1st
parent
32188bd8a5
commit
f41dfb2835
@ -0,0 +1,6 @@
|
||||
.Rproj.user
|
||||
.Rhistory
|
||||
.RData
|
||||
.Ruserdata
|
||||
.DS_Store
|
||||
*.Rproj
|
@ -0,0 +1,19 @@
|
||||
# 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
|
||||
)
|
||||
```
|
@ -0,0 +1,6 @@
|
||||
output_dir: "docs"
|
||||
book_filename: "a_new_instrument_for_microbial_epidemiology"
|
||||
language:
|
||||
ui:
|
||||
chapter_name: "Chapter "
|
||||
delete_merged_file: true
|
Binary file not shown.
After Width: | Height: | Size: 19 KiB |
@ -0,0 +1,22 @@
|
||||
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
|
@ -0,0 +1,230 @@
|
||||
<!DOCTYPE html>
|
||||
<html lang="" xml:lang="">
|
||||
<head>
|
||||
|
||||
<meta charset="utf-8" />
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge" />
|
||||
<title>Page not found | 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="Page not found | 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="Page not found | 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="date" content="2021-08-25" />
|
||||
|
||||
<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" />
|
||||
|
||||
|
||||
|
||||
|
||||
<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>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>
|
||||
<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="page-not-found" class="section level1">
|
||||
<h1>Page not found</h1>
|
||||
<p>The page you requested cannot be found (perhaps it was moved or renamed).</p>
|
||||
<p>You may want to try searching to find the page's new location, or use
|
||||
the table of contents to find the page you are looking for.</p>
|
||||
</div>
|
||||
</section>
|
||||
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
|
||||
</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>
|
Binary file not shown.
After Width: | Height: | Size: 19 KiB |
@ -0,0 +1,235 @@
|
||||
<!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" />
|
||||
|
||||
<meta property="og:title" content="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="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="date" content="2021-08-25" />
|
||||
|
||||
<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="next" href="intro.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>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>
|
||||
<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="header">
|
||||
<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>
|
||||
<p>txt</p>
|
||||
|
||||
</div>
|
||||
</section>
|
||||
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<a href="intro.html" class="navigation navigation-next navigation-unique" aria-label="Next page"><i class="fa fa-angle-right"></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>
|
@ -0,0 +1,397 @@
|
||||
<!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="date" content="2021-08-25" />
|
||||
|
||||
<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="index.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>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>
|
||||
<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="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">'b'</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="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">'Here is a nice table!'</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>
|
||||
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<a href="index.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>
|
@ -0,0 +1,5 @@
|
||||
/* Styles for section anchors */
|
||||
a.anchor-section {margin-left: 10px; visibility: hidden; color: inherit;}
|
||||
a.anchor-section::before {content: '#';}
|
||||
.hasAnchor:hover a.anchor-section {visibility: visible;}
|
||||
ul > li > .anchor-section {display: none;}
|
@ -0,0 +1,33 @@
|
||||
// Anchor sections v1.0 written by Atsushi Yasumoto on Oct 3rd, 2020.
|
||||
document.addEventListener('DOMContentLoaded', function() {
|
||||
// Do nothing if AnchorJS is used
|
||||
if (typeof window.anchors === 'object' && anchors.hasOwnProperty('hasAnchorJSLink')) {
|
||||
return;
|
||||
}
|
||||
|
||||
const h = document.querySelectorAll('h1, h2, h3, h4, h5, h6');
|
||||
|
||||
// Do nothing if sections are already anchored
|
||||
if (Array.from(h).some(x => x.classList.contains('hasAnchor'))) {
|
||||
return null;
|
||||
}
|
||||
|
||||
// Use section id when pandoc runs with --section-divs
|
||||
const section_id = function(x) {
|
||||
return ((x.classList.contains('section') || (x.tagName === 'SECTION'))
|
||||
? x.id : '');
|
||||
};
|
||||
|
||||
// Add anchors
|
||||
h.forEach(function(x) {
|
||||
const id = x.id || section_id(x.parentElement);
|
||||
if (id === '' || x.matches(':empty')) {
|
||||
return null;
|
||||
}
|
||||
let anchor = document.createElement('a');
|
||||
anchor.href = '#' + id;
|
||||
anchor.classList = ['anchor-section'];
|
||||
x.classList.add('hasAnchor');
|
||||
x.appendChild(anchor);
|
||||
});
|
||||
});
|
Binary file not shown.
