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# Introduction {#intro}
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# edit: https://github.com/msberends/a_new_instrument_for_microbial_epidemiology/edit/master/%s
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<li><a href="./">A New Instrument for Microbial Epidemiology</a></li>
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<li class="divider"></li>
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<li class="chapter" data-level="" data-path="index.html"><a href="index.html"><i class="fa fa-check"></i>Prerequisites</a></li>
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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>
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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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<i class="fa fa-circle-o-notch fa-spin"></i><a href="./">A New Instrument for Microbial Epidemiology</a>
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|
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<h2 class="subtitle"><em>Empowering Antimicrobial Resistance Data Analysis</em></h2>
|
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<p class="author"><em>Matthijs S. Berends</em></p>
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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>
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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>
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<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>
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<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>
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<span id="cb2-4"><a href="intro.html#cb2-4" aria-hidden="true" tabindex="-1"></a>)</span></code></pre></div>
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|
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|
||||
<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>
|
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<th align="left">Species</th>
|
||||
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|
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</thead>
|
||||
<tbody>
|
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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>
|
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<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>
|
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<tr class="even">
|
||||
<td align="right">4.6</td>
|
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<td align="right">3.1</td>
|
||||
<td align="right">1.5</td>
|
||||
<td align="right">0.2</td>
|
||||
<td align="left">setosa</td>
|
||||
</tr>
|
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<tr class="odd">
|
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<td align="right">5.0</td>
|
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<td align="right">3.6</td>
|
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<td align="right">1.4</td>
|
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<td align="right">0.2</td>
|
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<td align="left">setosa</td>
|
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|
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<tr class="even">
|
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<td align="right">5.4</td>
|
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<td align="right">3.9</td>
|
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<td align="right">1.7</td>
|
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<td align="right">0.4</td>
|
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<td align="left">setosa</td>
|
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<td align="right">4.6</td>
|
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<td align="right">3.4</td>
|
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<td align="right">1.4</td>
|
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<td align="right">0.3</td>
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<td align="left">setosa</td>
|
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<tr class="even">
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<td align="right">5.0</td>
|
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<td align="right">3.4</td>
|
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<td align="right">1.5</td>
|
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<td align="right">0.2</td>
|
||||
<td align="left">setosa</td>
|
||||
</tr>
|
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<tr class="odd">
|
||||
<td align="right">4.4</td>
|
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<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>
|
||||
5
docs/libs/anchor-sections-1.0.1/anchor-sections.css
Normal file
5
docs/libs/anchor-sections-1.0.1/anchor-sections.css
Normal file
@ -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;}
|
||||
33
docs/libs/anchor-sections-1.0.1/anchor-sections.js
Normal file
33
docs/libs/anchor-sections-1.0.1/anchor-sections.js
Normal file
@ -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);
|
||||
});
|
||||
});
|
||||
BIN
docs/libs/gitbook-2.6.7/css/fontawesome/fontawesome-webfont.ttf
Normal file
BIN
docs/libs/gitbook-2.6.7/css/fontawesome/fontawesome-webfont.ttf
Normal file
Binary file not shown.
105
docs/libs/gitbook-2.6.7/css/plugin-bookdown.css
Normal file
105
docs/libs/gitbook-2.6.7/css/plugin-bookdown.css
Normal file
@ -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;
|
||||
}
|
||||
18
docs/libs/gitbook-2.6.7/css/plugin-clipboard.css
Normal file
18
docs/libs/gitbook-2.6.7/css/plugin-clipboard.css
Normal file
@ -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;
|
||||
}
|
||||
303
docs/libs/gitbook-2.6.7/css/plugin-fontsettings.css
Normal file
303
docs/libs/gitbook-2.6.7/css/plugin-fontsettings.css
Normal file
@ -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,
|
||||
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|
||||
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;
|
||||
}
|
||||
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|
||||
background-color: #fbeecb;
|
||||
}
|
||||
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|
||||
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,
|
||||
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|
||||
color: #9dbed8;
|
||||
background: #2d3143;
|
||||
border-color: #2d3143;
|
||||
}
|
||||
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|
||||
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;
|
||||
}
|
||||
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|
||||
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;
|
||||
}
|
||||
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|
||||
color: #383f52;
|
||||
}
|
||||
.book.color-theme-2 .book-body .navigation:hover {
|
||||
color: #fffff5;
|
||||
}
|
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/*
|
||||
* 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;
|
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}
|
||||
.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;
|
||||
}
|
||||
426
docs/libs/gitbook-2.6.7/css/plugin-highlight.css
Normal file
426
docs/libs/gitbook-2.6.7/css/plugin-highlight.css
Normal file
@ -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 */
|
||||
}
|
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.book .book-body .page-wrapper .page-inner section.normal pre .hljs-comment,
|
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.book .book-body .page-wrapper .page-inner section.normal code .hljs-comment,
|
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|
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|
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color: #8e908c;
|
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|
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.book .book-body .page-wrapper .page-inner section.normal pre .hljs-variable,
|
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|
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|
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|
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|
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|
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.book .book-body .page-wrapper .page-inner section.normal pre .hljs-regexp,
|
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.book .book-body .page-wrapper .page-inner section.normal code .hljs-regexp,
|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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color: #eab700;
|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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color: #718c00;
|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
||||
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|
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|
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|
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|
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.book .book-body .page-wrapper .page-inner section.normal code .coffeescript .hljs-title {
|
||||
color: #4271ae;
|
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}
|
||||
.book .book-body .page-wrapper .page-inner section.normal pre .hljs-keyword,
|
||||
.book .book-body .page-wrapper .page-inner section.normal code .hljs-keyword,
|
||||
.book .book-body .page-wrapper .page-inner section.normal pre .javascript .hljs-function,
|
||||
.book .book-body .page-wrapper .page-inner section.normal code .javascript .hljs-function {
|
||||
color: #8959a8;
|
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}
|
||||
.book .book-body .page-wrapper .page-inner section.normal pre .hljs,
