parent 32188bd8a5
commit f41dfb2835

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.Rproj.user
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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"
book_filename: "a_new_instrument_for_microbial_epidemiology"
language:
ui:
chapter_name: "Chapter "
delete_merged_file: true

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bookdown::gitbook:
css: style.css
config:
toc:
before: |
<li><a href="./">A New Instrument for Microbial Epidemiology</a></li>
after: |
<li><a href="https://github.com/rstudio/bookdown" target="blank">Published with bookdown</a></li>
# edit: https://github.com/msberends/a_new_instrument_for_microbial_epidemiology/edit/master/%s
download: ["pdf", "epub"]
bookdown::pdf_book:
includes:
in_header: preamble.tex
latex_engine: xelatex
citation_package: natbib
keep_tex: yes
bookdown::epub_book: default
# no bootstrap 4 for now
# bookdown::bs4_book: default

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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>
<li class="divider"></li>
<li><a href="https://github.com/rstudio/bookdown" target="blank">Published with bookdown</a></li>
</ul>
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<h1>
<i class="fa fa-circle-o-notch fa-spin"></i><a href="./">A New Instrument for Microbial Epidemiology</a>
</h1>
</div>
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<p>You may want to try searching to find the page's new location, or use
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<!DOCTYPE html>
<html lang="" xml:lang="">
<head>
<meta charset="utf-8" />
<meta http-equiv="X-UA-Compatible" content="IE=edge" />
<title>A New Instrument for Microbial Epidemiology</title>
<meta name="description" content="This is the PhD thesis of the author." />
<meta name="generator" content="bookdown 0.24 and GitBook 2.6.7" />
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<meta name="twitter:title" content="A New Instrument for Microbial Epidemiology" />
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<meta name="author" content="Matthijs S. Berends" />
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<li><a href="./">A New Instrument for Microbial Epidemiology</a></li>
<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>
<li class="divider"></li>
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</h1>
</div>
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<section class="normal" id="section-">
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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">
<h1>Prerequisites</h1>
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<!DOCTYPE html>
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<i class="fa fa-circle-o-notch fa-spin"></i><a href="./">A New Instrument for Microbial Epidemiology</a>
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<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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<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>
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<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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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;
font-weight: normal;
}
.book.color-theme-1 .book-summary ul.summary li.active > a,
.book.color-theme-1 .book-summary ul.summary li a:hover {
color: #704214;
background: transparent;
font-weight: normal;
}
/*
* Theme 2
*/
.book.color-theme-2 .book-summary {
color: #bcc1d2;
background: #2d3143;
border-right: none;
}
.book.color-theme-2 .book-summary .book-search {
background: transparent;
}
.book.color-theme-2 .book-summary .book-search input,
.book.color-theme-2 .book-summary .book-search input:focus {
border: 1px solid transparent;
}
.book.color-theme-2 .book-summary ul.summary li.divider {
background: #272a3a;
box-shadow: none;
}
.book.color-theme-2 .book-summary ul.summary li i.fa-check {
color: #33cc33;
}
.book.color-theme-2 .book-summary ul.summary li.done > a {
color: #62687f;
}
.book.color-theme-2 .book-summary ul.summary li a,
.book.color-theme-2 .book-summary ul.summary li span {
color: #c1c6d7;
background: transparent;
font-weight: 600;
}
.book.color-theme-2 .book-summary ul.summary li.active > a,
.book.color-theme-2 .book-summary ul.summary li a:hover {
color: #f4f4f5;
background: #252737;
font-weight: 600;
}

@ -0,0 +1,426 @@
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/* http://jmblog.github.com/color-themes-for-google-code-highlightjs */
/* Tomorrow Comment */
/* Tomorrow Red */
/* Tomorrow Orange */
/* Tomorrow Yellow */
/* Tomorrow Green */
/* Tomorrow Aqua */
/* Tomorrow Blue */
/* Tomorrow Purple */
}
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.book .book-body .page-wrapper .page-inner section.normal pre .hljs-title,
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color: #8e908c;
}
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color: #c82829;
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color: #f5871f;
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