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core/week-11/workshop.html

@@ -414,7 +414,7 @@ <h1 class="title">Workshop</h1>
 <li>how to insert special characters and equations</li>
 </ul></section></section><section id="exercise" class="level1"><h1>Exercise</h1>
 <p>🎬 The example RStudio project containing this code here: <a href="https://github.com/3mmaRand/chaffinch">chaffinch</a>. You can download the project as a zip file from there but there is some code that will do that automatically for you. Since this is an RStudio Project, do not run the code from inside a project. You may want to navigate to a particular directory or edit the <code>destdir</code>:</p>
-<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="fu">usethis</span><span class="fu">::</span><span class="fu">use_course</span><span class="op">(</span>url <span class="op">=</span> <span class="st">"3mmaRand/chaffinch"</span>, destdir <span class="op">=</span> <span class="st">"."</span><span class="op">)</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="fu">usethis</span><span class="fu">::</span><span class="fu"><a href="https://usethis.r-lib.org/reference/zip-utils.html">use_course</a></span><span class="op">(</span>url <span class="op">=</span> <span class="st">"3mmaRand/chaffinch"</span>, destdir <span class="op">=</span> <span class="st">"."</span><span class="op">)</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 <p>You can agree to deleting the zip. You should find RStudio restarts and you have a new project called chaffinch-xxxxxx. The xxxxxx is a commit reference - you do not need to worry about that, it is just a way to tell you which version of the repo you downloaded. You can now run the code in the project.</p>
 <p>🎬 Make an outline of your compendium. This could be a sketch on paper or slide or from the mindmap software you usually use. Or it could be a skeleton of folders and files on your computer.</p>
 <p>🎬 Make a start on a quarto doc.</p>

core/week-2/study_before_workshop.html

@@ -576,13 +576,13 @@
 <p>If this is a good place to create a Project directory then…</p>
 <p>🎬 Create a project with:</p>
 <div class="cell">
-<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="fu">usethis</span><span class="fu">::</span><span class="fu">create_project</span><span class="op">(</span><span class="st">"bananas"</span><span class="op">)</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="fu">usethis</span><span class="fu">::</span><span class="fu"><a href="https://usethis.r-lib.org/reference/create_package.html">create_project</a></span><span class="op">(</span><span class="st">"bananas"</span><span class="op">)</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 </div>
 </section><section id="using-the-usethis-package-3" class="slide level2"><h2>Using the <strong><code>usethis</code></strong> package</h2>
 <p>Otherwise</p>
 <p>If you want the project directory elsewhere, you will need to give the relative path, e.g.</p>
 <div class="cell">
-<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="fu">usethis</span><span class="fu">::</span><span class="fu">create_project</span><span class="op">(</span><span class="st">"../Documents/bananas"</span><span class="op">)</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="fu">usethis</span><span class="fu">::</span><span class="fu"><a href="https://usethis.r-lib.org/reference/create_package.html">create_project</a></span><span class="op">(</span><span class="st">"../Documents/bananas"</span><span class="op">)</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 </div>
 </section><section id="using-the-usethis-package-4" class="slide level2"><h2>Using the <strong><code>usethis</code></strong> package</h2>
 <p>The output will look like this and a new RStudio session will start.</p>
@@ -639,7 +639,7 @@
 <div class="fragment">
 <p>🎬 We can add a README with:</p>
 <div class="cell">
-<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="fu">usethis</span><span class="fu">::</span><span class="fu">use_readme_md</span><span class="op">(</span><span class="op">)</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="fu">usethis</span><span class="fu">::</span><span class="fu"><a href="https://usethis.r-lib.org/reference/use_readme_rmd.html">use_readme_md</a></span><span class="op">(</span><span class="op">)</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 </div>
 </div>
 <div class="fragment">

