Readme.html

<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml" lang="" xml:lang="">
<head>
  <meta charset="utf-8" />
  <meta name="generator" content="pandoc" />
  <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes" />
  <title>Readme</title>
  <style type="text/css">
      code{white-space: pre-wrap;}
      span.smallcaps{font-variant: small-caps;}
      span.underline{text-decoration: underline;}
      div.column{display: inline-block; vertical-align: top; width: 50%;}
  </style>
  <style type="text/css">
a.sourceLine { display: inline-block; line-height: 1.25; }
a.sourceLine { pointer-events: none; color: inherit; text-decoration: inherit; }
a.sourceLine:empty { height: 1.2em; }
.sourceCode { overflow: visible; }
code.sourceCode { white-space: pre; position: relative; }
div.sourceCode { margin: 1em 0; }
pre.sourceCode { margin: 0; }
@media screen {
div.sourceCode { overflow: auto; }
}
@media print {
code.sourceCode { white-space: pre-wrap; }
a.sourceLine { text-indent: -1em; padding-left: 1em; }
}
pre.numberSource a.sourceLine
  { position: relative; left: -4em; }
pre.numberSource a.sourceLine::before
  { content: attr(title);
    position: relative; left: -1em; text-align: right; vertical-align: baseline;
    border: none; pointer-events: all; display: inline-block;
    -webkit-touch-callout: none; -webkit-user-select: none;
    -khtml-user-select: none; -moz-user-select: none;
    -ms-user-select: none; user-select: none;
    padding: 0 4px; width: 4em;
    color: #aaaaaa;
  }
pre.numberSource { margin-left: 3em; border-left: 1px solid #aaaaaa;  padding-left: 4px; }
div.sourceCode
  {  }
@media screen {
a.sourceLine::before { text-decoration: underline; }
}
code span.al { color: #ff0000; font-weight: bold; } /* Alert */
code span.an { color: #60a0b0; font-weight: bold; font-style: italic; } /* Annotation */
code span.at { color: #7d9029; } /* Attribute */
code span.bn { color: #40a070; } /* BaseN */
code span.bu { } /* BuiltIn */
code span.cf { color: #007020; font-weight: bold; } /* ControlFlow */
code span.ch { color: #4070a0; } /* Char */
code span.cn { color: #880000; } /* Constant */
code span.co { color: #60a0b0; font-style: italic; } /* Comment */
code span.cv { color: #60a0b0; font-weight: bold; font-style: italic; } /* CommentVar */
code span.do { color: #ba2121; font-style: italic; } /* Documentation */
code span.dt { color: #902000; } /* DataType */
code span.dv { color: #40a070; } /* DecVal */
code span.er { color: #ff0000; font-weight: bold; } /* Error */
code span.ex { } /* Extension */
code span.fl { color: #40a070; } /* Float */
code span.fu { color: #06287e; } /* Function */
code span.im { } /* Import */
code span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Information */
code span.kw { color: #007020; font-weight: bold; } /* Keyword */
code span.op { color: #666666; } /* Operator */
code span.ot { color: #007020; } /* Other */
code span.pp { color: #bc7a00; } /* Preprocessor */
code span.sc { color: #4070a0; } /* SpecialChar */
code span.ss { color: #bb6688; } /* SpecialString */
code span.st { color: #4070a0; } /* String */
code span.va { color: #19177c; } /* Variable */
code span.vs { color: #4070a0; } /* VerbatimString */
code span.wa { color: #60a0b0; font-weight: bold; font-style: italic; } /* Warning */
  </style>
  <!--[if lt IE 9]>
    <script src="//cdnjs.cloudflare.com/ajax/libs/html5shiv/3.7.3/html5shiv-printshiv.min.js"></script>
  <![endif]-->
  <div style="display: none">
  \[
  %%
  % Add your macros here; they'll be included in pdf and html output.
  %%
  
  \newcommand{\R}{\mathbb{R}}    % reals
  \newcommand{\E}{\mathbb{E}}    % expectation
  \renewcommand{\P}{\mathbb{P}}  % probability
  