|
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.book .book-body .page-wrapper .page-inner section.normal code .hljs {
|
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display: block;
|
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background: white;
|
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color: #4d4d4c;
|
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padding: 0.5em;
|
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}
|
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.book .book-body .page-wrapper .page-inner section.normal pre .coffeescript .javascript,
|
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.book .book-body .page-wrapper .page-inner section.normal code .coffeescript .javascript,
|
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.book .book-body .page-wrapper .page-inner section.normal pre .javascript .xml,
|
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|
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|
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|
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|
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.book .book-body .page-wrapper .page-inner section.normal code .xml .javascript,
|
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.book .book-body .page-wrapper .page-inner section.normal pre .xml .vbscript,
|
||||
.book .book-body .page-wrapper .page-inner section.normal code .xml .vbscript,
|
||||
.book .book-body .page-wrapper .page-inner section.normal pre .xml .css,
|
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.book .book-body .page-wrapper .page-inner section.normal code .xml .css,
|
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.book .book-body .page-wrapper .page-inner section.normal pre .xml .hljs-cdata,
|
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.book .book-body .page-wrapper .page-inner section.normal code .xml .hljs-cdata {
|
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opacity: 0.5;
|
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}
|
||||
.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 {
|
||||
/*
|
||||
|
||||
Orginal Style from ethanschoonover.com/solarized (c) Jeremy Hull <sourdrums@gmail.com>
|
||||
|
||||
*/
|
||||
/* Solarized Green */
|
||||
/* Solarized Cyan */
|
||||
/* Solarized Blue */
|
||||
/* Solarized Yellow */
|
||||
/* Solarized Orange */
|
||||
/* Solarized Red */
|
||||
/* Solarized Violet */
|
||||
}
|
||||
.book.color-theme-1 .book-body .page-wrapper .page-inner section.normal pre .hljs,
|
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.book.color-theme-1 .book-body .page-wrapper .page-inner section.normal code .hljs {
|
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display: block;
|
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padding: 0.5em;
|
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background: #fdf6e3;
|
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color: #657b83;
|
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}
|
||||
.book.color-theme-1 .book-body .page-wrapper .page-inner section.normal pre .hljs-comment,
|
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.book.color-theme-1 .book-body .page-wrapper .page-inner section.normal code .hljs-comment,
|
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.book.color-theme-1 .book-body .page-wrapper .page-inner section.normal pre .hljs-template_comment,
|
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.book.color-theme-1 .book-body .page-wrapper .page-inner section.normal code .hljs-template_comment,
|
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.book.color-theme-1 .book-body .page-wrapper .page-inner section.normal pre .diff .hljs-header,
|
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.book.color-theme-1 .book-body .page-wrapper .page-inner section.normal code .diff .hljs-header,
|
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.book.color-theme-1 .book-body .page-wrapper .page-inner section.normal pre .hljs-doctype,
|
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.book.color-theme-1 .book-body .page-wrapper .page-inner section.normal code .hljs-doctype,
|
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.book.color-theme-1 .book-body .page-wrapper .page-inner section.normal pre .hljs-pi,
|
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.book.color-theme-1 .book-body .page-wrapper .page-inner section.normal code .hljs-pi,
|
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.book.color-theme-1 .book-body .page-wrapper .page-inner section.normal pre .lisp .hljs-string,
|
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.book.color-theme-1 .book-body .page-wrapper .page-inner section.normal code .lisp .hljs-string,
|
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.book.color-theme-1 .book-body .page-wrapper .page-inner section.normal pre .hljs-javadoc,
|
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.book.color-theme-1 .book-body .page-wrapper .page-inner section.normal code .hljs-javadoc {
|
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color: #93a1a1;
|
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}
|
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.book.color-theme-1 .book-body .page-wrapper .page-inner section.normal pre .hljs-keyword,
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||||
background: black;
|
||||
color: #eaeaea;
|
||||
padding: 0.5em;
|
||||
}
|
||||
.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal pre .coffeescript .javascript,
|
||||
.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal code .coffeescript .javascript,
|
||||
.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal pre .javascript .xml,
|
||||
.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal code .javascript .xml,
|
||||
.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal pre .tex .hljs-formula,
|
||||
.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal code .tex .hljs-formula,
|
||||
.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal pre .xml .javascript,
|
||||
.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal code .xml .javascript,
|
||||
.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal pre .xml .vbscript,
|
||||
.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal code .xml .vbscript,
|
||||
.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal pre .xml .css,
|
||||
.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal code .xml .css,
|
||||
.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal pre .xml .hljs-cdata,
|
||||
.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal code .xml .hljs-cdata {
|
||||
opacity: 0.5;
|
||||
}
|
||||
31
docs/libs/gitbook-2.6.7/css/plugin-search.css
Normal file
31
docs/libs/gitbook-2.6.7/css/plugin-search.css
Normal file
@ -0,0 +1,31 @@
|
||||
.book .book-summary .book-search {
|
||||
padding: 6px;
|
||||
background: transparent;
|
||||
position: absolute;
|
||||
top: -50px;
|
||||
left: 0px;
|
||||
right: 0px;
|
||||
transition: top 0.5s ease;
|
||||
}
|
||||
.book .book-summary .book-search input,
|
||||
.book .book-summary .book-search input:focus,
|
||||
.book .book-summary .book-search input:hover {
|
||||
width: 100%;
|
||||
background: transparent;
|
||||
border: 1px solid #ccc;
|
||||
box-shadow: none;
|
||||
outline: none;
|
||||
line-height: 22px;
|
||||
padding: 7px 4px;
|
||||
color: inherit;
|
||||
box-sizing: border-box;
|
||||
}
|
||||
.book.with-search .book-summary .book-search {
|
||||
top: 0px;
|
||||
}
|
||||
.book.with-search .book-summary ul.summary {
|
||||
top: 50px;
|
||||
}
|
||||
.with-search .summary li[data-level] a[href*=".html#"] {
|
||||
display: none;
|
||||
}
|
||||
1
docs/libs/gitbook-2.6.7/css/plugin-table.css
Normal file
1
docs/libs/gitbook-2.6.7/css/plugin-table.css
Normal file
@ -0,0 +1 @@
|
||||
.book .book-body .page-wrapper .page-inner section.normal table{display:table;width:100%;border-collapse:collapse;border-spacing:0;overflow:auto}.book .book-body .page-wrapper .page-inner section.normal table td,.book .book-body .page-wrapper .page-inner section.normal table th{padding:6px 13px;border:1px solid #ddd}.book .book-body .page-wrapper .page-inner section.normal table tr{background-color:#fff;border-top:1px solid #ccc}.book .book-body .page-wrapper .page-inner section.normal table tr:nth-child(2n){background-color:#f8f8f8}.book .book-body .page-wrapper .page-inner section.normal table th{font-weight:700}
|
||||
15
docs/libs/gitbook-2.6.7/css/style.css
Normal file
15
docs/libs/gitbook-2.6.7/css/style.css
Normal file
File diff suppressed because one or more lines are too long
1
docs/libs/gitbook-2.6.7/js/app.min.js
vendored
Normal file
1
docs/libs/gitbook-2.6.7/js/app.min.js
vendored
Normal file
File diff suppressed because one or more lines are too long
7
docs/libs/gitbook-2.6.7/js/clipboard.min.js
vendored
Normal file
7
docs/libs/gitbook-2.6.7/js/clipboard.min.js
vendored
Normal file
File diff suppressed because one or more lines are too long
86
docs/libs/gitbook-2.6.7/js/jquery.highlight.js
Normal file
86
docs/libs/gitbook-2.6.7/js/jquery.highlight.js
Normal file
@ -0,0 +1,86 @@
|
||||
gitbook.require(["jQuery"], function(jQuery) {
|
||||
|
||||
/*
|
||||
* jQuery Highlight plugin
|
||||
*
|
||||
* Based on highlight v3 by Johann Burkard
|
||||
* http://johannburkard.de/blog/programming/javascript/highlight-javascript-text-higlighting-jquery-plugin.html
|
||||
*
|
||||
* Code a little bit refactored and cleaned (in my humble opinion).
|
||||
* Most important changes:
|
||||
* - has an option to highlight only entire words (wordsOnly - false by default),
|
||||
* - has an option to be case sensitive (caseSensitive - false by default)
|
||||
* - highlight element tag and class names can be specified in options
|
||||
*
|
||||
* Copyright (c) 2009 Bartek Szopka
|
||||
*
|
||||
* Licensed under MIT license.
