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index.html
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<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<meta name="generator" content="pandoc" />
<title>OxShef: RMarkdown Template Site</title>
<script src="site_libs/jquery-1.11.3/jquery.min.js"></script>
<meta name="viewport" content="width=device-width, initial-scale=1" />
<link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" />
<script src="site_libs/bootstrap-3.3.5/js/bootstrap.min.js"></script>
<script src="site_libs/bootstrap-3.3.5/shim/html5shiv.min.js"></script>
<script src="site_libs/bootstrap-3.3.5/shim/respond.min.js"></script>
<script src="site_libs/navigation-1.1/tabsets.js"></script>
<link href="site_libs/highlightjs-9.12.0/textmate.css" rel="stylesheet" />
<script src="site_libs/highlightjs-9.12.0/highlight.js"></script>
<script src="site_libs/htmlwidgets-0.9/htmlwidgets.js"></script>
<script src="site_libs/proj4js-2.3.15/proj4.js"></script>
<link href="site_libs/highcharts-5.0.6/css/motion.css" rel="stylesheet" />
<script src="site_libs/highcharts-5.0.6/highstock.js"></script>
<script src="site_libs/highcharts-5.0.6/highcharts-3d.js"></script>
<script src="site_libs/highcharts-5.0.6/highcharts-more.js"></script>
<script src="site_libs/highcharts-5.0.6/modules/annotations.js"></script>
<script src="site_libs/highcharts-5.0.6/modules/broken-axis.js"></script>
<script src="site_libs/highcharts-5.0.6/modules/data.js"></script>
<script src="site_libs/highcharts-5.0.6/modules/drilldown.js"></script>
<script src="site_libs/highcharts-5.0.6/modules/exporting.js"></script>
<script src="site_libs/highcharts-5.0.6/modules/funnel.js"></script>
<script src="site_libs/highcharts-5.0.6/modules/heatmap.js"></script>
<script src="site_libs/highcharts-5.0.6/modules/map.js"></script>
<script src="site_libs/highcharts-5.0.6/modules/no-data-to-display.js"></script>
<script src="site_libs/highcharts-5.0.6/modules/offline-exporting.js"></script>
<script src="site_libs/highcharts-5.0.6/modules/solid-gauge.js"></script>
<script src="site_libs/highcharts-5.0.6/modules/treemap.js"></script>
<script src="site_libs/highcharts-5.0.6/plugins/annotations.js"></script>
<script src="site_libs/highcharts-5.0.6/plugins/draggable-legend.js"></script>
<script src="site_libs/highcharts-5.0.6/plugins/draggable-points.js"></script>
<script src="site_libs/highcharts-5.0.6/plugins/export-csv.js"></script>
<script src="site_libs/highcharts-5.0.6/plugins/grouped-categories.js"></script>
<script src="site_libs/highcharts-5.0.6/plugins/motion.js"></script>
<script src="site_libs/highcharts-5.0.6/plugins/pattern-fill-v2.js"></script>
<script src="site_libs/highcharts-5.0.6/plugins/tooltip-delay.js"></script>
<script src="site_libs/highcharts-5.0.6/custom/reset.js"></script>
<script src="site_libs/highcharts-5.0.6/custom/symbols-extra.js"></script>
<script src="site_libs/highcharts-5.0.6/custom/text-symbols.js"></script>
<link href="site_libs/fontawesome-4.5.0/font-awesome.min.css" rel="stylesheet" />
<link href="site_libs/htmlwdgtgrid-1/htmlwdgtgrid.css" rel="stylesheet" />
<script src="site_libs/highchart-binding-0.5.0/highchart.js"></script>
<meta name="description" content="This is a template site using RMarkdown for the OxShef Project - a collaboration between University of Oxford and University of Sheffield" />
<link rel="icon" type="image/png" href="images/favicon.png" />
<script type="text/javascript" src="js/rmarkdown.js"></script>
<style type="text/css">code{white-space: pre;}</style>
<style type="text/css">
pre:not([class]) {
background-color: white;
}
</style>
<script type="text/javascript">
if (window.hljs) {
hljs.configure({languages: []});
hljs.initHighlightingOnLoad();