@ -0,0 +1,105 @@
|
||||
.book .book-header h1 {
|
||||
padding-left: 20px;
|
||||
padding-right: 20px;
|
||||
}
|
||||
.book .book-header.fixed {
|
||||
position: fixed;
|
||||
right: 0;
|
||||
top: 0;
|
||||
left: 0;
|
||||
border-bottom: 1px solid rgba(0,0,0,.07);
|
||||
}
|
||||
span.search-highlight {
|
||||
background-color: #ffff88;
|
||||
}
|
||||
@media (min-width: 600px) {
|
||||
.book.with-summary .book-header.fixed {
|
||||
left: 300px;
|
||||
}
|
||||
}
|
||||
@media (max-width: 1240px) {
|
||||
.book .book-body.fixed {
|
||||
top: 50px;
|
||||
}
|
||||
.book .book-body.fixed .body-inner {
|
||||
top: auto;
|
||||
}
|
||||
}
|
||||
@media (max-width: 600px) {
|
||||
.book.with-summary .book-header.fixed {
|
||||
left: calc(100% - 60px);
|
||||
min-width: 300px;
|
||||
}
|
||||
.book.with-summary .book-body {
|
||||
transform: none;
|
||||
left: calc(100% - 60px);
|
||||
min-width: 300px;
|
||||
}
|
||||
.book .book-body.fixed {
|
||||
top: 0;
|
||||
}
|
||||
}
|
||||
|
||||
.book .book-body.fixed .body-inner {
|
||||
top: 50px;
|
||||
}
|
||||
.book .book-body .page-wrapper .page-inner section.normal sub, .book .book-body .page-wrapper .page-inner section.normal sup {
|
||||
font-size: 85%;
|
||||
}
|
||||
|
||||
@media print {
|
||||
.book .book-summary, .book .book-body .book-header, .fa {
|
||||
display: none !important;
|
||||
}
|
||||
.book .book-body.fixed {
|
||||
left: 0px;
|
||||
}
|
||||
.book .book-body,.book .book-body .body-inner, .book.with-summary {
|
||||
overflow: visible !important;
|
||||
}
|
||||
}
|
||||
.kable_wrapper {
|
||||
border-spacing: 20px 0;
|
||||
border-collapse: separate;
|
||||
border: none;
|
||||
margin: auto;
|
||||
}
|
||||
.kable_wrapper > tbody > tr > td {
|
||||
vertical-align: top;
|
||||
}
|
||||
.book .book-body .page-wrapper .page-inner section.normal table tr.header {
|
||||
border-top-width: 2px;
|
||||
}
|
||||
.book .book-body .page-wrapper .page-inner section.normal table tr:last-child td {
|
||||
border-bottom-width: 2px;
|
||||
}
|
||||
.book .book-body .page-wrapper .page-inner section.normal table td, .book .book-body .page-wrapper .page-inner section.normal table th {
|
||||
border-left: none;
|
||||
border-right: none;
|
||||
}
|
||||
.book .book-body .page-wrapper .page-inner section.normal table.kable_wrapper > tbody > tr, .book .book-body .page-wrapper .page-inner section.normal table.kable_wrapper > tbody > tr > td {
|
||||
border-top: none;
|
||||
}
|
||||
.book .book-body .page-wrapper .page-inner section.normal table.kable_wrapper > tbody > tr:last-child > td {
|
||||
border-bottom: none;
|
||||
}
|
||||
|
||||
div.theorem, div.lemma, div.corollary, div.proposition, div.conjecture {
|
||||
font-style: italic;
|
||||
}
|
||||
span.theorem, span.lemma, span.corollary, span.proposition, span.conjecture {
|
||||
font-style: normal;
|
||||
}
|
||||
div.proof>*:last-child:after {
|
||||
content: "\25a2";
|
||||
float: right;
|
||||
}
|
||||
.header-section-number {
|
||||
padding-right: .5em;
|
||||
}
|
||||
#header .multi-author {
|
||||
