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<meta name="author" content="Peter Ralph">
<meta name="dcterms.date" content="2020-09-29">
<title>Writing reproducible, re-usable reports, with R + markdown</title>
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<div class="reveal">
<div class="slides">
<section id="title-slide">
<h1 class="title">Writing reproducible, re-usable reports, with R + markdown</h1>
<p class="author">Peter Ralph</p>
<p class="date">September 29, 2020</p>
</section>
<section><section id="markdown" class="title-slide slide level1"><h1>Markdown</h1></section><section id="goal" class="slide level2">
<h2>Goal:</h2>
<p>Communicate your thoughts to your collaborators and your future self,</p>
<div class="fragment">
<p>combining text, math, documented code,</p>
</div>
<div class="fragment">
<p>and <strong>no fuss</strong>.</p>
</div>
</section><section class="slide level2">
<p>No fussing about layout:</p>
<ul>
<li>unformatted text</li>
<li><a href="http://commonmark.org/">markdown</a></li>
<li><a href="http://latex-project.org/intro.html">LaTeX</a></li>
</ul>
<p>Markdown aims to be readable as-is,<br />
but has methods to produce beautiful output.</p>
<div class="fragment">
<blockquote>
<p>A Markdown-formatted document should be publishable as-is, as plain text, without looking like it’s been marked up with tags or formatting instructions. – <a href="http://daringfireball.net/projects/markdown/syntax#philosophy">John Gruber</a></p>
</blockquote>
</div>
</section><section id="no-really-dont-think-about-the-layout" class="slide level2">
<h2>No, really, don’t think about the layout</h2>
<p>Don’t even <em>think</em> about the layout, just the content.</p>
<blockquote>
<p>[…] it is better to leave document design to document designers, and to let authors get on with writing documents – <a href="http://latex-project.org/intro.html">intro to LaTeX</a></p>
</blockquote>
</section><section class="slide level2">
<p>Today’s goal:</p>
<ol type="1">
<li>Learn a few simple rules</li>
<li>and get going producing content.</li>
</ol>
</section><section id="structuring-text" class="slide level2">
<h2>Structuring text</h2>
<ol type="1">
<li>Separate things with empty lines.</li>
<li>Wrap lines whenever you feel like it.</li>
</ol>
<figure>
<img data-src="Erika_9_typewriter.jpg" alt="your laptop?" /><figcaption>your laptop?</figcaption>
</figure>
<!--
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carriage return
always does the same thing.
But, it's nice to have different (semantic) levels of spaces.
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</section><section id="source" class="slide level2">
<h2>Source</h2>
<div class="sourceCode" id="cb1"><pre class="sourceCode markdown"><code class="sourceCode markdown"><a class="sourceLine" id="cb1-1" title="1">Text formatting</a>
<a class="sourceLine" id="cb1-2" title="2">===============</a>
<a class="sourceLine" id="cb1-3" title="3"></a>
<a class="sourceLine" id="cb1-4" title="4">Inline markup</a>
<a class="sourceLine" id="cb1-5" title="5">-------------</a>
<a class="sourceLine" id="cb1-6" title="6"></a>
<a class="sourceLine" id="cb1-7" title="7">**Paragraphs** begin and end </a>
<a class="sourceLine" id="cb1-8" title="8">with empty lines, and are *not* indented.</a>
<a class="sourceLine" id="cb1-9" title="9"></a>
<a class="sourceLine" id="cb1-10" title="10">- **bold** and *emphasis*</a>
<a class="sourceLine" id="cb1-11" title="11">- ~~strikeout~~</a>
<a class="sourceLine" id="cb1-12" title="12"><span class="fl">- super^scripts^ and sub~scripts~</span></a>