if (document.readyState && document.readyState === "complete") {
window.setTimeout(function() { hljs.initHighlighting(); }, 0);
}
}
</script>
<style type="text/css">
h1 {
font-size: 34px;
}
h1.title {
font-size: 38px;
}
h2 {
font-size: 30px;
}
h3 {
font-size: 24px;
}
h4 {
font-size: 18px;
}
h5 {
font-size: 16px;
}
h6 {
font-size: 12px;
}
.table th:not([align]) {
text-align: left;
}
</style>
<link rel="stylesheet" href="css/rmarkdown.css" type="text/css" />
</head>
<body>
<style type = "text/css">
.main-container {
max-width: 940px;
margin-left: auto;
margin-right: auto;
}
code {
color: inherit;
background-color: rgba(0, 0, 0, 0.04);
}
img {
max-width:100%;
height: auto;
}
.tabbed-pane {
padding-top: 12px;
}
button.code-folding-btn:focus {
outline: none;
}
</style>
<div class="container-fluid main-container">
<!-- tabsets -->
<script>
$(document).ready(function () {
window.buildTabsets("TOC");
});
</script>
<!-- code folding -->
<div id="rStudioHeader" class="alwaysShrunk">
<div class="innards bandContent">
<div>
<a class="menuItem" href="index.html">OxShef: Rmd Template Site</a>
</div>
<div id="menu">
<div id="menuToggler"></div>
<div id="menuItems">
<a class="menuItem" href="example-page.html">Example Page</a>
<a class="menuItem" href="idn_info.html">Support for Oxford Researchers</a>
<a class="menuItem" href="orda_info.html">Support for Sheffield Researchers</a>
<a class="menuItem gitHub" href="https://github.com/OxShef/oxshef_rmd_template"></a>
<a class="menuItem gitHubText" href="https://github.com/OxShef/oxshef_rmd_template">Source on GitHub</a>
</div>
</div>
</div>
</div>
<style type="text/css">
#TOC {
margin-left: 35px;
margin-top: 90px;
}
</style>
<script type="text/javascript">
$(".main-container").removeClass("main-container").removeClass("container-fluid").addClass("footerPushDown");
</script>
<div id="pageContent" class="standardPadding">
<div class="articleBandContent">
<div class="alert alert-warning alert-dismissible" role="alert">
<div class='container-fluid'>
<button type="button" class="close" data-dismiss="alert" aria-label="Close"><span aria-hidden="true">×</span></button>
</div>
<div class='row'>
<div class='col-md-6 align-self-center'>
<div class='row'>
<div class='col-sm-6 align-self-center'>
<span>Researchers at <strong>University of Oxford</strong> can use the ORDA service XXX to host interactive visualisations produced with XXX.</span>
See <a href='idn_info.html' style='color:#fff;font-weight:bold'>here for further details</a>.</span>
<p></p>
</div>
<div class='col-sm-6 align-self-center'>
<center>
<img src='images/logo_university-of-oxford_web.png' width='100px'></img>
</center>
<p></p>
</div>
</div>
</div>
<div class='col-md-6 align-self-center'>
<div class='row'>
<div class='col-sm-6 align-self-center'>
<span>Researchers at <strong>University of Sheffield</strong> can use the ORDA service XXX to host interactive visualisations produced with XXX.</span>
See <a href='orda_info.html' style='color:#fff;font-weight:bold'>here for further details</a>.</span>
<p></p>
</div>
<div class='col-sm-6 align-self-center'>
<center>
<img src='images/logo_university-of-sheffield_web_white.svg' width='250px'></img>
</center>
</div>
</div>
</div>
</div>
</div>
<div class="fluid-row" id="header">
<h1 class="title toc-ignore">OxShef: RMarkdown Template Site</h1>
</div>
<p>This is a template RMarkdown website for the OxShef project, please consider using this template if you are adding a new website to the project that will be written using RMarkdown files.</p>
<p>Current websites in OxShef that use this template include:</p>
<ul>
<li><a href="https://oxshef.github.io/oxshef_charts/">OxShef Charts</a>: A guide to different visualisation options for visualising research data</li>