|
||||
*
|
||||
*/
|
||||
|
||||
jQuery.extend({
|
||||
highlight: function (node, re, nodeName, className) {
|
||||
if (node.nodeType === 3) {
|
||||
var match = node.data.match(re);
|
||||
if (match) {
|
||||
var highlight = document.createElement(nodeName || 'span');
|
||||
highlight.className = className || 'highlight';
|
||||
var wordNode = node.splitText(match.index);
|
||||
wordNode.splitText(match[0].length);
|
||||
var wordClone = wordNode.cloneNode(true);
|
||||
highlight.appendChild(wordClone);
|
||||
wordNode.parentNode.replaceChild(highlight, wordNode);
|
||||
return 1; //skip added node in parent
|
||||
}
|
||||
} else if ((node.nodeType === 1 && node.childNodes) && // only element nodes that have children
|
||||
!/(script|style)/i.test(node.tagName) && // ignore script and style nodes
|
||||
!(node.tagName === nodeName.toUpperCase() && node.className === className)) { // skip if already highlighted
|
||||
for (var i = 0; i < node.childNodes.length; i++) {
|
||||
i += jQuery.highlight(node.childNodes[i], re, nodeName, className);
|
||||
}
|
||||
}
|
||||
return 0;
|
||||
}
|
||||
});
|
||||
|
||||
jQuery.fn.unhighlight = function (options) {
|
||||
var settings = { className: 'highlight', element: 'span' };
|
||||
jQuery.extend(settings, options);
|
||||
|
||||
return this.find(settings.element + "." + settings.className).each(function () {
|
||||
var parent = this.parentNode;
|
||||
parent.replaceChild(this.firstChild, this);
|
||||
parent.normalize();
|
||||
}).end();
|
||||
};
|
||||
|
||||
jQuery.fn.highlight = function (words, options) {
|
||||
var settings = { className: 'highlight', element: 'span', caseSensitive: false, wordsOnly: false };
|
||||
jQuery.extend(settings, options);
|
||||
|
||||
if (words.constructor === String) {
|
||||
words = [words];
|
||||
// also match 'foo-bar' if search for 'foo bar'
|
||||
if (/\s/.test(words[0])) words.push(words[0].replace(/\s+/, '-'));
|
||||
}
|
||||
words = jQuery.grep(words, function(word, i){
|
||||
return word !== '';
|
||||
});
|
||||
words = jQuery.map(words, function(word, i) {
|
||||
return word.replace(/[-[\]{}()*+?.,\\^$|#\s]/g, "\\$&");
|
||||
});
|
||||
if (words.length === 0) { return this; }
|
||||
|
||||
var flag = settings.caseSensitive ? "" : "i";
|
||||
var pattern = "(" + words.join("|") + ")";
|
||||
if (settings.wordsOnly) {
|
||||
pattern = "\\b" + pattern + "\\b";
|
||||
}
|
||||
var re = new RegExp(pattern, flag);
|
||||
|
||||
return this.each(function () {
|
||||
jQuery.highlight(this, re, settings.element, settings.className);
|
||||
});
|
||||
};
|
||||
|
||||
});
|
||||
259
docs/libs/gitbook-2.6.7/js/plugin-bookdown.js
Normal file
259
docs/libs/gitbook-2.6.7/js/plugin-bookdown.js
Normal file
@ -0,0 +1,259 @@
|
||||
gitbook.require(["gitbook", "lodash", "jQuery"], function(gitbook, _, $) {
|
||||
|
||||
var gs = gitbook.storage;
|
||||
|
||||
gitbook.events.bind("start", function(e, config) {
|
||||
|
||||
// add the Edit button (edit on Github)
|
||||
var edit = config.edit;
|
||||
if (edit && edit.link) gitbook.toolbar.createButton({
|
||||
icon: 'fa fa-edit',
|
||||
label: edit.text || 'Edit',
|
||||
position: 'left',
|
||||
onClick: function(e) {
|
||||
e.preventDefault();
|
||||
window.open(edit.link);
|
||||
}
|
||||
});
|
||||
|
||||
// add the History button (file history on Github)
|
||||
var history = config.history;
|
||||
if (history && history.link) gitbook.toolbar.createButton({
|
||||
icon: 'fa fa-history',
|
||||
label: history.text || 'History',
|
||||
position: 'left',
|
||||
onClick: function(e) {
|
||||
e.preventDefault();
|
||||
window.open(history.link);
|
||||
}
|
||||
});
|
||||
|
||||
// add the View button (file view on Github)
|
||||
var view = config.view;
|
||||
if (view && view.link) gitbook.toolbar.createButton({
|
||||
icon: 'fa fa-eye',
|
||||
label: view.text || 'View Source',
|
||||
position: 'left',
|
||||
onClick: function(e) {
|
||||
e.preventDefault();
|
||||
window.open(view.link);
|
||||
}
|
||||
});
|
||||
|
||||
// add the Download button
|
||||
var down = config.download;
|
||||
var normalizeDownload = function() {
|
||||
if (!down || !(down instanceof Array) || down.length === 0) return;
|
||||
if (down[0] instanceof Array) return down;
|
||||
return $.map(down, function(file, i) {
|
||||
return [[file, file.replace(/.*[.]/g, '').toUpperCase()]];
|
||||
});
|
||||
};
|
||||
down = normalizeDownload(down);
|
||||
if (down) if (down.length === 1 && /[.]pdf$/.test(down[0][0])) {
|
||||
gitbook.toolbar.createButton({
|
||||
icon: 'fa fa-file-pdf-o',
|
||||
label: down[0][1],
|
||||
position: 'left',
|
||||
onClick: function(e) {
|
||||
e.preventDefault();
|
||||
window.open(down[0][0]);
|
||||
}
|
||||
});
|
||||
} else {
|
||||
gitbook.toolbar.createButton({
|
||||
icon: 'fa fa-download',
|
||||
label: 'Download',
|
||||
position: 'left',
|
||||
dropdown: $.map(down, function(item, i) {
|
||||
return {
|
||||
text: item[1],
|
||||
onClick: function(e) {
|
||||
e.preventDefault();
|
||||
window.open(item[0]);
|
||||
}
|
||||
};
|
||||
})
|
||||
});
|
||||
}
|
||||
|
||||
// add the Information button
|
||||
var info = ['Keyboard shortcuts (<> indicates arrow keys):',
|
||||
'<left>/<right>: navigate to previous/next page',
|
||||
's: Toggle sidebar'];
|
||||
if (config.search !== false) info.push('f: Toggle search input ' +
|
||||
'(use <up>/<down>/Enter in the search input to navigate through search matches; ' +
|
||||
'press Esc to cancel search)');
|
||||
if (config.info !== false) gitbook.toolbar.createButton({
|
||||
icon: 'fa fa-info',
|
||||
label: 'Information about the toolbar',
|
||||
position: 'left',
|
||||
onClick: function(e) {
|
||||
e.preventDefault();
|
||||
window.alert(info.join('\n\n'));
|
||||
}
|
||||
});
|
||||
|
||||
// highlight the current section in TOC
|
||||
var href = window.location.pathname;
|
||||
href = href.substr(href.lastIndexOf('/') + 1);
|
||||
// accentuated characters need to be decoded (#819)
|
||||
href = decodeURIComponent(href);
|
||||
if (href === '') href = 'index.html';
|
||||
var li = $('a[href^="' + href + location.hash + '"]').parent('li.chapter').first();
|
||||
var summary = $('ul.summary'), chaps = summary.find('li.chapter');
|
||||
if (li.length === 0) li = chaps.first();
|
||||
li.addClass('active');
|
||||
chaps.on('click', function(e) {
|
||||
chaps.removeClass('active');
|
||||
$(this).addClass('active');
|
||||
gs.set('tocScrollTop', summary.scrollTop());
|
||||
});
|
||||
|
||||
var toc = config.toc;
|
||||
// collapse TOC items that are not for the current chapter
|
||||
if (toc && toc.collapse) (function() {
|
||||
var type = toc.collapse;
|
||||
if (type === 'none') return;
|
||||
if (type !== 'section' && type !== 'subsection') return;
|
||||
// sections under chapters
|
||||
var toc_sub = summary.children('li[data-level]').children('ul');
|
||||
if (type === 'section') {
|
||||
toc_sub.hide()
|
||||
.parent().has(li).children('ul').show();
|
||||
} else {
|
||||
toc_sub.children('li').children('ul').hide()
|
||||
.parent().has(li).children('ul').show();
|
||||
}
|
||||
li.children('ul').show();
|
||||
var toc_sub2 = toc_sub.children('li');
|
||||
if (type === 'section') toc_sub2.children('ul').hide();
|
||||
summary.children('li[data-level]').find('a')
|
||||
.on('click.bookdown', function(e) {
|
||||
if (href === $(this).attr('href').replace(/#.*/, ''))
|
||||
$(this).parent('li').children('ul').toggle();
|
||||
});
|
||||
})();
|
||||
|
||||
// add tooltips to the <a>'s that are truncated
|
||||
$('a').each(function(i, el) {
|
||||
if (el.offsetWidth >= el.scrollWidth) return;
|
||||
if (typeof el.title === 'undefined') return;
|
||||
el.title = el.text;
|
||||
});
|
||||
|
||||
// restore TOC scroll position
|
||||
var pos = gs.get('tocScrollTop');
|
||||
