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0__make.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> Make</title>
<script src="library/jquery-1.11.3/jquery.min.js"></script>
<meta name="viewport" content="width=device-width, initial-scale=1" />
<link href="library/bootstrap-3.3.5/css/paper.min.css" rel="stylesheet" />
<script src="library/bootstrap-3.3.5/js/bootstrap.min.js"></script>
<script src="library/bootstrap-3.3.5/shim/html5shiv.min.js"></script>
<script src="library/bootstrap-3.3.5/shim/respond.min.js"></script>
<script src="library/navigation-1.1/tabsets.js"></script>
<style type="text/css">code{white-space: pre;}</style>
<style type="text/css">
div.sourceCode { overflow-x: auto; }
table.sourceCode, tr.sourceCode, td.lineNumbers, td.sourceCode {
margin: 0; padding: 0; vertical-align: baseline; border: none; }
table.sourceCode { width: 100%; line-height: 100%; }
td.lineNumbers { text-align: right; padding-right: 4px; padding-left: 4px; color: #aaaaaa; border-right: 1px solid #aaaaaa; }
td.sourceCode { padding-left: 5px; }
code > span.kw { color: #007020; font-weight: bold; } /* Keyword */
code > span.dt { color: #902000; } /* DataType */
code > span.dv { color: #40a070; } /* DecVal */
code > span.bn { color: #40a070; } /* BaseN */
code > span.fl { color: #40a070; } /* Float */
code > span.ch { color: #4070a0; } /* Char */
code > span.st { color: #4070a0; } /* String */
code > span.co { color: #60a0b0; font-style: italic; } /* Comment */
code > span.ot { color: #007020; } /* Other */
code > span.al { color: #ff0000; font-weight: bold; } /* Alert */
code > span.fu { color: #06287e; } /* Function */
code > span.er { color: #ff0000; font-weight: bold; } /* Error */
code > span.wa { color: #60a0b0; font-weight: bold; font-style: italic; } /* Warning */
code > span.cn { color: #880000; } /* Constant */
code > span.sc { color: #4070a0; } /* SpecialChar */
code > span.vs { color: #4070a0; } /* VerbatimString */
code > span.ss { color: #bb6688; } /* SpecialString */
code > span.im { } /* Import */
code > span.va { color: #19177c; } /* Variable */
code > span.cf { color: #007020; font-weight: bold; } /* ControlFlow */
code > span.op { color: #666666; } /* Operator */
code > span.bu { } /* BuiltIn */
code > span.ex { } /* Extension */
code > span.pp { color: #bc7a00; } /* Preprocessor */
code > span.at { color: #7d9029; } /* Attribute */
code > span.do { color: #ba2121; font-style: italic; } /* Documentation */
code > span.an { color: #60a0b0; font-weight: bold; font-style: italic; } /* Annotation */
code > span.cv { color: #60a0b0; font-weight: bold; font-style: italic; } /* CommentVar */
code > span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Information */
</style>
<style type="text/css">
pre:not([class]) {
background-color: white;
}
</style>
<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;
}
</style>
</head>
<body>
<div class="container-fluid main-container">
<div class="row">
<div class="col-md-2" style="border-top:solid #E2A674 20px"></div>
<div class="col-md-2 rpqa" style="border-top:solid #9F3B2B 20px"></div>
<div class="col-md-4" style="background:black;text-align:center"><a href="index.html" style="color:white"><i class="glyphicon glyphicon-th-list"></i> Back to index</a></div>
<div class="col-md-2 hist_sweden" style="border-top:solid #21523B 20px"></div>
<div class="col-md-2 mod_sweden" style="border-top:solid #8A846C 20px"></div>
</div>
</div>
<div class="container-fluid main-container">
<div id="make" class="section level1">
<h1>Make</h1>
<p>load helpers</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">source</span>(<span class="st">"0__helpers.R"</span>)
<span class="kw">render_web</span>(<span class="st">"index.Rmd"</span>, <span class="dt">include_top =</span> <span class="ot">NULL</span>)</code></pre></div>
<div id="spin-all-r-scripts" class="section level3">
<h3>spin all R scripts</h3>
