This is my full PhD thesis in R Markdown (using the bookdown package), containing a PDF and EPUB file, and a website in the ‘docs’ folder with the integral content of the book. https://git.io/PhDthesisAMR
You can not select more than 25 topics Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.
 
 
phd_thesis/docs/introduction.html

400 lines
14 KiB

<!DOCTYPE html>
<html lang="" xml:lang="">
<head>
<meta charset="utf-8" />
<meta http-equiv="X-UA-Compatible" content="IE=edge" />
<title>1 Introduction | 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" />
<meta property="og:title" content="1 Introduction | A New Instrument for Microbial Epidemiology" />
<meta property="og:type" content="book" />
<meta property="og:description" content="This is the PhD thesis of the author." />
<meta name="github-repo" content="msberends/a_new_instrument_for_microbial_epidemiology" />
<meta name="twitter:card" content="summary" />
<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" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<meta name="apple-mobile-web-app-capable" content="yes" />
<meta name="apple-mobile-web-app-status-bar-style" content="black" />
<link rel="prev" href="colophon.html"/>
<script src="libs/header-attrs-2.10/header-attrs.js"></script>
<script src="libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
<script src="https://cdn.jsdelivr.net/npm/fuse.js@6.4.6/dist/fuse.min.js"></script>
<link href="libs/gitbook-2.6.7/css/style.css" rel="stylesheet" />
<link href="libs/gitbook-2.6.7/css/plugin-table.css" rel="stylesheet" />
<link href="libs/gitbook-2.6.7/css/plugin-bookdown.css" rel="stylesheet" />
<link href="libs/gitbook-2.6.7/css/plugin-highlight.css" rel="stylesheet" />
<link href="libs/gitbook-2.6.7/css/plugin-search.css" rel="stylesheet" />
<link href="libs/gitbook-2.6.7/css/plugin-fontsettings.css" rel="stylesheet" />
<link href="libs/gitbook-2.6.7/css/plugin-clipboard.css" rel="stylesheet" />
<link href="libs/anchor-sections-1.0.1/anchor-sections.css" rel="stylesheet" />
<script src="libs/anchor-sections-1.0.1/anchor-sections.js"></script>
<style type="text/css">
pre > code.sourceCode { white-space: pre; position: relative; }
pre > code.sourceCode > span { display: inline-block; line-height: 1.25; }
pre > code.sourceCode > span:empty { height: 1.2em; }
.sourceCode { overflow: visible; }
code.sourceCode > span { color: inherit; text-decoration: inherit; }
pre.sourceCode { margin: 0; }
@media screen {
div.sourceCode { overflow: auto; }
}
@media print {
pre > code.sourceCode { white-space: pre-wrap; }
pre > code.sourceCode > span { text-indent: -5em; padding-left: 5em; }
}
pre.numberSource code
{ counter-reset: source-line 0; }
pre.numberSource code > span
{ position: relative; left: -4em; counter-increment: source-line; }
pre.numberSource code > span > a:first-child::before
{ content: counter(source-line);
position: relative; left: -1em; text-align: right; vertical-align: baseline;
border: none; display: inline-block;
-webkit-touch-callout: none; -webkit-user-select: none;
-khtml-user-select: none; -moz-user-select: none;
-ms-user-select: none; user-select: none;
padding: 0 4px; width: 4em;
color: #aaaaaa;
}
pre.numberSource { margin-left: 3em; border-left: 1px solid #aaaaaa; padding-left: 4px; }
div.sourceCode
{ }
@media screen {
pre > code.sourceCode > span > a:first-child::before { text-decoration: underline; }
}
code span.al { color: #ff0000; font-weight: bold; } /* Alert */
code span.an { color: #60a0b0; font-weight: bold; font-style: italic; } /* Annotation */
code span.at { color: #7d9029; } /* Attribute */
code span.bn { color: #40a070; } /* BaseN */
code span.bu { } /* BuiltIn */
code span.cf { color: #007020; font-weight: bold; } /* ControlFlow */
code span.ch { color: #4070a0; } /* Char */
code span.cn { color: #880000; } /* Constant */
code span.co { color: #60a0b0; font-style: italic; } /* Comment */
code span.cv { color: #60a0b0; font-weight: bold; font-style: italic; } /* CommentVar */
code span.do { color: #ba2121; font-style: italic; } /* Documentation */
code span.dt { color: #902000; } /* DataType */
code span.dv { color: #40a070; } /* DecVal */
code span.er { color: #ff0000; font-weight: bold; } /* Error */