if (typeof pos !== 'undefined') summary.scrollTop(pos);
|
||||
|
||||
// highlight the TOC item that has same text as the heading in view as scrolling
|
||||
if (toc && toc.scroll_highlight !== false && li.length > 0) (function() {
|
||||
// scroll the current TOC item into viewport
|
||||
var ht = $(window).height(), rect = li[0].getBoundingClientRect();
|
||||
if (rect.top >= ht || rect.top <= 0 || rect.bottom <= 0) {
|
||||
summary.scrollTop(li[0].offsetTop);
|
||||
}
|
||||
// current chapter TOC items
|
||||
var items = $('a[href^="' + href + '"]').parent('li.chapter'),
|
||||
m = items.length;
|
||||
if (m === 0) {
|
||||
items = summary.find('li.chapter');
|
||||
m = items.length;
|
||||
}
|
||||
if (m === 0) return;
|
||||
// all section titles on current page
|
||||
var hs = bookInner.find('.page-inner').find('h1,h2,h3'), n = hs.length,
|
||||
ts = hs.map(function(i, el) { return $(el).text(); });
|
||||
if (n === 0) return;
|
||||
var scrollHandler = function(e) {
|
||||
var ht = $(window).height();
|
||||
clearTimeout($.data(this, 'scrollTimer'));
|
||||
$.data(this, 'scrollTimer', setTimeout(function() {
|
||||
// find the first visible title in the viewport
|
||||
for (var i = 0; i < n; i++) {
|
||||
var rect = hs[i].getBoundingClientRect();
|
||||
if (rect.top >= 0 && rect.bottom <= ht) break;
|
||||
}
|
||||
if (i === n) return;
|
||||
items.removeClass('active');
|
||||
for (var j = 0; j < m; j++) {
|
||||
if (items.eq(j).children('a').first().text() === ts[i]) break;
|
||||
}
|
||||
if (j === m) j = 0; // highlight the chapter title
|
||||
// search bottom-up for a visible TOC item to highlight; if an item is
|
||||
// hidden, we check if its parent is visible, and so on
|
||||
while (j > 0 && items.eq(j).is(':hidden')) j--;
|
||||
items.eq(j).addClass('active');
|
||||
}, 250));
|
||||
};
|
||||
bookInner.on('scroll.bookdown', scrollHandler);
|
||||
bookBody.on('scroll.bookdown', scrollHandler);
|
||||
})();
|
||||
|
||||
// do not refresh the page if the TOC item points to the current page
|
||||
$('a[href="' + href + '"]').parent('li.chapter').children('a')
|
||||
.on('click', function(e) {
|
||||
bookInner.scrollTop(0);
|
||||
bookBody.scrollTop(0);
|
||||
return false;
|
||||
});
|
||||
|
||||
var toolbar = config.toolbar;
|
||||
if (!toolbar || toolbar.position !== 'static') {
|
||||
var bookHeader = $('.book-header');
|
||||
bookBody.addClass('fixed');
|
||||
bookHeader.addClass('fixed')
|
||||
.css('background-color', bookBody.css('background-color'))
|
||||
.on('click.bookdown', function(e) {
|
||||
// the theme may have changed after user clicks the theme button
|
||||
bookHeader.css('background-color', bookBody.css('background-color'));
|
||||
});
|
||||
}
|
||||
|
||||
});
|
||||
|
||||
gitbook.events.bind("page.change", function(e) {
|
||||
// store TOC scroll position
|
||||
var summary = $('ul.summary');
|
||||
gs.set('tocScrollTop', summary.scrollTop());
|
||||
});
|
||||
|
||||
var bookBody = $('.book-body'), bookInner = bookBody.find('.body-inner');
|
||||
var chapterTitle = function() {
|
||||
return bookInner.find('.page-inner').find('h1,h2').first().text();
|
||||
};
|
||||
var saveScrollPos = function(e) {
|
||||
// save scroll position before page is reloaded
|
||||
gs.set('bodyScrollTop', {
|
||||
body: bookBody.scrollTop(),
|
||||
inner: bookInner.scrollTop(),
|
||||
focused: document.hasFocus(),
|
||||
title: chapterTitle()
|
||||
});
|
||||
};
|
||||
$(document).on('servr:reload', saveScrollPos);
|
||||
|
||||
// check if the page is loaded in an iframe (e.g. the RStudio preview window)
|
||||
var inIFrame = function() {
|
||||
var inIframe = true;
|
||||
try { inIframe = window.self !== window.top; } catch (e) {}
|
||||
return inIframe;
|
||||
};
|
||||
if (inIFrame()) {
|
||||
$(window).on('blur unload', saveScrollPos);
|
||||
}
|
||||
|
||||
$(function(e) {
|
||||
var pos = gs.get('bodyScrollTop');
|
||||
if (pos) {
|
||||
if (pos.title === chapterTitle()) {
|
||||
if (pos.body !== 0) bookBody.scrollTop(pos.body);
|
||||
if (pos.inner !== 0) bookInner.scrollTop(pos.inner);
|
||||
}
|
||||
}
|
||||
if ((pos && pos.focused) || !inIFrame()) bookInner.find('.page-wrapper').focus();
|
||||
// clear book body scroll position
|
||||
gs.remove('bodyScrollTop');
|
||||
});
|
||||
|
||||
});
|
||||
29
docs/libs/gitbook-2.6.7/js/plugin-clipboard.js
Normal file
29
docs/libs/gitbook-2.6.7/js/plugin-clipboard.js
Normal file
@ -0,0 +1,29 @@
|
||||
gitbook.require(["gitbook", "jQuery"], function(gitbook, $) {
|
||||
|
||||
var copyButton = '<button type="button" class="copy-to-clipboard-button" title="Copy to clipboard" aria-label="Copy to clipboard"><i class="fa fa-copy"></i></button>';
|
||||
var clipboard;
|
||||
|
||||
gitbook.events.bind("page.change", function() {
|
||||
|
||||
if (!ClipboardJS.isSupported()) return;
|
||||
|
||||
// the page.change event is thrown twice: before and after the page changes
|
||||
if (clipboard) {
|
||||
// clipboard is already defined
|
||||
// we can deduct that we are before page changes
|
||||
clipboard.destroy(); // destroy the previous events listeners
|
||||
clipboard = undefined; // reset the clipboard object
|
||||
return;
|
||||
}
|
||||
|
||||
$(copyButton).prependTo("div.sourceCode");
|
||||
|
||||
clipboard = new ClipboardJS(".copy-to-clipboard-button", {
|
||||
text: function(trigger) {
|
||||
return trigger.parentNode.textContent;
|
||||
}
|
||||
});
|
||||
|
||||
});
|
||||
|
||||
});
|
||||
152
docs/libs/gitbook-2.6.7/js/plugin-fontsettings.js
Normal file
152
docs/libs/gitbook-2.6.7/js/plugin-fontsettings.js
Normal file
@ -0,0 +1,152 @@
|
||||
gitbook.require(["gitbook", "lodash", "jQuery"], function(gitbook, _, $) {
|
||||
var fontState;
|
||||
|
||||
var THEMES = {
|
||||
"white": 0,
|
||||
"sepia": 1,
|
||||
"night": 2
|
||||
};
|
||||
|
||||
var FAMILY = {
|
||||
"serif": 0,
|
||||
"sans": 1
|
||||
};
|
||||
|
||||
// Save current font settings
|
||||
function saveFontSettings() {
|
||||
gitbook.storage.set("fontState", fontState);
|
||||
update();
|
||||
}
|
||||
|
||||
// Increase font size
|
||||
function enlargeFontSize(e) {
|
||||
e.preventDefault();
|
||||
if (fontState.size >= 4) return;
|
||||
|
||||
fontState.size++;
|
||||
saveFontSettings();
|
||||
};
|
||||
|
||||
// Decrease font size
|
||||
function reduceFontSize(e) {
|
||||
e.preventDefault();
|
||||
if (fontState.size <= 0) return;
|
||||
|
||||
fontState.size--;
|
||||
saveFontSettings();
|
||||
};
|
||||
|
||||
// Change font family
|
||||
function changeFontFamily(index, e) {
|
||||
e.preventDefault();
|
||||
|
||||
fontState.family = index;
|
||||
saveFontSettings();
|
||||
};
|
||||
|
||||
// Change type of color
|
||||
function changeColorTheme(index, e) {
|
||||
e.preventDefault();
|
||||
|
||||
var $book = $(".book");
|
||||
|
||||
if (fontState.theme !== 0)
|
||||
$book.removeClass("color-theme-"+fontState.theme);
|
||||
|
||||
fontState.theme = index;
|
||||
if (fontState.theme !== 0)
|
||||
$book.addClass("color-theme-"+fontState.theme);
|
||||
|
||||
saveFontSettings();
|
||||
};
|
||||
|
||||
function update() {
|
||||
var $book = gitbook.state.$book;
|
||||
|
||||
$(".font-settings .font-family-list li").removeClass("active");
|
||||
$(".font-settings .font-family-list li:nth-child("+(fontState.family+1)+")").addClass("active");
|
||||
|
||||
$book[0].className = $book[0].className.replace(/\bfont-\S+/g, '');
|
||||
$book.addClass("font-size-"+fontState.size);
|
||||
$book.addClass("font-family-"+fontState.family);
|
||||
|
||||
if(fontState.theme !== 0) {
|
||||
$book[0].className = $book[0].className.replace(/\bcolor-theme-\S+/g, '');
|
||||
$book.addClass("color-theme-"+fontState.theme);
|
||||
}
|
||||
};
|
||||
|
||||
function init(config) {
|
||||
var $bookBody, $book;
|
||||
|
||||
//Find DOM elements.