<p>since all R scripts are either source files or meant for the cluster we just want to document R scripts</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">just_document =<span class="st"> </span>all_Rs =<span class="st"> </span><span class="kw">c</span>(<span class="kw">list.files</span>(<span class="dt">pattern =</span> <span class="st">"</span><span class="ch">\\</span><span class="st">.R$"</span>, <span class="dt">full.names =</span> <span class="ot">TRUE</span>), <span class="kw">list.files</span>(<span class="dt">path =</span> <span class="st">"cluster"</span>, <span class="dt">pattern =</span> <span class="st">"</span><span class="ch">\\</span><span class="st">.R$"</span>, <span class="dt">full.names =</span> <span class="ot">TRUE</span>))
for(i in <span class="kw">seq_along</span>(all_Rs)) {
just_document[i] =<span class="st"> </span><span class="kw">spin</span>(all_Rs[i],<span class="dt">knit=</span><span class="ot">FALSE</span>,<span class="dt">envir =</span> <span class="kw">new.env</span>(), <span class="dt">format =</span> <span class="st">"Rmd"</span>, )
}</code></pre></div>
<p>after spinning into Rmds, render them, but don’t evaluate code</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">opts_chunk$<span class="kw">set</span>(<span class="dt">eval=</span><span class="ot">FALSE</span>, <span class="dt">cache=</span><span class="ot">FALSE</span>)
for(i in <span class="kw">seq_along</span>(just_document)) {
if (<span class="kw">dirname</span>(just_document[i]) ==<span class="st"> "cluster"</span>) {
<span class="kw">file.rename</span>(just_document[i], <span class="kw">basename</span>(just_document[i]))
just_document[i] =<span class="st"> </span><span class="kw">basename</span>(just_document[i])
}
<span class="kw">render_web</span>(just_document[i], <span class="dt">auto_tab =</span> <span class="ot">FALSE</span>)
}</code></pre></div>
<p>remove the temporary Rmd files left over from spinning</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">unlink</span>(just_document)</code></pre></div>
<p>now render the md files. these are usually from scripts I had to run on the cluster for memory reasons</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">all_mds =<span class="st"> </span><span class="kw">list.files</span>(<span class="dt">pattern =</span> <span class="st">"</span><span class="ch">\\</span><span class="st">.md$"</span>)
for(i in <span class="kw">seq_along</span>(all_mds)) {
<span class="kw">render_web</span>(all_mds[i])
}</code></pre></div>
<p>all other scripts should be evaluated</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">opts_chunk$<span class="kw">set</span>(<span class="dt">eval=</span><span class="ot">TRUE</span>, <span class="dt">cache =</span> <span class="ot">TRUE</span>)
<span class="kw">library</span>(stringr)
done =<span class="st"> </span><span class="kw">str_sub</span>(all_mds,<span class="dv">1</span>, -<span class="dv">4</span>)
all_rmds =<span class="st"> </span><span class="kw">list.files</span>(<span class="dt">pattern =</span> <span class="st">".Rmd$"</span>)
todo =<span class="st"> </span><span class="kw">str_sub</span>(all_rmds, <span class="dv">1</span>, -<span class="dv">5</span>)
rmds_left =<span class="st"> </span>all_rmds[ !todo %in%<span class="st"> </span>done ]
rmds_left =<span class="st"> </span><span class="kw">list.files</span>(<span class="dt">pattern =</span> <span class="st">"^2[^e]+_main_.+.Rmd$"</span>)
for(i in <span class="kw">seq_along</span>(rmds_left)) {
<span class="kw">render_web</span>(rmds_left[i])
}</code></pre></div>
</div>
</div>
</div>
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// add bootstrap table styles to pandoc tables
$(document).ready(function () {
$('tr.header').parent('thead').parent('table').addClass('table table-condensed');
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</body>
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