Initial updates following Neale's review

html_outputs/index.html

@@ -725,7 +725,7 @@ <h1 class="title">The Epidemiologist R Handbook</h1>
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     <div class="quarto-title-meta-heading">Last updated</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">Oct 2, 2024</p>
+      <p class="date">Oct 18, 2024</p>
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@@ -1463,7 +1463,7 @@ <h3 class="unnumbered anchored" data-anchor-id="contribution">Contribution</h3>
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html_outputs/new_pages/basics.html

@@ -1249,7 +1249,7 @@ <h3 class="unnumbered anchored" data-anchor-id="functions-with-multiple-argument
 <ul>
 <li>Show proportions instead of counts (set <code>proportional = TRUE</code> when the default is <code>FALSE</code>)<br>
 </li>
-<li>Specify the two colors to use (<code>pal =</code> is short for “palette” and is supplied with a vector of two color names. See the <a href="https://epirhandbook.com/new_pages/basics.html#objects">objects</a> page for how the function <code>c()</code> makes a vector)</li>
+<li>Specify the two colors to use (<code>pal =</code> is short for “palette” and is supplied with a vector of two color names. See the <a href="../new_pages/basics.html#objects">objects</a> page for how the function <code>c()</code> makes a vector)</li>
 </ul>
 <p><span style="color: black;"><strong><em>NOTE:</em></strong> For arguments that you specify with both parts of the argument (e.g.&nbsp;<code>proportional = TRUE</code>), their order among all the arguments does not matter.</span></p>
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@@ -1327,7 +1327,7 @@ <h3 class="unnumbered anchored" data-anchor-id="install-and-load">Install and lo
 </ol>
 <section id="your-library" class="level4 unnumbered">
 <h4 class="unnumbered anchored" data-anchor-id="your-library">Your library</h4>
-<p>Your “library” is actually a folder on your computer, containing a folder for each package that has been installed. Find out where R is installed in your computer, and look for a folder called “win-library”. For example: <code>R\win-library\4.4.1</code> (the 4.4.1 is the R version - you’ll have a different library for each R version you’ve downloaded).</p>
+<p>Your “library” is actually a folder on your computer, containing a folder for each package that has been installed. Find out where R is installed in your computer, and look for a folder called “library”. For example: <code>R\4.4.1\library</code> (the 4.4.1 is the R version - you’ll have a different library for each R version you’ve downloaded).</p>
 <p>You can print the file path to your library by entering <code>.libPaths()</code> (empty parentheses). This becomes especially important if working with <a href="../new_pages/network_drives.html">R on network drives</a>.</p>
 </section>
 <section id="install-from-cran" class="level4 unnumbered">
@@ -1364,7 +1364,7 @@ <h4 class="unnumbered anchored" data-anchor-id="how-to-install-and-load">How to
 </div>
 <p>To check whether a package is installed or loaded, you can view the Packages pane in RStudio. If the package is installed, it is shown there with version number. If its box is checked, it is loaded for the current session.</p>
 <p><strong>Install from Github</strong></p>
-<p>Sometimes, you need to install a package that is not yet available from CRAN. Or perhaps the package is available on CRAN but you want the <em>development version</em> with new features not yet offered in the more stable published CRAN version. These are often hosted on the website <a href="https://github.com/">github.com</a> in a free, public-facing code “repository”. Read more about Github in the handbook page on <a href="https://epirhandbook.com/new_pages/collaboration.html">Version control and collaboration with Git and Github</a>.</p>
+<p>Sometimes, you need to install a package that is not yet available from CRAN. Or perhaps the package is available on CRAN but you want the <em>development version</em> with new features not yet offered in the more stable published CRAN version. These are often hosted on the website <a href="https://github.com/">github.com</a> in a free, public-facing code “repository”. Read more about Github in the handbook page on <a href="../new_pages/collaboration.html">Version control and collaboration with Git and Github</a>.</p>
 <p>To download R packages from Github, you can use the function <code>p_load_gh()</code> from <strong>pacman</strong>, which will install the package if necessary, and load it for use in your current R session. Alternatives to install include using the <strong>remotes</strong> or <strong>devtools</strong> packages. Read more about all the <strong>pacman</strong> functions in the <a href="https://cran.r-project.org/web/packages/pacman/pacman.pdf">package documentation</a>.</p>
 <p>To install from Github, you have to provide more information. You must provide:</p>
 <ol type="1">
@@ -1738,7 +1738,7 @@ <h3 class="unnumbered anchored" data-anchor-id="defining-objects--">Defining obj
 </div>
 </div>
 <p><strong>Columns</strong></p>
-<p>Columns in a dataset are also objects and can be defined, over-written, and created as described below in the section on <a href="https://epirhandbook.com/new_pages/basics.html#columnsvariables">Columns</a>.</p>
+<p>Columns in a dataset are also objects and can be defined, over-written, and created as described below in the section on <a href="../new_pages/basics.html#columnsvariables">Columns</a>.</p>
 <p>You can use the assignment operator from <strong>base</strong> R to create a new column. Below, the new column <code>bmi</code> (Body Mass Index) is created, and for each row the new value is result of a mathematical operation on the row’s value in the <code>wt_kg</code> and <code>ht_cm</code> columns.</p>
 <div class="cell">
 <div class="sourceCode cell-code" id="cb34"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb34-1"><a href="#cb34-1" aria-hidden="true" tabindex="-1"></a><span class="co"># create new "bmi" column using base R syntax</span></span>
@@ -3348,7 +3348,7 @@ <h3 class="unnumbered anchored" data-anchor-id="code-assists">Code assists</h3>
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