code span.ex { } /* Extension */
code span.fl { color: #40a070; } /* Float */
code span.fu { color: #06287e; } /* Function */
code span.im { } /* Import */
code span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Information */
code span.kw { color: #007020; font-weight: bold; } /* Keyword */
code span.op { color: #666666; } /* Operator */
code span.ot { color: #007020; } /* Other */
code span.pp { color: #bc7a00; } /* Preprocessor */
code span.sc { color: #4070a0; } /* SpecialChar */
code span.ss { color: #bb6688; } /* SpecialString */
code span.st { color: #4070a0; } /* String */
code span.va { color: #19177c; } /* Variable */
code span.vs { color: #4070a0; } /* VerbatimString */
code span.wa { color: #60a0b0; font-weight: bold; font-style: italic; } /* Warning */
</style>
<link rel="stylesheet" href="style.css" type="text/css" />
</head>
<body>
<div class="book without-animation with-summary font-size-2 font-family-1" data-basepath=".">
<div class="book-summary">
<nav role="navigation">
<ul class="summary">
<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>Preamble</a>
<ul>
<li class="chapter" data-level="" data-path="index.html"><a href="index.html#short-summary-250-words"><i class="fa fa-check"></i>Short summary (250 words)</a></li>
</ul></li>
<li class="chapter" data-level="" data-path="colophon.html"><a href="colophon.html"><i class="fa fa-check"></i>Colophon</a></li>
<li class="chapter" data-level="1" data-path="introduction.html"><a href="introduction.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>
</nav>
</div>
<div class="book-body">
<div class="body-inner">
<div class="book-header" role="navigation">
<h1>
<i class="fa fa-circle-o-notch fa-spin"></i><a href="./">A New Instrument for Microbial Epidemiology</a>
</h1>
</div>
<div class="page-wrapper" tabindex="-1" role="main">
<div class="page-inner">
<section class="normal" id="section-">
<div id="introduction" 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="introduction.html#introduction">1</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="introduction.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="introduction.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>
</div>
<p>Reference a figure by its code chunk label with the <code>fig:</code> prefix, e.g., see Figure <a href="introduction.html#fig:nice-fig">1.1</a>. Similarly, you can reference tables generated from <code>knitr::kable()</code>, e.g., see Table <a href="introduction.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="introduction.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="introduction.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="introduction.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="introduction.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>
</div>
</div>
</div>
<a href="colophon.html" class="navigation navigation-prev navigation-unique" aria-label="Previous page"><i class="fa fa-angle-left"></i></a>
</div>
</div>
<script src="libs/gitbook-2.6.7/js/app.min.js"></script>
<script src="libs/gitbook-2.6.7/js/clipboard.min.js"></script>
<script src="libs/gitbook-2.6.7/js/plugin-search.js"></script>
<script src="libs/gitbook-2.6.7/js/plugin-sharing.js"></script>
<script src="libs/gitbook-2.6.7/js/plugin-fontsettings.js"></script>
<script src="libs/gitbook-2.6.7/js/plugin-bookdown.js"></script>
<script src="libs/gitbook-2.6.7/js/jquery.highlight.js"></script>
<script src="libs/gitbook-2.6.7/js/plugin-clipboard.js"></script>
<script>
gitbook.require(["gitbook"], function(gitbook) {
gitbook.start({
"sharing": {
"github": false,
"facebook": true,
"twitter": true,
"linkedin": false,
"weibo": false,
"instapaper": false,
"vk": false,
"whatsapp": false,
"all": ["facebook", "twitter", "linkedin", "weibo", "instapaper"]
},
"fontsettings": {
"theme": "white",
"family": "sans",
"size": 2
},
"edit": {
"link": null,
"text": null
},
"history": {
"link": null,
"text": null
},
"view": {
"link": null,
"text": null
},
"download": ["a_new_instrument_for_microbial_epidemiology.pdf", "a_new_instrument_for_microbial_epidemiology.epub"],
"search": {
"engine": "fuse",
"options": null
},
"toc": {
"collapse": "subsection"
}
});
});
</script>
</body>
</html>