|
||||
$book = gitbook.state.$book;
|
||||
$bookBody = $book.find(".book-body");
|
||||
|
||||
// Instantiate font state object
|
||||
fontState = gitbook.storage.get("fontState", {
|
||||
size: config.size || 2,
|
||||
family: FAMILY[config.family || "sans"],
|
||||
theme: THEMES[config.theme || "white"]
|
||||
});
|
||||
|
||||
update();
|
||||
};
|
||||
|
||||
|
||||
gitbook.events.bind("start", function(e, config) {
|
||||
var opts = config.fontsettings;
|
||||
if (!opts) return;
|
||||
|
||||
// Create buttons in toolbar
|
||||
gitbook.toolbar.createButton({
|
||||
icon: 'fa fa-font',
|
||||
label: 'Font Settings',
|
||||
className: 'font-settings',
|
||||
dropdown: [
|
||||
[
|
||||
{
|
||||
text: 'A',
|
||||
className: 'font-reduce',
|
||||
onClick: reduceFontSize
|
||||
},
|
||||
{
|
||||
text: 'A',
|
||||
className: 'font-enlarge',
|
||||
onClick: enlargeFontSize
|
||||
}
|
||||
],
|
||||
[
|
||||
{
|
||||
text: 'Serif',
|
||||
onClick: _.partial(changeFontFamily, 0)
|
||||
},
|
||||
{
|
||||
text: 'Sans',
|
||||
onClick: _.partial(changeFontFamily, 1)
|
||||
}
|
||||
],
|
||||
[
|
||||
{
|
||||
text: 'White',
|
||||
onClick: _.partial(changeColorTheme, 0)
|
||||
},
|
||||
{
|
||||
text: 'Sepia',
|
||||
onClick: _.partial(changeColorTheme, 1)
|
||||
},
|
||||
{
|
||||
text: 'Night',
|
||||
onClick: _.partial(changeColorTheme, 2)
|
||||
}
|
||||
]
|
||||
]
|
||||
});
|
||||
|
||||
|
||||
// Init current settings
|
||||
init(opts);
|
||||
});
|
||||
});
|
||||
|
||||
|
||||
270
docs/libs/gitbook-2.6.7/js/plugin-search.js
Normal file
270
docs/libs/gitbook-2.6.7/js/plugin-search.js
Normal file
@ -0,0 +1,270 @@
|
||||
gitbook.require(["gitbook", "lodash", "jQuery"], function(gitbook, _, $) {
|
||||
var index = null;
|
||||
var fuse = null;
|
||||
var _search = {engine: 'lunr', opts: {}};
|
||||
var $searchInput, $searchLabel, $searchForm;
|
||||
var $highlighted = [], hi, hiOpts = { className: 'search-highlight' };
|
||||
var collapse = false, toc_visible = [];
|
||||
|
||||
function init(config) {
|
||||
// Instantiate search settings
|
||||
_search = gitbook.storage.get("search", {
|
||||
engine: config.search.engine || 'lunr',
|
||||
opts: config.search.options || {},
|
||||
});
|
||||
};
|
||||
|
||||
// Save current search settings
|
||||
function saveSearchSettings() {
|
||||
gitbook.storage.set("search", _search);
|
||||
}
|
||||
|
||||
// Use a specific index
|
||||
function loadIndex(data) {
|
||||
// [Yihui] In bookdown, I use a character matrix to store the chapter
|
||||
// content, and the index is dynamically built on the client side.
|
||||
// Gitbook prebuilds the index data instead: https://github.com/GitbookIO/plugin-search
|
||||
// We can certainly do that via R packages V8 and jsonlite, but let's
|
||||
// see how slow it really is before improving it. On the other hand,
|
||||
// lunr cannot handle non-English text very well, e.g. the default
|
||||
// tokenizer cannot deal with Chinese text, so we may want to replace
|
||||
// lunr with a dumb simple text matching approach.
|
||||
if (_search.engine === 'lunr') {
|
||||
index = lunr(function () {
|
||||
this.ref('url');
|
||||
this.field('title', { boost: 10 });
|
||||
this.field('body');
|
||||
});
|
||||
data.map(function(item) {
|
||||
index.add({
|
||||
url: item[0],
|
||||
title: item[1],
|
||||
body: item[2]
|
||||
});
|
||||
});
|
||||
return;
|
||||
}
|
||||
fuse = new Fuse(data.map((_data => {
|
||||
return {
|
||||
url: _data[0],
|
||||
title: _data[1],
|
||||
body: _data[2]
|
||||
};
|
||||
})), Object.assign(
|
||||
{
|
||||
includeScore: true,
|
||||
threshold: 0.1,
|
||||
ignoreLocation: true,
|
||||
keys: ["title", "body"]
|
||||
},
|
||||
_search.opts
|
||||
));
|
||||
}
|
||||
|
||||
// Fetch the search index
|
||||
function fetchIndex() {
|
||||
return $.getJSON(gitbook.state.basePath+"/search_index.json")
|
||||
.then(loadIndex); // [Yihui] we need to use this object later
|
||||
}
|
||||
|
||||
// Search for a term and return results
|
||||
function search(q) {
|
||||
let results = [];
|
||||
switch (_search.engine) {
|
||||
case 'fuse':
|
||||
if (!fuse) return;
|
||||
results = fuse.search(q).map(function(result) {
|
||||
var parts = result.item.url.split('#');
|
||||
return {
|
||||
path: parts[0],
|
||||
hash: parts[1]
|
||||
};
|
||||
});
|
||||
break;
|
||||
case 'lunr':
|
||||
default:
|
||||
if (!index) return;
|
||||
results = _.chain(index.search(q)).map(function(result) {
|
||||
var parts = result.ref.split("#");
|
||||
return {
|
||||
path: parts[0],
|
||||
hash: parts[1]
|
||||
};
|
||||
})
|
||||
.value();
|
||||
}
|
||||
|
||||
// [Yihui] Highlight the search keyword on current page
|
||||
$highlighted = $('.page-inner')
|
||||
.unhighlight(hiOpts).highlight(q, hiOpts).find('span.search-highlight');
|
||||
scrollToHighlighted(0);
|
||||
|
||||
return results;
|
||||
}
|
||||
|
||||
// [Yihui] Scroll the chapter body to the i-th highlighted string
|
||||
function scrollToHighlighted(d) {
|
||||
var n = $highlighted.length;
|
||||
hi = hi === undefined ? 0 : hi + d;
|
||||
// navignate to the previous/next page in the search results if reached the top/bottom
|
||||
var b = hi < 0;
|
||||
if (d !== 0 && (b || hi >= n)) {
|
||||
var path = currentPath(), n2 = toc_visible.length;
|
||||
if (n2 === 0) return;
|
||||
for (var i = b ? 0 : n2; (b && i < n2) || (!b && i >= 0); i += b ? 1 : -1) {
|
||||
if (toc_visible.eq(i).data('path') === path) break;
|
||||
}
|
||||
i += b ? -1 : 1;
|
||||
if (i < 0) i = n2 - 1;
|
||||
if (i >= n2) i = 0;
|
||||
var lnk = toc_visible.eq(i).find('a[href$=".html"]');
|
||||
if (lnk.length) lnk[0].click();
|
||||
return;
|
||||
}
|
||||
if (n === 0) return;
|
||||
var $p = $highlighted.eq(hi);
|
||||
$p[0].scrollIntoView();
|
||||
$highlighted.css('background-color', '');
|
||||
// an orange background color on the current item and removed later
|
||||
$p.css('background-color', 'orange');
|
||||
setTimeout(function() {
|
||||
$p.css('background-color', '');
|
||||
}, 2000);
|
||||
}
|
||||
|
||||
function currentPath() {
|
||||
var href = window.location.pathname;
|
||||
href = href.substr(href.lastIndexOf('/') + 1);
|
||||
return href === '' ? 'index.html' : href;
|
||||
}
|
||||
|
||||
// Create search form
|
||||
function createForm(value) {
|
||||
if ($searchForm) $searchForm.remove();
|
||||
if ($searchLabel) $searchLabel.remove();
|
||||
if ($searchInput) $searchInput.remove();
|
||||
|
||||
$searchForm = $('<div>', {
|
||||
'class': 'book-search',
|
||||
'role': 'search'
|
||||
});
|
||||
|
||||
$searchLabel = $('<label>', {
|
||||
'for': 'search-box',
|
||||
'aria-hidden': 'false',
|
||||
'hidden': ''
|
||||
});
|
||||
|
||||
$searchInput = $('<input>', {
|
||||
'id': 'search-box',
|
||||
'type': 'search',
|
||||
'class': 'form-control',
|
||||
'val': value,
|
||||
'placeholder': 'Type to search (Enter for navigation)',
|
||||
'title': 'Use Enter or the <Down> key to navigate to the next match, or the <Up> key to the previous match'
|
||||
});
|
||||
|
||||
$searchLabel.append("Type to search");
|
||||
$searchLabel.appendTo($searchForm);
|
||||
