281/zenodo.5960048</a>.
+</div>
 <div id="ref-baggerly2009" class="csl-entry" role="listitem">
 Baggerly, Keith A, and Kevin R Coombes. 2009. <span>“DERIVING CHEMOSENSITIVITY FROM CELL LINES: FORENSIC BIOINFORMATICS AND REPRODUCIBLE RESEARCH IN HIGH-THROUGHPUT BIOLOGY.”</span> <em>Ann. Appl. Stat.</em> 3 (4): 1309–34. <a href="https://doi.org/10.2307/27801549">https://doi.org/10.2307/27801549</a>.
 </div>
@@ -588,6 +591,9 @@ <h1>Independent study following the workshop</h1>
 <div id="ref-sessioninfo" class="csl-entry" role="listitem">
 Wickham, Hadley, Winston Chang, Robert Flight, Kirill Müller, and Jim Hester. 2021. <em>Sessioninfo: R Session Information</em>. <a href="https://github.com/r-lib/sessioninfo#readme">https://github.com/r-lib/sessioninfo#readme</a>.
 </div>
+<div id="ref-knitr1" class="csl-entry" role="listitem">
+Xie, Yihui. 2024. <em>Knitr: A General-Purpose Package for Dynamic Report Generation in r</em>. <a href="https://yihui.org/knitr/">https://yihui.org/knitr/</a>.
+</div>
 <div id="ref-kableExtra" class="csl-entry" role="listitem">
 Zhu, Hao. 2021. <span>“kableExtra: Construct Complex Table with ’Kable’ and Pipe Syntax.”</span> <a href="https://CRAN.R-project.org/package=kableExtra">https://CRAN.R-project.org/package=kableExtra</a>.
 </div>

images/images.html

@@ -218,7 +218,7 @@ <h1 class="title">Image Data Analysis for Group Project</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">13 September, 2024</p>
+      <p class="date">17 September, 2024</p>
     </div>
   </div>