<a class="sourceLine" id="cb1-13" title="13"><span class="fl">- and </span><span class="bn">`inline_code($fixed.width)`</span></a></code></pre></div>
</section><section id="result" class="slide level2">
<h2>Result</h2>
<h3 id="text-formatting">Text formatting</h3>
<h4 id="inline-markup">Inline markup</h4>
<p><strong>Paragraphs</strong> begin and end with empty lines, and are <em>not</em> indented.</p>
<ul>
<li><strong>bold</strong> and <em>emphasis</em></li>
<li><del>strikeout</del></li>
<li>super<sup>scripts</sup> and sub<sub>scripts</sub></li>
<li>and <code>inline_code($fixed.width)</code></li>
</ul>
</section><section id="source-1" class="slide level2">
<h2>Source</h2>
<div class="sourceCode" id="cb2"><pre class="sourceCode markdown"><code class="sourceCode markdown"><a class="sourceLine" id="cb2-1" title="1">Lists must be preceded by an empty line,</a>
<a class="sourceLine" id="cb2-2" title="2"></a>
<a class="sourceLine" id="cb2-3" title="3">1. <span class="fl"> ordered or unordered.</span></a>
<a class="sourceLine" id="cb2-4" title="4"><span class="fl">2. Indenting subsequent content</span></a>
<a class="sourceLine" id="cb2-5" title="5"><span class="fl"> </span></a>
<a class="sourceLine" id="cb2-6" title="6"><span class="fl"> - will continue the list</span></a>
<a class="sourceLine" id="cb2-7" title="7"></a>
<a class="sourceLine" id="cb2-8" title="8"><span class="bn"> * and nest</span></a>
<a class="sourceLine" id="cb2-9" title="9"><span class="bn"> * other lists.</span></a>
<a class="sourceLine" id="cb2-10" title="10"></a>
<a class="sourceLine" id="cb2-11" title="11">3. <span class="fl"> *Indenting* means one tab, or four spaces.</span></a>
<a class="sourceLine" id="cb2-12" title="12"></a>
<a class="sourceLine" id="cb2-13" title="13">After using markdown for a bit, </a>
<a class="sourceLine" id="cb2-14" title="14">go read <span class="ot">[pandoc's documentation](http://pandoc.org/README.html)</span>.</a></code></pre></div>
</section><section class="slide level2">
<p>Lists must be preceded by an empty line,</p>
<ol type="1">
<li>ordered or unordered.</li>
<li><p>Indenting subsequent content</p>
<ul>
<li><p>will continue the list</p>
<ul>
<li>and nest</li>
<li>other lists.</li>
</ul></li>
</ul></li>
<li><p><em>Indenting</em> means one tab, or four spaces.</p></li>
</ol>
<p>After using markdown for a bit, go read <a href="http://pandoc.org/README.html">pandoc’s documentation</a>.</p>
</section><section id="math" class="slide level2">
<h2>Math</h2>
<pre><code>Math goes between `$`, single ($\pi$), or double:
$$ \frac{\pi}{4} = \sum_{n=0}^\infty \frac{(-1)^n}{2k+1} .$$</code></pre>
<p>Math goes between <code>$</code>, single (<span class="math inline">\(\pi\)</span>), or double: <span class="math display">\[\frac{\pi}{4} = \sum_{n=0}^\infty \frac{(-1)^n}{2k+1} .\]</span></p>
</section><section class="slide level2">
<p>Even math environments <em>inside</em> double dollar signs:</p>
<div class="sourceCode" id="cb4"><pre class="sourceCode md"><code class="sourceCode markdown"><a class="sourceLine" id="cb4-1" title="1">$$</a>
<a class="sourceLine" id="cb4-2" title="2">\begin{align}</a>
<a class="sourceLine" id="cb4-3" title="3"><span class="bn"> x &= (a+b)^2 - (a-b)^2 \\</span></a>
<a class="sourceLine" id="cb4-4" title="4"><span class="bn"> &= 4ab</span></a>
<a class="sourceLine" id="cb4-5" title="5">\end{align}</a>
<a class="sourceLine" id="cb4-6" title="6">$$</a></code></pre></div>
<p><span class="math display">\[\begin{align}
x &= (a+b)^2 - (a-b)^2 \\
&= 4ab
\end{align}\]</span></p>
</section><section id="code-blocks" class="slide level2">
<h2>Code blocks</h2>
<pre><code>```{.r}
msg <- "Hello, world."