  \]
  </div>
</head>
<body>
<h1 id="a-quick-introduction-to-rmarkdown">A quick introduction to R/markdown</h1>
<p>These are notes and materials for a short (2-hour) course on using R/markdown to generate reports and dynamic documents.</p>
<p>Here’s a link to <a href="http://petrelharp.github.io/r-markdown-tutorial/using-rmarkdown.slides.html">the slides</a>. Here is also a document with some <a href="http://petrelharp.github.io/r-markdown-tutorial/gotchas.html">gotchas</a> that I’ve figured out my way around, and some <a href="http://petrelharp.github.io/r-markdown-tutorial/technical-notes.html">technical notes</a> on getting pandoc, R+markdown, and this presentation to work.</p>
<h2 id="outline">Outline</h2>
<ol type="1">
<li><p>Markdown</p>
<ul>
<li>philosophy: just write</li>
<li>structure: headers, breaks</li>
<li>formatting: <strong>bold</strong>, <em>emphasis</em></li>
<li><a href="Outline">links</a></li>
<li>math</li>
<li>code blocks</li>
<li>images</li>
<li><a href="https://github.com/jgm/pandoc/issues/851">metadata</a></li>
<li>the <a href="http://en.wikipedia.org/wiki/Markdown">wider</a> <a href="http://blog.codinghorror.com/standard-flavored-markdown/">world</a> of <a href="http://commonmark.org/">markdown(s)</a></li>
</ul></li>
<li><p>Rendering markdown with <a href="http://pandoc.org">pandoc</a></p>
<ul>
<li>bare-bones</li>
<li>adding style</li>
<li>metadata/YAML headers</li>
<li>self-contained documents (+local mathjax)</li>
<li>gotchas</li>
<li>the <a href="http://pandoc.org/README.html">documentation</a> and <a href="http://stackoverflow.com/questions/tagged/pandoc?sort=frequent&amp;pageSize=15">where to look for help</a></li>
</ul></li>
<li><p>Adding <a href="http://r-project.org/">R</a></p>
<ul>
<li>what <a href="http://yihui.name/knitr/">knitr</a> does</li>
<li>code chunks</li>
<li>figures</li>
<li>tables</li>
<li>chunk options</li>
<li>inline <code>R</code></li>
<li>rmarkdown and rstudio</li>
</ul></li>
<li><p>One report, many documents: a working example</p>
<ul>
<li>one subdirectory per dataset</li>
<li>json configuration + simulated data</li>
<li>external variables with knitr</li>
<li>using <code>Rscript</code> instead</li>
</ul></li>
</ol>
<h2 id="compiling-the-presentation-yourself">Compiling the presentation yourself</h2>
<p>The presentation uses <a href="http://lab.hakim.se/reveal-js/">reveal.js</a>. You can get this repository along with reveal.js like so:</p>
<div class="sourceCode" id="cb1"><pre class="sourceCode sh"><code class="sourceCode bash"><a class="sourceLine" id="cb1-1" title="1"><span class="fu">git</span> clone https://github.com/petrelharp/r-markdown-tutorial.git</a>
<a class="sourceLine" id="cb1-2" title="2"><span class="bu">cd</span> r-markdown-turoial</a>
<a class="sourceLine" id="cb1-3" title="3"><span class="fu">git</span> submodule init <span class="kw">&amp;&amp;</span> <span class="fu">git</span> submodule update</a></code></pre></div>
<p>With an up-to-date version of pandoc, R, and knitr, you should be able to compile the presentation like so:</p>
<div class="sourceCode" id="cb2"><pre class="sourceCode sh"><code class="sourceCode bash"><a class="sourceLine" id="cb2-1" title="1"><span class="fu">make</span> using-rmarkdown.slides.html</a></code></pre></div>
<p><em>Note:</em> OSX, for some reason, passes strings through make differently, so you need to uncomment a line in the Makefile, so it looks like this:</p>
<pre><code># or, uncomment for OSX:
KNITR_PATTERNS = list( chunk.begin=&quot;^```+\\\\s*\\\\{[.]?(r[a-zA-Z]*.*)\\\\}\\\\s*$$&quot;, chunk.end=&quot;^```+\\\\s*$$&quot;, inline.code=&quot;`r +([^`]+)\\\\s*`&quot;)</code></pre>
<p>(the only difference is an extra level of escaping the slashes).</p>
<p>Since I give presentations sometimes not on the internet, this by default relies on a local installation of MathJax, so unless you’ve installed this on Debian/Ubuntu (<code>aptitude install libjs-mathjax</code>), to view the maths properly you need to change the location in the Makefile.</p>
<p>The presentation will not render in Rstudio because: by default, <code>knitr</code> tries to process all code blocks; so to have example code in the document you have to munge your own code. To keep my document processable by just pandoc, and prettier (except the inline code) I am rendering the presentation after modifying the regular expression knitr uses to identify code chunks to require exactly three backticks, at the start of the line, and the identifier <code>r</code> (by default it is much more lax). See the Makefile for how this is done.</p>
</body>
</html>