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<title>1 Introduction | A New Instrument for Microbial Epidemiology</title>
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<meta property="og:title" content="1 Introduction | A New Instrument for Microbial Epidemiology" />
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<meta name="twitter:title" content="1 Introduction | A New Instrument for Microbial Epidemiology" />
<meta name="twitter:description" content="This is the PhD thesis of the author." />
<meta name="author" content="Matthijs S. Berends" />
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<li><a href="./">A New Instrument for Microbial Epidemiology</a></li>
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<li class="chapter" data-level="" data-path="index.html"><a href="index.html"><i class="fa fa-check"></i>Prerequisites</a></li>
<li class="chapter" data-level="1" data-path="intro.html"><a href="intro.html"><i class="fa fa-check"></i><b>1</b> Introduction</a></li>
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<h1>
<i class="fa fa-circle-o-notch fa-spin"></i><a href="./">A New Instrument for Microbial Epidemiology</a>
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<section class="normal" id="section-">
<div id="intro" class="section level1" number="1">
<h1><span class="header-section-number">1</span> Introduction</h1>
<p>You can label chapter and section titles using <code>{#label}</code> after them, e.g., we can reference Chapter <a href="intro.html#intro">1</a>. If you do not manually label them, there will be automatic labels anyway, e.g., Chapter <a href="#methods"><strong>??</strong></a>.</p>
<p>Figures and tables with captions will be placed in <code>figure</code> and <code>table</code> environments, respectively.</p>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb1-1"><a href="intro.html#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="fu">par</span>(<span class="at">mar =</span> <span class="fu">c</span>(<span class="dv">4</span>, <span class="dv">4</span>, .<span class="dv">1</span>, .<span class="dv">1</span>))</span>
<span id="cb1-2"><a href="intro.html#cb1-2" aria-hidden="true" tabindex="-1"></a><span class="fu">plot</span>(pressure, <span class="at">type =</span> <span class="st">&#39;b&#39;</span>, <span class="at">pch =</span> <span class="dv">19</span>)</span></code></pre></div>
<div class="figure" style="text-align: center"><span style="display:block;" id="fig:nice-fig"></span>
<img src="a_new_instrument_for_microbial_epidemiology_files/figure-html/nice-fig-1.png" alt="Here is a nice figure!" width="80%" />
<p class="caption">
Figure 1.1: Here is a nice figure!
</p>
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<p>Reference a figure by its code chunk label with the <code>fig:</code> prefix, e.g., see Figure <a href="intro.html#fig:nice-fig">1.1</a>. Similarly, you can reference tables generated from <code>knitr::kable()</code>, e.g., see Table <a href="intro.html#tab:nice-tab">1.1</a>.</p>
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb2-1"><a href="intro.html#cb2-1" aria-hidden="true" tabindex="-1"></a>knitr<span class="sc">::</span><span class="fu">kable</span>(</span>
<span id="cb2-2"><a href="intro.html#cb2-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">head</span>(iris, <span class="dv">20</span>), <span class="at">caption =</span> <span class="st">&#39;Here is a nice table!&#39;</span>,</span>
<span id="cb2-3"><a href="intro.html#cb2-3" aria-hidden="true" tabindex="-1"></a> <span class="at">booktabs =</span> <span class="cn">TRUE</span></span>
<span id="cb2-4"><a href="intro.html#cb2-4" aria-hidden="true" tabindex="-1"></a>)</span></code></pre></div>
<table>
<caption><span id="tab:nice-tab">Table 1.1: </span>Here is a nice table!</caption>
<thead>
<tr class="header">
<th align="right">Sepal.Length</th>
<th align="right">Sepal.Width</th>
<th align="right">Petal.Length</th>
<th align="right">Petal.Width</th>
<th align="left">Species</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td align="right">5.1</td>
<td align="right">3.5</td>
<td align="right">1.4</td>
<td align="right">0.2</td>
<td align="left">setosa</td>
</tr>
<tr class="even">
<td align="right">4.9</td>
<td align="right">3.0</td>
<td align="right">1.4</td>
<td align="right">0.2</td>
<td align="left">setosa</td>
</tr>
<tr class="odd">
<td align="right">4.7</td>
<td align="right">3.2</td>
<td align="right">1.3</td>
<td align="right">0.2</td>
<td align="left">setosa</td>
</tr>
<tr class="even">
<td align="right">4.6</td>
<td align="right">3.1</td>
<td align="right">1.5</td>
<td align="right">0.2</td>
<td align="left">setosa</td>
</tr>
<tr class="odd">
<td align="right">5.0</td>
<td align="right">3.6</td>
<td align="right">1.4</td>
<td align="right">0.2</td>
<td align="left">setosa</td>
</tr>
<tr class="even">
<td align="right">5.4</td>
<td align="right">3.9</td>
<td align="right">1.7</td>
<td align="right">0.4</td>
<td align="left">setosa</td>
</tr>
<tr class="odd">
<td align="right">4.6</td>
<td align="right">3.4</td>
<td align="right">1.4</td>
<td align="right">0.3</td>
<td align="left">setosa</td>
</tr>
<tr class="even">
<td align="right">5.0</td>
<td align="right">3.4</td>
<td align="right">1.5</td>
<td align="right">0.2</td>
<td align="left">setosa</td>
</tr>
<tr class="odd">
<td align="right">4.4</td>
<td align="right">2.9</td>
<td align="right">1.4</td>
<td align="right">0.2</td>
<td align="left">setosa</td>
</tr>
<tr class="even">
<td align="right">4.9</td>
<td align="right">3.1</td>
<td align="right">1.5</td>
<td align="right">0.1</td>
<td align="left">setosa</td>
</tr>
<tr class="odd">
<td align="right">5.4</td>
<td align="right">3.7</td>
<td align="right">1.5</td>
<td align="right">0.2</td>
<td align="left">setosa</td>
</tr>
<tr class="even">
<td align="right">4.8</td>
<td align="right">3.4</td>
<td align="right">1.6</td>
<td align="right">0.2</td>
<td align="left">setosa</td>
</tr>
<tr class="odd">
<td align="right">4.8</td>
<td align="right">3.0</td>
<td align="right">1.4</td>
<td align="right">0.1</td>
<td align="left">setosa</td>
</tr>
<tr class="even">
<td align="right">4.3</td>
<td align="right">3.0</td>
<td align="right">1.1</td>
<td align="right">0.1</td>
<td align="left">setosa</td>
</tr>
<tr class="odd">
<td align="right">5.8</td>
<td align="right">4.0</td>
<td align="right">1.2</td>
<td align="right">0.2</td>
<td align="left">setosa</td>
</tr>
<tr class="even">
<td align="right">5.7</td>
<td align="right">4.4</td>
<td align="right">1.5</td>
<td align="right">0.4</td>
<td align="left">setosa</td>
</tr>
<tr class="odd">
<td align="right">5.4</td>
<td align="right">3.9</td>
<td align="right">1.3</td>
<td align="right">0.4</td>
<td align="left">setosa</td>
</tr>
<tr class="even">
<td align="right">5.1</td>
<td align="right">3.5</td>
<td align="right">1.4</td>
<td align="right">0.3</td>
<td align="left">setosa</td>
</tr>
<tr class="odd">
<td align="right">5.7</td>
<td align="right">3.8</td>
<td align="right">1.7</td>
<td align="right">0.3</td>
<td align="left">setosa</td>
</tr>
<tr class="even">
<td align="right">5.1</td>
<td align="right">3.8</td>
<td align="right">1.5</td>
<td align="right">0.3</td>
<td align="left">setosa</td>
</tr>
</tbody>
</table>
</div>
</section>
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