core/week-2/workshop.html

@@ -502,52 +502,52 @@ <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 Mar 28 13:59 data
-drwxr-xr-x 2 runner docker  4096 Mar 28 13:59 images
--rw-r--r-- 1 runner docker  1597 Mar 28 13:59 overview.qmd
--rw-r--r-- 1 runner docker   184 Mar 28 13:59 study_after_workshop.qmd
--rw-r--r-- 1 runner docker  4807 Mar 28 13:59 study_before_workshop.ipynb
--rw-r--r-- 1 runner docker 13029 Mar 28 13:59 study_before_workshop.qmd
--rw-r--r-- 1 runner docker 58063 Mar 28 13:59 workshop.html
--rw-r--r-- 1 runner docker  8550 Mar 28 13:59 workshop.qmd
--rw-r--r-- 1 runner docker  8564 Mar 28 14:23 workshop.rmarkdown
-drwxr-xr-x 3 runner docker  4096 Mar 28 13:59 workshop_files</code></pre>
+drwxr-xr-x 2 runner docker  4096 Mar 28 17:29 data
+drwxr-xr-x 2 runner docker  4096 Mar 28 17:29 images
+-rw-r--r-- 1 runner docker  1597 Mar 28 17:29 overview.qmd
+-rw-r--r-- 1 runner docker   184 Mar 28 17:29 study_after_workshop.qmd
+-rw-r--r-- 1 runner docker  4807 Mar 28 17:29 study_before_workshop.ipynb
+-rw-r--r-- 1 runner docker 13029 Mar 28 17:29 study_before_workshop.qmd
+-rw-r--r-- 1 runner docker 58063 Mar 28 17:29 workshop.html
+-rw-r--r-- 1 runner docker  8550 Mar 28 17:29 workshop.qmd
+-rw-r--r-- 1 runner docker  8564 Mar 28 17:32 workshop.rmarkdown
+drwxr-xr-x 3 runner docker  4096 Mar 28 17:29 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 Mar 28 13:59 data
-drwxr-xr-x 2 runner docker 4.0K Mar 28 13:59 images
--rw-r--r-- 1 runner docker 1.6K Mar 28 13:59 overview.qmd
--rw-r--r-- 1 runner docker  184 Mar 28 13:59 study_after_workshop.qmd
--rw-r--r-- 1 runner docker 4.7K Mar 28 13:59 study_before_workshop.ipynb
--rw-r--r-- 1 runner docker  13K Mar 28 13:59 study_before_workshop.qmd
--rw-r--r-- 1 runner docker  57K Mar 28 13:59 workshop.html
--rw-r--r-- 1 runner docker 8.4K Mar 28 13:59 workshop.qmd
--rw-r--r-- 1 runner docker 8.4K Mar 28 14:23 workshop.rmarkdown
-drwxr-xr-x 3 runner docker 4.0K Mar 28 13:59 workshop_files</code></pre>
+drwxr-xr-x 2 runner docker 4.0K Mar 28 17:29 data
+drwxr-xr-x 2 runner docker 4.0K Mar 28 17:29 images
+-rw-r--r-- 1 runner docker 1.6K Mar 28 17:29 overview.qmd
+-rw-r--r-- 1 runner docker  184 Mar 28 17:29 study_after_workshop.qmd
+-rw-r--r-- 1 runner docker 4.7K Mar 28 17:29 study_before_workshop.ipynb
+-rw-r--r-- 1 runner docker  13K Mar 28 17:29 study_before_workshop.qmd
+-rw-r--r-- 1 runner docker  57K Mar 28 17:29 workshop.html
+-rw-r--r-- 1 runner docker 8.4K Mar 28 17:29 workshop.qmd
+-rw-r--r-- 1 runner docker 8.4K Mar 28 17:32 workshop.rmarkdown
+drwxr-xr-x 3 runner docker 4.0K Mar 28 17:29 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 Mar 28 14:23 .
-drwxr-xr-x 6 runner docker 4.0K Mar 28 13:59 ..
-drwxr-xr-x 2 runner docker 4.0K Mar 28 13:59 data
-drwxr-xr-x 2 runner docker 4.0K Mar 28 13:59 images
--rw-r--r-- 1 runner docker 1.6K Mar 28 13:59 overview.qmd
--rw-r--r-- 1 runner docker  184 Mar 28 13:59 study_after_workshop.qmd
--rw-r--r-- 1 runner docker 4.7K Mar 28 13:59 study_before_workshop.ipynb
--rw-r--r-- 1 runner docker  13K Mar 28 13:59 study_before_workshop.qmd
--rw-r--r-- 1 runner docker  57K Mar 28 13:59 workshop.html
--rw-r--r-- 1 runner docker 8.4K Mar 28 13:59 workshop.qmd
--rw-r--r-- 1 runner docker 8.4K Mar 28 14:23 workshop.rmarkdown
-drwxr-xr-x 3 runner docker 4.0K Mar 28 13:59 workshop_files</code></pre>
+drwxr-xr-x 5 runner docker 4.0K Mar 28 17:32 .
+drwxr-xr-x 6 runner docker 4.0K Mar 28 17:29 ..
+drwxr-xr-x 2 runner docker 4.0K Mar 28 17:29 data
+drwxr-xr-x 2 runner docker 4.0K Mar 28 17:29 images
+-rw-r--r-- 1 runner docker 1.6K Mar 28 17:29 overview.qmd
+-rw-r--r-- 1 runner docker  184 Mar 28 17:29 study_after_workshop.qmd
+-rw-r--r-- 1 runner docker 4.7K Mar 28 17:29 study_before_workshop.ipynb
+-rw-r--r-- 1 runner docker  13K Mar 28 17:29 study_before_workshop.qmd
+-rw-r--r-- 1 runner docker  57K Mar 28 17:29 workshop.html
+-rw-r--r-- 1 runner docker 8.4K Mar 28 17:29 workshop.qmd
+-rw-r--r-- 1 runner docker 8.4K Mar 28 17:32 workshop.rmarkdown
+drwxr-xr-x 3 runner docker 4.0K Mar 28 17:29 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>

images/images.html

@@ -332,7 +332,7 @@ <h1 class="title">Image Data Analysis for Group Project</h1>
 <p>You now have a dataframe with all the tracking data which is relatively easy to summarise and plot using tools you know.</p>
 <p>There is an example RStudio project containing this code here: <a href="https://github.com/3mmaRand/tips">tips</a>. You can also download the project as a zip file from there but there is some code that will do that automatically for you. Since this is an RStudio Project, do not run the code from inside a project. You may want to navigate to a particular directory or edit the <code>destdir</code>:</p>
 <div class="cell">
-<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="fu">usethis</span><span class="fu">::</span><span class="fu">use_course</span><span class="op">(</span>url <span class="op">=</span> <span class="st">"3mmaRand/tips"</span>, destdir <span class="op">=</span> <span class="st">"."</span><span class="op">)</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="fu">usethis</span><span class="fu">::</span><span class="fu"><a href="https://usethis.r-lib.org/reference/zip-utils.html">use_course</a></span><span class="op">(</span>url <span class="op">=</span> <span class="st">"3mmaRand/tips"</span>, destdir <span class="op">=</span> <span class="st">"."</span><span class="op">)</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 </div>
 <p>You can agree to deleting the zip. You should find RStudio restarts and you have a new project called tips-xxxxxx. The xxxxxx is a commit reference - you do not need to worry about that, it is just a way to tell you which version of the repo you downloaded. You can now run the code in the project.</p>