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# Introduction {#intro}
You can label chapter and section titles using `{#label}` after them, e.g., we can reference Chapter \@ref(intro). If you do not manually label them, there will be automatic labels anyway, e.g., Chapter \@ref(methods).
Figures and tables with captions will be placed in `figure` and `table` environments, respectively.
```{r nice-fig, fig.cap='Here is a nice figure!', out.width='80%', fig.asp=.75, fig.align='center'}
par(mar = c(4, 4, .1, .1))
plot(pressure, type = 'b', pch = 19)
```
Reference a figure by its code chunk label with the `fig:` prefix, e.g., see Figure \@ref(fig:nice-fig). Similarly, you can reference tables generated from `knitr::kable()`, e.g., see Table \@ref(tab:nice-tab).
```{r nice-tab, tidy=FALSE}
knitr::kable(
head(iris, 20), caption = 'Here is a nice table!',
booktabs = TRUE
)
```

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output_dir: "docs"
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language:
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bookdown::gitbook:
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# edit: https://github.com/msberends/a_new_instrument_for_microbial_epidemiology/edit/master/%s
download: ["pdf", "epub"]
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<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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<p>You may want to try searching to find the page's new location, or use
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<li class="divider"></li>
<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 class="title">A New Instrument for Microbial Epidemiology</h1>
<h2 class="subtitle"><em>Empowering Antimicrobial Resistance Data Analysis</em></h2>
<p class="author"><em>Matthijs S. Berends</em></p>
<p class="date"><em>25 August 2021</em></p>
</div>
<div id="prerequisites" class="section level1 unnumbered">
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<li><a href="./">A New Instrument for Microbial Epidemiology</a></li>
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<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>
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<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%" />
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Figure 1.1: Here is a nice figure!
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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>
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}
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.book.color-theme-1 .book-body .page-wrapper .page-inner section.normal table td {
border-color: #f5d06c;
}
.book.color-theme-1 .book-body .page-wrapper .page-inner section.normal table tr {
color: inherit;
background-color: #fdf6e3;
border-color: #444444;
}
.book.color-theme-1 .book-body .page-wrapper .page-inner section.normal table tr:nth-child(2n) {
background-color: #fbeecb;
}
.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal {
color: #bdcadb;
}
.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal a {
color: #3eb1d0;
}
.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal h1,
.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal h2,
.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal h3,
.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal h4,
.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal h5,
.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal h6 {
color: #fffffa;
}
.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal h1,
.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal h2 {
border-color: #373b4e;
}
.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal h6 {
color: #373b4e;
}
.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal hr {
background-color: #373b4e;
}
.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal blockquote {
border-color: #373b4e;
}
.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal pre,
.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal code {
color: #9dbed8;
background: #2d3143;
border-color: #2d3143;
}
.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal .highlight {
background-color: #282a39;
}
.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal table th,
.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal table td {
border-color: #3b3f54;
}
.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal table tr {
color: #b6c2d2;
background-color: #2d3143;
border-color: #3b3f54;
}
.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal table tr:nth-child(2n) {
background-color: #35394b;
}
.book.color-theme-1 .book-header {
color: #afa790;
background: transparent;
}
.book.color-theme-1 .book-header .btn {
color: #afa790;
}
.book.color-theme-1 .book-header .btn:hover {
color: #73553c;
background: none;
}
.book.color-theme-1 .book-header h1 {
color: #704214;
}
.book.color-theme-2 .book-header {
color: #7e888b;
background: transparent;
}
.book.color-theme-2 .book-header .btn {
color: #3b3f54;
}
.book.color-theme-2 .book-header .btn:hover {
color: #fffff5;
background: none;
}
.book.color-theme-2 .book-header h1 {
color: #bdcadb;
}
.book.color-theme-1 .book-body .navigation {
color: #afa790;
}
.book.color-theme-1 .book-body .navigation:hover {
color: #73553c;
}
.book.color-theme-2 .book-body .navigation {
color: #383f52;
}
.book.color-theme-2 .book-body .navigation:hover {
color: #fffff5;
}
/*
* Theme 1
*/
.book.color-theme-1 .book-summary {
color: #afa790;
background: #111111;
border-right: 1px solid rgba(0, 0, 0, 0.07);
}
.book.color-theme-1 .book-summary .book-search {
background: transparent;
}
.book.color-theme-1 .book-summary .book-search input,
.book.color-theme-1 .book-summary .book-search input:focus {
border: 1px solid transparent;
}
.book.color-theme-1 .book-summary ul.summary li.divider {
background: #7e888b;
box-shadow: none;
}
.book.color-theme-1 .book-summary ul.summary li i.fa-check {
color: #33cc33;
}
.book.color-theme-1 .book-summary ul.summary li.done > a {
color: #877f6a;
}
.book.color-theme-1 .book-summary ul.summary li a,
.book.color-theme-1 .book-summary ul.summary li span {
color: #877f6a;
background: transparent;