$searchInput.appendTo($searchForm);
|
||||
$searchForm.prependTo(gitbook.state.$book.find('.book-summary'));
|
||||
}
|
||||
|
||||
// Return true if search is open
|
||||
function isSearchOpen() {
|
||||
return gitbook.state.$book.hasClass("with-search");
|
||||
}
|
||||
|
||||
// Toggle the search
|
||||
function toggleSearch(_state) {
|
||||
if (isSearchOpen() === _state) return;
|
||||
if (!$searchInput) return;
|
||||
|
||||
gitbook.state.$book.toggleClass("with-search", _state);
|
||||
|
||||
// If search bar is open: focus input
|
||||
if (isSearchOpen()) {
|
||||
gitbook.sidebar.toggle(true);
|
||||
$searchInput.focus();
|
||||
} else {
|
||||
$searchInput.blur();
|
||||
$searchInput.val("");
|
||||
gitbook.storage.remove("keyword");
|
||||
gitbook.sidebar.filter(null);
|
||||
$('.page-inner').unhighlight(hiOpts);
|
||||
}
|
||||
}
|
||||
|
||||
function sidebarFilter(results) {
|
||||
gitbook.sidebar.filter(_.pluck(results, "path"));
|
||||
toc_visible = $('ul.summary').find('li:visible');
|
||||
}
|
||||
|
||||
// Recover current search when page changed
|
||||
function recoverSearch() {
|
||||
var keyword = gitbook.storage.get("keyword", "");
|
||||
|
||||
createForm(keyword);
|
||||
|
||||
if (keyword.length > 0) {
|
||||
if(!isSearchOpen()) {
|
||||
toggleSearch(true); // [Yihui] open the search box
|
||||
}
|
||||
sidebarFilter(search(keyword));
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
gitbook.events.bind("start", function(e, config) {
|
||||
// [Yihui] disable search
|
||||
if (config.search === false) return;
|
||||
init(config);
|
||||
collapse = !config.toc || config.toc.collapse === 'section' ||
|
||||
config.toc.collapse === 'subsection';
|
||||
|
||||
// Pre-fetch search index and create the form
|
||||
fetchIndex()
|
||||
// [Yihui] recover search after the page is loaded
|
||||
.then(recoverSearch);
|
||||
|
||||
|
||||
// Type in search bar
|
||||
$(document).on("keyup", ".book-search input", function(e) {
|
||||
var key = (e.keyCode ? e.keyCode : e.which);
|
||||
// [Yihui] Escape -> close search box; Up/Down/Enter: previous/next highlighted
|
||||
if (key == 27) {
|
||||
e.preventDefault();
|
||||
toggleSearch(false);
|
||||
} else if (key == 38) {
|
||||
scrollToHighlighted(-1);
|
||||
} else if (key == 40 || key == 13) {
|
||||
scrollToHighlighted(1);
|
||||
}
|
||||
}).on("input", ".book-search input", function(e) {
|
||||
var q = $(this).val().trim();
|
||||
if (q.length === 0) {
|
||||
gitbook.sidebar.filter(null);
|
||||
gitbook.storage.remove("keyword");
|
||||
$('.page-inner').unhighlight(hiOpts);
|
||||
} else {
|
||||
var results = search(q);
|
||||
sidebarFilter(results);
|
||||
gitbook.storage.set("keyword", q);
|
||||
}
|
||||
});
|
||||
|
||||
// Create the toggle search button
|
||||
gitbook.toolbar.createButton({
|
||||
icon: 'fa fa-search',
|
||||
label: 'Search',
|
||||
position: 'left',
|
||||
onClick: toggleSearch
|
||||
});
|
||||
|
||||
// Bind keyboard to toggle search
|
||||
gitbook.keyboard.bind(['f'], toggleSearch);
|
||||
});
|
||||
|
||||
// [Yihui] do not try to recover search; always start fresh
|
||||
// gitbook.events.bind("page.change", recoverSearch);
|
||||
});
|
||||
116
docs/libs/gitbook-2.6.7/js/plugin-sharing.js
Normal file
116
docs/libs/gitbook-2.6.7/js/plugin-sharing.js
Normal file
@ -0,0 +1,116 @@
|
||||
gitbook.require(["gitbook", "lodash", "jQuery"], function(gitbook, _, $) {
|
||||
var SITES = {
|
||||
'github': {
|
||||
'label': 'Github',
|
||||
'icon': 'fa fa-github',
|
||||
'onClick': function(e) {
|
||||
e.preventDefault();
|
||||
var repo = $('meta[name="github-repo"]').attr('content');
|
||||
if (typeof repo === 'undefined') throw("Github repo not defined");
|
||||
window.open("https://github.com/"+repo);
|
||||
}
|
||||
},
|
||||
'facebook': {
|
||||
'label': 'Facebook',
|
||||
'icon': 'fa fa-facebook',
|
||||
'onClick': function(e) {
|
||||
e.preventDefault();
|
||||
window.open("http://www.facebook.com/sharer/sharer.php?u="+encodeURIComponent(location.href));
|
||||
}
|
||||
},
|
||||
'twitter': {
|
||||
'label': 'Twitter',
|
||||
'icon': 'fa fa-twitter',
|
||||
'onClick': function(e) {
|
||||
e.preventDefault();
|
||||
window.open("http://twitter.com/intent/tweet?text="+encodeURIComponent(document.title)+"&url="+encodeURIComponent(location.href)+"&hashtags=rmarkdown,bookdown");
|
||||
}
|
||||
},
|
||||
'linkedin': {
|
||||
'label': 'LinkedIn',
|
||||
'icon': 'fa fa-linkedin',
|
||||
'onClick': function(e) {
|
||||
e.preventDefault();
|
||||
window.open("https://www.linkedin.com/shareArticle?mini=true&url="+encodeURIComponent(location.href)+"&title="+encodeURIComponent(document.title));
|
||||
}
|
||||
},
|
||||
'weibo': {
|
||||
'label': 'Weibo',
|
||||
'icon': 'fa fa-weibo',
|
||||
'onClick': function(e) {
|
||||
e.preventDefault();
|
||||
window.open("http://service.weibo.com/share/share.php?content=utf-8&url="+encodeURIComponent(location.href)+"&title="+encodeURIComponent(document.title));
|
||||
}
|
||||
},
|
||||
'instapaper': {
|
||||
'label': 'Instapaper',
|
||||
'icon': 'fa fa-italic',
|
||||
'onClick': function(e) {
|
||||
e.preventDefault();
|
||||
window.open("http://www.instapaper.com/text?u="+encodeURIComponent(location.href));
|
||||
}
|
||||
},
|
||||
'vk': {
|
||||
'label': 'VK',
|
||||
'icon': 'fa fa-vk',
|
||||
'onClick': function(e) {
|
||||
e.preventDefault();
|
||||
window.open("http://vkontakte.ru/share.php?url="+encodeURIComponent(location.href));
|
||||
}
|
||||
},
|
||||
'whatsapp': {
|
||||
'label': 'Whatsapp',
|
||||
'icon': 'fa fa-whatsapp',
|
||||
'onClick': function(e) {
|
||||
e.preventDefault();
|
||||
var url = encodeURIComponent(location.href);
|
||||
window.open((isMobile() ? "whatsapp://send" : "https://web.whatsapp.com/send") + "?text=" + url);
|
||||
}
|
||||
},
|
||||
};
|
||||
|
||||
function isMobile() {
|
||||
return !!navigator.maxTouchPoints;
|
||||
}
|
||||
|
||||
gitbook.events.bind("start", function(e, config) {
|
||||
var opts = config.sharing;
|
||||
if (!opts) return;
|
||||
|
||||
// Create dropdown menu
|
||||
var menu = _.chain(opts.all)
|
||||
.map(function(id) {
|
||||
var site = SITES[id];
|
||||
if (!site) return;
|
||||
return {
|
||||
text: site.label,
|
||||
onClick: site.onClick
|
||||
};
|
||||
})
|
||||
.compact()
|
||||
.value();
|
||||
|
||||
// Create main button with dropdown
|
||||
if (menu.length > 0) {
|
||||
gitbook.toolbar.createButton({
|
||||
icon: 'fa fa-share-alt',
|
||||
label: 'Share',
|
||||
position: 'right',
|
||||
dropdown: [menu]
|
||||
});
|
||||
}
|
||||
|
||||
// Direct actions to share
|
||||
_.each(SITES, function(site, sideId) {
|
||||
if (!opts[sideId]) return;
|
||||
|
||||
gitbook.toolbar.createButton({
|
||||
icon: site.icon,
|
||||
label: site.label,
|
||||
title: site.label,
|
||||
position: 'right',
|
||||
onClick: site.onClick
|
||||
});
|
||||
});
|
||||
});
|
||||
});
|
||||
12
docs/libs/header-attrs-2.10/header-attrs.js
Normal file
12
docs/libs/header-attrs-2.10/header-attrs.js
Normal file
@ -0,0 +1,12 @@
|
||||
// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
|
||||
// be compatible with the behavior of Pandoc < 2.8).