</ul>
<p>There is a more thorough overview of the features of this website template (and how to use it) in the <a href="https://github.com/OxShef/oxshef_rmd_template">github readme</a>.</p>
<hr>
<div id="site-features" class="section level1">
<h1>Site Features</h1>
<ul>
<li><p>Bootstrap 4.0: Bootstrap is an awesome framework for building responsively designed websites, i.e. content that <em>reflows</em> as the size of the browser window changes, beautifully supporting a wide range of mobile devices. The main utility of Bootstrap in this template is for laying out grids, an example of which you can see above.</p></li>
<li><p>includes/include_institutional-support.html: The purple alert at the top of this page contains links to institutional support for the service/tool described within the website itself, linking to idn_info.html and orda_info.html respectively. Note that this is optionall included in the YAML header as follows:</p></li>
</ul>
<pre class="yaml"><code>output:
html_document:
toc_float: false
includes:
before_body: [includes/include_header.html, includes/include_institutional-support.html]</code></pre>
<hr>
</div>
<div id="bootstrap-grid-example" class="section level1">
<h1>Bootstrap grid example</h1>
<div class="row align-items-center">
<div class="col-md-6 align-self-center">
<p>Note that HTML to can be included verbatim within the .Rmd files that generate each webpage, however the markdown engine does interpret content within HTML tags. This allows Markdown like this **bold** to be used to <strong>embolden</strong> text.</p>
<p>To guaranantee that HTML is rendered without any <em>attempted magic</em> you can make use of these special comments around the html:</p>
<p><–html_preserve–></p>
<p><–/html_preserve–></p>
</div>
<div class="col-md-6 align-self-center">
<p>This section of the site should appear either directly to the right or underneath the information about <code>html_preserve</code> tags, as it is in another column of the bootstrap grid. The barchart below is generated using the <code>highcharter</code> library:</p>
<div id="htmlwidget-772e5f5283473938eb77" style="width:100%;height:500px;" class="highchart html-widget"></div>
<script type="application/json" data-for="htmlwidget-772e5f5283473938eb77">{"x":{"hc_opts":{"title":{"text":"Median height of species from dplyr::starwars"},"yAxis":{"title":{"text":"Median height (cm)"},"type":"linear"},"credits":{"enabled":false},"exporting":{"enabled":false},"plotOptions":{"series":{"turboThreshold":0,"showInLegend":false,"marker":{"enabled":true}},"treemap":{"layoutAlgorithm":"squarified"},"bubble":{"minSize":5,"maxSize":25},"scatter":{"marker":{"symbol":"circle"}}},"annotationsOptions":{"enabledButtons":false},"tooltip":{"delayForDisplay":10},"series":[{"group":"group","data":[{"species":"Quermian","median.height":264,"y":264,"name":"Quermian"},{"species":"Wookiee","median.height":231,"y":231,"name":"Wookiee"},{"species":"Kaminoan","median.height":221,"y":221,"name":"Kaminoan"},{"species":"Kaleesh","median.height":216,"y":216,"name":"Kaleesh"},{"species":"Gungan","median.height":206,"y":206,"name":"Gungan"},{"species":"Pau'an","median.height":206,"y":206,"name":"Pau'an"},{"species":"Besalisk","median.height":198,"y":198,"name":"Besalisk"},{"species":"Cerean","median.height":198,"y":198,"name":"Cerean"},{"species":"Chagrian","median.height":196,"y":196,"name":"Chagrian"},{"species":"Nautolan","median.height":196,"y":196,"name":"Nautolan"},{"species":"Skakoan","median.height":193,"y":193,"name":"Skakoan"},{"species":"Muun","median.height":191,"y":191,"name":"Muun"},{"species":"Neimodian","median.height":191,"y":191,"name":"Neimodian"},{"species":"Trandoshan","median.height":190,"y":190,"name":"Trandoshan"},{"species":"Iktotchi","median.height":188,"y":188,"name":"Iktotchi"},{"species":"Kel