margin: 0.5em 0 -0.5em 0;
|
||||
}
|
||||
#header .date {
|
||||
margin-top: 1.5em;
|
||||
}
|
@ -0,0 +1,18 @@
|
||||
div.sourceCode {
|
||||
position: relative;
|
||||
}
|
||||
|
||||
.copy-to-clipboard-button {
|
||||
position: absolute;
|
||||
right: 0;
|
||||
top: 0;
|
||||
visibility: hidden;
|
||||
}
|
||||
|
||||
.copy-to-clipboard-button:focus {
|
||||
outline: 0;
|
||||
}
|
||||
|
||||
div.sourceCode:hover > .copy-to-clipboard-button {
|
||||
visibility: visible;
|
||||
}
|
@ -0,0 +1,303 @@
|
||||
/*
|
||||
* Theme 1
|
||||
*/
|
||||
.color-theme-1 .dropdown-menu {
|
||||
background-color: #111111;
|
||||
border-color: #7e888b;
|
||||
}
|
||||
.color-theme-1 .dropdown-menu .dropdown-caret .caret-inner {
|
||||
border-bottom: 9px solid #111111;
|
||||
}
|
||||
.color-theme-1 .dropdown-menu .buttons {
|
||||
border-color: #7e888b;
|
||||
}
|
||||
.color-theme-1 .dropdown-menu .button {
|
||||
color: #afa790;
|
||||
}
|
||||
.color-theme-1 .dropdown-menu .button:hover {
|
||||
color: #73553c;
|
||||
}
|
||||
/*
|
||||
* Theme 2
|
||||
*/
|
||||
.color-theme-2 .dropdown-menu {
|
||||
background-color: #2d3143;
|
||||
border-color: #272a3a;
|
||||
}
|
||||
.color-theme-2 .dropdown-menu .dropdown-caret .caret-inner {
|
||||
border-bottom: 9px solid #2d3143;
|
||||
}
|
||||
.color-theme-2 .dropdown-menu .buttons {
|
||||
border-color: #272a3a;
|
||||
}
|
||||
.color-theme-2 .dropdown-menu .button {
|
||||
color: #62677f;
|
||||
}
|
||||
.color-theme-2 .dropdown-menu .button:hover {
|
||||
color: #f4f4f5;
|
||||
}
|
||||
.book .book-header .font-settings .font-enlarge {
|
||||
line-height: 30px;
|
||||
font-size: 1.4em;
|
||||
}
|
||||
.book .book-header .font-settings .font-reduce {
|
||||
line-height: 30px;
|
||||
font-size: 1em;
|
||||
}
|
||||
|
||||
/* sidebar transition background */
|
||||
div.book.color-theme-1 {
|
||||
background: #f3eacb;
|
||||
}
|
||||
.book.color-theme-1 .book-body {
|
||||
color: #704214;
|
||||
background: #f3eacb;
|
||||
}
|
||||
.book.color-theme-1 .book-body .page-wrapper .page-inner section {
|
||||
background: #f3eacb;
|
||||
}
|
||||
|
||||
/* sidebar transition background */
|
||||
div.book.color-theme-2 {
|
||||
background: #1c1f2b;
|
||||
}
|
||||
|
||||
.book.color-theme-2 .book-body {
|
||||
color: #bdcadb;
|
||||
background: #1c1f2b;
|
||||
}
|
||||
.book.color-theme-2 .book-body .page-wrapper .page-inner section {
|
||||
background: #1c1f2b;
|
||||
}
|
||||
.book.font-size-0 .book-body .page-inner section {
|
||||
font-size: 1.2rem;
|
||||
}
|
||||
.book.font-size-1 .book-body .page-inner section {
|
||||
font-size: 1.4rem;
|
||||
}
|
||||
.book.font-size-2 .book-body .page-inner section {
|
||||
font-size: 1.6rem;
|
||||
}
|
||||
.book.font-size-3 .book-body .page-inner section {
|
||||
font-size: 2.2rem;
|
||||
}
|
||||
.book.font-size-4 .book-body .page-inner section {
|
||||
font-size: 4rem;
|
||||
}
|
||||
.book.font-family-0 {
|
||||
font-family: Georgia, serif;
|
||||
}
|
||||
.book.font-family-1 {
|
||||
font-family: "Helvetica Neue", Helvetica, Arial, sans-serif;