|
||||
document.addEventListener('DOMContentLoaded', function(e) {
|
||||
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
|
||||
var i, h, a;
|
||||
for (i = 0; i < hs.length; i++) {
|
||||
h = hs[i];
|
||||
if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
|
||||
a = h.attributes;
|
||||
while (a.length > 0) h.removeAttribute(a[0].name);
|
||||
}
|
||||
});
|
||||
2
docs/libs/jquery-3.6.0/jquery-3.6.0.min.js
vendored
Normal file
2
docs/libs/jquery-3.6.0/jquery-3.6.0.min.js
vendored
Normal file
File diff suppressed because one or more lines are too long
3
docs/reference-keys.txt
Normal file
3
docs/reference-keys.txt
Normal file
@ -0,0 +1,3 @@
|
||||
fig:nice-fig
|
||||
tab:nice-tab
|
||||
intro
|
||||
1
docs/search_index.json
Normal file
1
docs/search_index.json
Normal file
@ -0,0 +1 @@
|
||||
[["index.html", "A New Instrument for Microbial Epidemiology Empowering Antimicrobial Resistance Data Analysis Prerequisites", " A New Instrument for Microbial Epidemiology Empowering Antimicrobial Resistance Data Analysis Matthijs S. Berends 25 August 2021 Prerequisites txt "],["intro.html", "1 Introduction", " 1 Introduction You can label chapter and section titles using {#label} after them, e.g., we can reference Chapter 1. If you do not manually label them, there will be automatic labels anyway, e.g., Chapter ??. Figures and tables with captions will be placed in figure and table environments, respectively. par(mar = c(4, 4, .1, .1)) plot(pressure, type = 'b', pch = 19) Figure 1.1: Here is a nice figure! Reference a figure by its code chunk label with the fig: prefix, e.g., see Figure 1.1. Similarly, you can reference tables generated from knitr::kable(), e.g., see Table 1.1. knitr::kable( head(iris, 20), caption = 'Here is a nice table!', booktabs = TRUE ) Table 1.1: Here is a nice table! Sepal.Length Sepal.Width Petal.Length Petal.Width Species 5.1 3.5 1.4 0.2 setosa 4.9 3.0 1.4 0.2 setosa 4.7 3.2 1.3 0.2 setosa 4.6 3.1 1.5 0.2 setosa 5.0 3.6 1.4 0.2 setosa 5.4 3.9 1.7 0.4 setosa 4.6 3.4 1.4 0.3 setosa 5.0 3.4 1.5 0.2 setosa 4.4 2.9 1.4 0.2 setosa 4.9 3.1 1.5 0.1 setosa 5.4 3.7 1.5 0.2 setosa 4.8 3.4 1.6 0.2 setosa 4.8 3.0 1.4 0.1 setosa 4.3 3.0 1.1 0.1 setosa 5.8 4.0 1.2 0.2 setosa 5.7 4.4 1.5 0.4 setosa 5.4 3.9 1.3 0.4 setosa 5.1 3.5 1.4 0.3 setosa 5.7 3.8 1.7 0.3 setosa 5.1 3.8 1.5 0.3 setosa "],["404.html", "Page not found", " Page not found The page you requested cannot be found (perhaps it was moved or renamed). 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. "]]
|
||||
14
docs/style.css
Normal file
14
docs/style.css
Normal file
@ -0,0 +1,14 @@
|
||||
p.caption {
|
||||
color: #777;
|
||||
margin-top: 10px;
|
||||
}
|
||||
p code {
|
||||
white-space: inherit;
|
||||
}
|
||||
pre {
|
||||
word-break: normal;
|
||||
word-wrap: normal;
|
||||
}
|
||||
pre code {
|
||||
white-space: inherit;
|
||||
}
|
||||
19
index.Rmd
Normal file
19
index.Rmd
Normal file
@ -0,0 +1,19 @@
|
||||
---
|
||||
title: "A New Instrument for Microbial Epidemiology"
|
||||
subtitle: "Empowering Antimicrobial Resistance Data Analysis"
|
||||
author: "Matthijs S. Berends"
|
||||
date: "25 August 2021"
|
||||
site: bookdown::bookdown_site
|
||||
output: bookdown::gitbook
|
||||
documentclass: book
|
||||
# bibliography: [book.bib, packages.bib]
|
||||
bibliography: [packages.bib]
|
||||
biblio-style: apalike
|
||||
link-citations: yes
|
||||
github-repo: msberends/a_new_instrument_for_microbial_epidemiology
|
||||
description: "This is the PhD thesis of the author."
|
||||
---
|
||||
|
||||
# Prerequisites {-}
|
||||
|
||||
txt
|
||||
102
packages.bib
Normal file
102
packages.bib
Normal file
@ -0,0 +1,102 @@
|
||||
@Manual{R-AMR,
|
||||
title = {AMR: Antimicrobial Resistance Data Analysis},
|
||||
author = {Matthijs S. Berends and Christian F. Luz and Alexander W. Friedrich and Bhanu N. M. Sinha and Casper J. Albers and Corinna Glasner},
|
||||
year = {2021},
|
||||
note = {https://github.com/msberends/AMR, https://msberends.github.io/AMR},
|
||||
}
|
||||
|
||||
@Manual{R-base,
|
||||
title = {R: A Language and Environment for Statistical Computing},
|
||||
author = {{R Core Team}},
|
||||
organization = {R Foundation for Statistical Computing},
|
||||
address = {Vienna, Austria},
|
||||
year = {2021},
|
||||
url = {https://www.R-project.org/},
|
||||
}
|
||||
|
||||
@Manual{R-bookdown,
|
||||
title = {bookdown: Authoring Books and Technical Documents with R Markdown},
|
||||
author = {Yihui Xie},
|
||||
year = {2021},
|
||||
note = {R package version 0.24},
|
||||
url = {https://CRAN.R-project.org/package=bookdown},
|
||||
}
|
||||
|
||||
@Manual{R-knitr,
|
||||
title = {knitr: A General-Purpose Package for Dynamic Report Generation in R},
|
||||
author = {Yihui Xie},
|
||||
year = {2021},
|
||||
note = {R package version 1.33},
|
||||
url = {https://yihui.org/knitr/},
|
||||
}
|
||||
|
||||
@Manual{R-rmarkdown,
|
||||
title = {rmarkdown: Dynamic Documents for R},
|
||||
author = {JJ Allaire and Yihui Xie and Jonathan McPherson and Javier Luraschi and Kevin Ushey and Aron Atkins and Hadley Wickham and Joe Cheng and Winston Chang and Richard Iannone},
|
||||
year = {2021},
|
||||
note = {R package version 2.10},
|
||||
url = {https://CRAN.R-project.org/package=rmarkdown},
|
||||
}
|
||||
|
||||
@Article{AMR2021,
|
||||
title = {AMR - An R Package for Working with Antimicrobial Resistance Data},
|
||||
author = {M S Berends and C F Luz and A W Friedrich and B N M Sinha and C J Albers and C Glasner},
|
||||
doi = {10.1101/810622},
|
||||
journal = {Journal of Statistical Software},
|
||||
pages = {Accepted for publication},
|
||||
year = {2021},
|
||||
url = {https://www.biorxiv.org/content/10.1101/810622v4},
|
||||
}
|
||||
|
||||
@Book{bookdown2016,
|
||||