Dor","median.height":188,"y":188,"name":"Kel Dor"},{"species":"Tholothian","median.height":184,"y":184,"name":"Tholothian"},{"species":"Geonosian","median.height":183,"y":183,"name":"Geonosian"},{"species":"Human","median.height":180,"y":180,"name":"Human"},{"species":"Mon Calamari","median.height":180,"y":180,"name":"Mon Calamari"},{"species":"Twi'lek","median.height":179,"y":179,"name":"Twi'lek"},{"species":"Togruta","median.height":178,"y":178,"name":"Togruta"},{"species":"Hutt","median.height":175,"y":175,"name":"Hutt"},{"species":"Rodian","median.height":173,"y":173,"name":"Rodian"},{"species":"Zabrak","median.height":173,"y":173,"name":"Zabrak"},{"species":"Clawdite","median.height":168,"y":168,"name":"Clawdite"},{"species":"Mirialan","median.height":168,"y":168,"name":"Mirialan"},{"species":"Toong","median.height":163,"y":163,"name":"Toong"},{"species":"Sullustan","median.height":160,"y":160,"name":"Sullustan"},{"species":"Toydarian","median.height":137,"y":137,"name":"Toydarian"},{"species":"Droid","median.height":132,"y":132,"name":"Droid"},{"species":"Xexto","median.height":122,"y":122,"name":"Xexto"},{"species":"Dug","median.height":112,"y":112,"name":"Dug"},{"species":"Vulptereen","median.height":94,"y":94,"name":"Vulptereen"},{"species":"Ewok","median.height":88,"y":88,"name":"Ewok"},{"species":"Aleena","median.height":79,"y":79,"name":"Aleena"},{"species":"Yoda's species","median.height":66,"y":66,"name":"Yoda's species"}],"type":"bar"}],"xAxis":{"type":"category","title":{"text":"species"},"categories":null}},"theme":{"chart":{"backgroundColor":"transparent"}},"conf_opts":{"global":{"Date":null,"VMLRadialGradientURL":"http =//code.highcharts.com/list(version)/gfx/vml-radial-gradient.png","canvasToolsURL":"http =//code.highcharts.com/list(version)/modules/canvas-tools.js","getTimezoneOffset":null,"timezoneOffset":0,"useUTC":true},"lang":{"contextButtonTitle":"Chart context menu","decimalPoint":".","downloadJPEG":"Download JPEG image","downloadPDF":"Download PDF document","downloadPNG":"Download PNG image","downloadSVG":"Download SVG vector image","drillUpText":"Back to {series.name}","invalidDate":null,"loading":"Loading...","months":["January","February","March","April","May","June","July","August","September","October","November","December"],"noData":"No data to display","numericSymbols":["k","M","G","T","P","E"],"printChart":"Print chart","resetZoom":"Reset zoom","resetZoomTitle":"Reset zoom level 1:1","shortMonths":["Jan","Feb","Mar","Apr","May","Jun","Jul","Aug","Sep","Oct","Nov","Dec"],"thousandsSep":" ","weekdays":["Sunday","Monday","Tuesday","Wednesday","Thursday","Friday","Saturday"]}},"type":"chart","fonts":[],"debug":false},"evals":[],"jsHooks":[]}</script>
</div>
<hr>
</div>
</div>
</div> <!-- articleBandContent -->
</div> <!-- pageContent -->
<div id="rStudioFooter" class="band full">
<div class="bandContent">
<h4><a href="oxshef.github.io" target="_blank" style="color:#fff;font-weight:bold">OxShef</a></h4>
<div id="logos">
<!--<a href="https://twitter.com/rstudio" class="footerLogo twitter"></a>!-->
<a href="https://github.com/OxShef/oxshef_rmd_template" class="footerLogo gitHub"></a>
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</div>
</div>
</div>
<!-- bizible -->
<script type="text/javascript" src="//cdn.bizible.com/scripts/bizible.js" async=""></script>
</div>
<script>
// add bootstrap table styles to pandoc tables
function bootstrapStylePandocTables() {
$('tr.header').parent('thead').parent('table').addClass('table table-condensed');
}
$(document).ready(function () {
bootstrapStylePandocTables();
});
</script>
</body>
</html>