|
||||
}
|
||||
.book.color-theme-1 .book-body .page-wrapper .page-inner section.normal {
|
||||
color: #704214;
|
||||
}
|
||||
.book.color-theme-1 .book-body .page-wrapper .page-inner section.normal a {
|
||||
color: inherit;
|
||||
}
|
||||
.book.color-theme-1 .book-body .page-wrapper .page-inner section.normal h1,
|
||||
.book.color-theme-1 .book-body .page-wrapper .page-inner section.normal h2,
|
||||
.book.color-theme-1 .book-body .page-wrapper .page-inner section.normal h3,
|
||||
.book.color-theme-1 .book-body .page-wrapper .page-inner section.normal h4,
|
||||
.book.color-theme-1 .book-body .page-wrapper .page-inner section.normal h5,
|
||||
.book.color-theme-1 .book-body .page-wrapper .page-inner section.normal h6 {
|
||||
color: inherit;
|
||||
}
|
||||
.book.color-theme-1 .book-body .page-wrapper .page-inner section.normal h1,
|
||||
.book.color-theme-1 .book-body .page-wrapper .page-inner section.normal h2 {
|
||||
border-color: inherit;
|
||||
}
|
||||
.book.color-theme-1 .book-body .page-wrapper .page-inner section.normal h6 {
|
||||
color: inherit;
|
||||
}
|
||||
.book.color-theme-1 .book-body .page-wrapper .page-inner section.normal hr {
|
||||
background-color: inherit;
|
||||
}
|
||||
.book.color-theme-1 .book-body .page-wrapper .page-inner section.normal blockquote {
|
||||
border-color: #c4b29f;
|
||||
opacity: 0.9;
|
||||
}
|
||||
.book.color-theme-1 .book-body .page-wrapper .page-inner section.normal pre,
|
||||
.book.color-theme-1 .book-body .page-wrapper .page-inner section.normal code {
|
||||
background: #fdf6e3;
|
||||
color: #657b83;
|
||||
border-color: #f8df9c;
|
||||
}
|
||||
.book.color-theme-1 .book-body .page-wrapper .page-inner section.normal .highlight {
|
||||
background-color: inherit;
|
||||
}
|
||||
.book.color-theme-1 .book-body .page-wrapper .page-inner section.normal table th,
|
||||
.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;
|
||||
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 @@
|
||||
.book .book-body .page-wrapper .page-inner section.normal pre,
|
||||
.book .book-body .page-wrapper .page-inner section.normal code {
|
||||
/* 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 */
|
||||
}
|
||||
.book .book-body .page-wrapper .page-inner section.normal pre .hljs-comment,
|
||||
.book .book-body .page-wrapper .page-inner section.normal code .hljs-comment,
|
||||
.book .book-body .page-wrapper .page-inner section.normal pre .hljs-title,
|
||||
.book .book-body .page-wrapper .page-inner section.normal code .hljs-title {
|
||||
color: #8e908c;
|
||||
}
|
||||
.book .book-body .page-wrapper .page-inner section.normal pre .hljs-variable,
|
||||
.book .book-body .page-wrapper .page-inner section.normal code .hljs-variable,
|
||||
.book .book-body .page-wrapper .page-inner section.normal pre .hljs-attribute,
|
||||
.book .book-body .page-wrapper .page-inner section.normal code .hljs-attribute,
|
||||
.book .book-body .page-wrapper .page-inner section.normal pre .hljs-tag,
|
||||
.book .book-body .page-wrapper .page-inner section.normal code .hljs-tag,