print(msg)
```</code></pre>
<p><strong>produces</strong></p>
<div class="sourceCode" id="cb6"><pre class="sourceCode R"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" title="1">msg <-<span class="st"> "Hello, world."</span></a>
<a class="sourceLine" id="cb6-2" title="2"><span class="kw">print</span>(msg)</a></code></pre></div>
</section><section id="blockquotes" class="slide level2">
<h2>Blockquotes</h2>
<pre><code>> I also dream about a modern replacement for LaTeX
> designed from the ground up to target multiple output formats
> (at least PDF, HTML, EPUB). -- [John MacFarlane](http://john.macfarlane.usesthis.com/)</code></pre>
<p><strong>produces</strong></p>
<blockquote>
<p>I also dream about a modern replacement for LaTeX designed from the ground up to target multiple output formats (at least PDF, HTML, EPUB). – <a href="http://john.macfarlane.usesthis.com/">John MacFarlane</a></p>
</blockquote>
</section><section id="links-and-images" class="slide level2">
<h2>Links and Images</h2>
<p><a href="http://www.w3.org/">Links</a> just go in parentheses, and can be <a href="#/links-and-images">internal</a>.</p>
<div class="sourceCode" id="cb8"><pre class="sourceCode markdown"><code class="sourceCode markdown"><a class="sourceLine" id="cb8-1" title="1"><span class="ot">[Links](http://www.w3.org/)</span> just go in parentheses, </a>
<a class="sourceLine" id="cb8-2" title="2">and can be <span class="ot">[internal](#links-and-images)</span>.</a></code></pre></div>
</section><section class="slide level2">
<p>Images are <strong>the same</strong> but with a <code>!</code> in front.<br />
Setting width and height are optional.</p>
<div class="sourceCode" id="cb9"><pre class="sourceCode markdown"><code class="sourceCode markdown"><a class="sourceLine" id="cb9-1" title="1"><span class="al"></span>{width=300px height=300px}</a></code></pre></div>
<figure>
<img data-src="cat-pandoc.jpg" alt="oh, internet" width="300" height="300" /><figcaption>oh, internet</figcaption>
</figure>
</section></section>
<section><section id="rendering-markdown-with-pandoc" class="title-slide slide level1"><h1>Rendering markdown with <a href="http://pandoc.org">pandoc</a></h1></section><section id="get-started" class="slide level2">
<h2>Get started!</h2>
<p>Directions / in Rstudio.</p>
<ol start="0" type="1">
<li>Make a directory for this workshop<br />
/ start a new project.</li>
<li>Open a text editor<br />
/ open a new Rmarkdown file and delete everything.</li>
<li>Write some text.</li>
<li>Save it as <code>notes.Rmd</code>.</li>
</ol>
</section><section class="slide level2">
<p>To compile, either:</p>
<ul>
<li><p>Open <code>R</code>, run</p>
<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" title="1"><span class="kw">library</span>(knitr)</a>
<a class="sourceLine" id="cb10-2" title="2"><span class="kw">knit2html</span>(<span class="st">"notes.Rmd"</span>)</a></code></pre></div>
<p>and open <code>notes.html</code> in your web browser.</p></li>
<li><p><strong>or</strong> in <code>Rstudio</code>, save the file (with suffix <code>.Rmd</code>) and click on <em>knit</em>.</p></li>
</ul>
<p><em>Where is it?</em> Use <code>getwd()</code> to tell you.</p>
</section><section id="wait-but-the-layout" class="slide level2">
<h2>Wait, but the layout?</h2>
<p>Remember,</p>
<blockquote>
<p>[…] it is better to leave document design to document designers, and to let authors get on with writing documents.</p>
</blockquote>
<div class="fragment">
<p>If you <strong>must</strong>, then:</p>
<ul>
<li>tweak the css</li>
<li>modify a <a href="http://rmarkdown.rstudio.com/developer_custom_formats.html">rmarkdown format</a></li>
<li>or a <a href="http://pandoc.org/README.html#templates">pandoc template</a></li>
</ul>
</div>
</section><section id="gotchas" class="slide level2">
<h2>Gotchas</h2>
<ol type="1">
<li>many things need to begin with an empty line</li>
<li>carriage returns don’t (usually) mean anything</li>