title = {bookdown: Authoring Books and Technical Documents with {R} Markdown},
|
||||
author = {Yihui Xie},
|
||||
publisher = {Chapman and Hall/CRC},
|
||||
address = {Boca Raton, Florida},
|
||||
year = {2016},
|
||||
note = {ISBN 978-1138700109},
|
||||
url = {https://bookdown.org/yihui/bookdown},
|
||||
}
|
||||
|
||||
@Book{knitr2015,
|
||||
title = {Dynamic Documents with {R} and knitr},
|
||||
author = {Yihui Xie},
|
||||
publisher = {Chapman and Hall/CRC},
|
||||
address = {Boca Raton, Florida},
|
||||
year = {2015},
|
||||
edition = {2nd},
|
||||
note = {ISBN 978-1498716963},
|
||||
url = {https://yihui.org/knitr/},
|
||||
}
|
||||
|
||||
@InCollection{knitr2014,
|
||||
booktitle = {Implementing Reproducible Computational Research},
|
||||
editor = {Victoria Stodden and Friedrich Leisch and Roger D. Peng},
|
||||
title = {knitr: A Comprehensive Tool for Reproducible Research in {R}},
|
||||
author = {Yihui Xie},
|
||||
publisher = {Chapman and Hall/CRC},
|
||||
year = {2014},
|
||||
note = {ISBN 978-1466561595},
|
||||
url = {http://www.crcpress.com/product/isbn/9781466561595},
|
||||
}
|
||||
|
||||
@Book{rmarkdown2018,
|
||||
title = {R Markdown: The Definitive Guide},
|
||||
author = {Yihui Xie and J.J. Allaire and Garrett Grolemund},
|
||||
publisher = {Chapman and Hall/CRC},
|
||||
address = {Boca Raton, Florida},
|
||||
year = {2018},
|
||||
note = {ISBN 9781138359338},
|
||||
url = {https://bookdown.org/yihui/rmarkdown},
|
||||
}
|
||||
|
||||
@Book{rmarkdown2020,
|
||||
title = {R Markdown Cookbook},
|
||||
author = {Yihui Xie and Christophe Dervieux and Emily Riederer},
|
||||
publisher = {Chapman and Hall/CRC},
|
||||
address = {Boca Raton, Florida},
|
||||
year = {2020},
|
||||
note = {ISBN 9780367563837},
|
||||
url = {https://bookdown.org/yihui/rmarkdown-cookbook},
|
||||
}
|
||||
|
||||
8
preamble.tex
Normal file
8
preamble.tex
Normal file
@ -0,0 +1,8 @@
|
||||
\usepackage{booktabs}
|
||||
\usepackage{amsthm}
|
||||
\makeatletter
|
||||
\def\thm@space@setup{%
|
||||
\thm@preskip=8pt plus 2pt minus 4pt
|
||||
\thm@postskip=\thm@preskip
|
||||
}
|
||||
\makeatother
|
||||
14
style.css
Normal file
14
style.css
Normal file
@ -0,0 +1,14 @@
|
||||
p.caption {
|
||||
color: #777;
|
||||
margin-top: 10px;
|
||||
}
|
||||
p code {
|
||||
white-space: inherit;
|
||||
}
|
||||
pre {
|
||||
word-break: normal;
|
||||
word-wrap: normal;
|
||||
}
|
||||
pre code {
|
||||
white-space: inherit;
|
||||
}
|
||||
127
toc.css
Normal file
127
toc.css
Normal file
@ -0,0 +1,127 @@
|
||||
#TOC ul,
|
||||
#TOC li,
|
||||
#TOC span,
|
||||
#TOC a {
|
||||
margin: 0;
|
||||
padding: 0;
|
||||
position: relative;
|
||||
}
|
||||
#TOC {
|
||||
line-height: 1;
|
||||
border-radius: 5px 5px 0 0;
|
||||
background: #141414;
|
||||
background: linear-gradient(to bottom, #333333 0%, #141414 100%);
|
||||
border-bottom: 2px solid #0fa1e0;
|
||||
width: auto;
|
||||
}
|
||||
#TOC:after,
|
||||
#TOC ul:after {
|
||||
content: '';
|
||||
display: block;
|
||||
clear: both;
|
||||
}
|
||||
#TOC a {
|
||||
background: #141414;
|
||||
background: linear-gradient(to bottom, #333333 0%, #141414 100%);
|
||||
color: #ffffff;
|
||||
display: block;
|
||||
padding: 19px 20px;
|
||||
text-decoration: none;
|
||||
text-shadow: none;
|
||||
}
|
||||
#TOC ul {
|
||||
list-style: none;
|
||||
}
|
||||
#TOC > ul > li {
|
||||
display: inline-block;
|
||||
float: left;
|
||||
margin: 0;
|
||||
}
|
||||
#TOC > ul > li > a {
|
||||
color: #ffffff;
|
||||
}
|
||||
#TOC > ul > li:hover:after {
|
||||
content: '';
|
||||
display: block;
|
||||
width: 0;
|
||||
height: 0;
|
||||
position: absolute;
|
||||
left: 50%;
|
||||
bottom: 0;
|
||||
border-left: 10px solid transparent;
|
||||
border-right: 10px solid transparent;
|
||||
border-bottom: 10px solid #0fa1e0;
|
||||
margin-left: -10px;
|
||||
}
|
||||
#TOC > ul > li:first-child > a {
|
||||
border-radius: 5px 0 0 0;
|
||||
}
|
||||
#TOC.align-right > ul > li:first-child > a,
|
||||
#TOC.align-center > ul > li:first-child > a {
|
||||
border-radius: 0;
|
||||
}
|
||||
#TOC.align-right > ul > li:last-child > a {
|
||||
border-radius: 0 5px 0 0;
|
||||
}
|
||||
#TOC > ul > li.active > a,
|
||||
#TOC > ul > li:hover > a {
|
||||
color: #ffffff;
|
||||
box-shadow: inset 0 0 3px #000000;
|
||||
background: #070707;
|
||||
background: linear-gradient(to bottom, #262626 0%, #070707 100%);
|
||||
}
|
||||
#TOC .has-sub {
|
||||
z-index: 1;
|
||||
}
|
||||
#TOC .has-sub:hover > ul {
|
||||
display: block;
|
||||
}
|
||||
#TOC .has-sub ul {
|
||||
display: none;
|
||||
position: absolute;
|
||||
width: 200px;
|
||||
top: 100%;
|
||||
left: 0;
|
||||
}
|
||||
#TOC .has-sub ul li a {
|
||||
background: #0fa1e0;
|
||||
border-bottom: 1px dotted #31b7f1;
|
||||
filter: none;
|
||||
display: block;
|
||||
line-height: 120%;
|
||||
padding: 10px;
|
||||
color: #ffffff;
|
||||
}
|
||||
#TOC .has-sub ul li:hover a {
|
||||
background: #0c7fb0;
|
||||
}
|
||||
#TOC ul ul li:hover > a {
|
||||
color: #ffffff;
|
||||
}
|
||||
#TOC .has-sub .has-sub:hover > ul {
|
||||
display: block;
|
||||
}
|
||||
#TOC .has-sub .has-sub ul {
|
||||
display: none;
|
||||
position: absolute;
|
||||
left: 100%;
|
||||
top: 0;
|
||||
}
|
||||
#TOC .has-sub .has-sub ul li a {
|
||||
background: #0c7fb0;
|
||||
border-bottom: 1px dotted #31b7f1;
|
||||
}
|
||||
#TOC .has-sub .has-sub ul li a:hover {
|
||||
background: #0a6d98;
|
||||
}
|
||||
#TOC ul ul li.last > a,
|
||||
#TOC ul ul li:last-child > a,
|
||||
#TOC ul ul ul li.last > a,
|
||||
#TOC ul ul ul li:last-child > a,
|
||||
#TOC .has-sub ul li:last-child > a,
|
||||
#TOC .has-sub ul li.last > a {
|
||||
border-bottom: 0;
|
||||
}
|
||||
#TOC ul {
|
||||
font-size: 1.2rem;
|
||||
}
|
||||
Loading…
Reference in New Issue
Block a user