|
||||
.book .book-body .page-wrapper .page-inner section.normal pre .hljs-regexp,
|
||||
.book .book-body .page-wrapper .page-inner section.normal code .hljs-regexp,
|
||||
.book .book-body .page-wrapper .page-inner section.normal pre .ruby .hljs-constant,
|
||||
.book .book-body .page-wrapper .page-inner section.normal code .ruby .hljs-constant,
|
||||
.book .book-body .page-wrapper .page-inner section.normal pre .xml .hljs-tag .hljs-title,
|
||||
.book .book-body .page-wrapper .page-inner section.normal code .xml .hljs-tag .hljs-title,
|
||||
.book .book-body .page-wrapper .page-inner section.normal pre .xml .hljs-pi,
|
||||
.book .book-body .page-wrapper .page-inner section.normal code .xml .hljs-pi,
|
||||
.book .book-body .page-wrapper .page-inner section.normal pre .xml .hljs-doctype,
|
||||
.book .book-body .page-wrapper .page-inner section.normal code .xml .hljs-doctype,
|
||||
.book .book-body .page-wrapper .page-inner section.normal pre .html .hljs-doctype,
|
||||
.book .book-body .page-wrapper .page-inner section.normal code .html .hljs-doctype,
|
||||
.book .book-body .page-wrapper .page-inner section.normal pre .css .hljs-id,
|
||||
.book .book-body .page-wrapper .page-inner section.normal code .css .hljs-id,
|
||||
.book .book-body .page-wrapper .page-inner section.normal pre .css .hljs-class,
|
||||
.book .book-body .page-wrapper .page-inner section.normal code .css .hljs-class,
|
||||
.book .book-body .page-wrapper .page-inner section.normal pre .css .hljs-pseudo,
|
||||
.book .book-body .page-wrapper .page-inner section.normal code .css .hljs-pseudo {
|
||||
color: #c82829;
|
||||
}
|
||||
.book .book-body .page-wrapper .page-inner section.normal pre .hljs-number,
|
||||
.book .book-body .page-wrapper .page-inner section.normal code .hljs-number,
|
||||
.book .book-body .page-wrapper .page-inner section.normal pre .hljs-preprocessor,
|
||||
.book .book-body .page-wrapper .page-inner section.normal code .hljs-preprocessor,
|
||||
.book .book-body .page-wrapper .page-inner section.normal pre .hljs-pragma,
|
||||
.book .book-body .page-wrapper .page-inner section.normal code .hljs-pragma,
|
||||
.book .book-body .page-wrapper .page-inner section.normal pre .hljs-built_in,
|
||||
.book .book-body .page-wrapper .page-inner section.normal code .hljs-built_in,
|
||||
.book .book-body .page-wrapper .page-inner section.normal pre .hljs-literal,
|
||||
.book .book-body .page-wrapper .page-inner section.normal code .hljs-literal,
|
||||
.book .book-body .page-wrapper .page-inner section.normal pre .hljs-params,
|
||||
.book .book-body .page-wrapper .page-inner section.normal code .hljs-params,
|
||||
.book .book-body .page-wrapper .page-inner section.normal pre .hljs-constant,
|
||||
.book .book-body .page-wrapper .page-inner section.normal code .hljs-constant {
|
||||
color: #f5871f;
|
||||
}
|
||||
.book .book-body .page-wrapper .page-inner section.normal pre .ruby .hljs-class .hljs-title,
|
||||
.book .book-body .page-wrapper .page-inner section.normal code .ruby .hljs-class .hljs-title |