<li>but indentations do (<em>by at least four spaces</em>)</li>
</ol>
<div class="fragment">
<p>For more info see <a href="http://pandoc.org/README.html#the-four-space-rule">the documentation</a>.</p>
</div>
</section><section id="metadata" class="slide level2">
<h2>Metadata</h2>
<p>At the top of your document, add</p>
<div class="sourceCode" id="cb11"><pre class="sourceCode yaml"><code class="sourceCode yaml"><a class="sourceLine" id="cb11-1" title="1"><span class="ot">---</span></a>
<a class="sourceLine" id="cb11-2" title="2"><span class="fu">title:</span><span class="at"> YOUR TITLE HERE</span></a>
<a class="sourceLine" id="cb11-3" title="3"><span class="fu">author:</span><span class="at"> YOUR NAME HERE</span></a>
<a class="sourceLine" id="cb11-4" title="4"><span class="fu">date:</span><span class="at"> August 23, 2017</span></a>
<a class="sourceLine" id="cb11-5" title="5"><span class="ot">---</span></a></code></pre></div>
<p>… the <a href="http://yaml.org/">YAML</a> metadata,<br />
delimited by <strong>exactly three</strong> dashes.</p>
</section><section class="slide level2">
<p><strong>Note:</strong> Besides setting the title, you can control the <strong>output</strong> in <a href="http://tex.stackexchange.com/questions/139139/adding-headers-and-footers-using-pandoc/139205#139205">many</a> <a href="http://rmarkdown.rstudio.com/html_document_format.html#pandoc-arguments">ways</a> here.</p>
<p><em>For example</em>: add</p>
<div class="sourceCode" id="cb12"><pre class="sourceCode yaml"><code class="sourceCode yaml"><a class="sourceLine" id="cb12-1" title="1"><span class="fu">output_format :</span><span class="at"> pdf_document</span></a></code></pre></div>
<p>and render with <code>rmarkdown::render("notes.md")</code>.</p>
<div class="fragment">
<p><strong>or even:</strong></p>
<div class="sourceCode" id="cb13"><pre class="sourceCode yaml"><code class="sourceCode yaml"><a class="sourceLine" id="cb13-1" title="1"><span class="fu">output_format :</span><span class="at"> word_document</span></a></code></pre></div>
</div>
</section><section id="under-the-hood" class="slide level2">
<h2>Under the hood</h2>
<p><a href="http://pandoc.org/README.html"><code>pandoc</code></a></p>
<div class="sourceCode" id="cb14"><pre class="sourceCode sh"><code class="sourceCode bash"><a class="sourceLine" id="cb14-1" title="1"><span class="ex">pandoc</span> --help</a></code></pre></div>
<figure>
<img data-src="jgm.png" alt="jgm" width="567" height="339" /><figcaption>jgm</figcaption>
</figure>
</section></section>
<section><section id="adding-in-r" class="title-slide slide level1"><h1>Adding in R</h1></section><section class="slide level2">
<p><strong>Goal:</strong> add R code to the document, <em>along with its output</em>.</p>
<div class="fragment">
<figure>
<img data-src="knitr-screenshot.png" alt="knitr" /><figcaption>knitr</figcaption>
</figure>
</div>
</section><section id="go-ahead" class="slide level2">
<h2>Go ahead</h2>
<p>Just add a <em>chunk</em> of R code, wrapped in</p>
<pre class="Rmd"><code> ```{r}
# PUT ARBITRARY R CODE HERE
```</code></pre>
<div class="fragment">
<p><strong>Try it!</strong></p>
</div>
</section><section class="slide level2">
<pre class="Rmd"><code>Powers of two?
```{r}
2^(0:10)
```</code></pre>
<div class="fragment">
<p>Powers of two?</p>
<div class="sourceCode" id="cb17"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb17-1" title="1"><span class="dv">2</span><span class="op">^</span>(<span class="dv">0</span><span class="op">:</span><span class="dv">10</span>)</a></code></pre></div>
<pre><code>## [1] 1 2 4 8 16 32 64 128 256 512 1024</code></pre>
</div>
</section><section class="slide level2">
<pre class="Rmd"><code>How about this?
$$ \lim_{n \to \infty} 4 \sum_{k=1}^n \frac{ (-1)^n }{ 2n+1 } = \pi , $$
```{r}
cumsum( 4 * (-1)^(0:20) / (2*(0:20)+1) )
```</code></pre>
<div class="fragment">
<p>How about this? <span class="math display">\[ \lim_{n \to \infty} 4 \sum_{k=0}^n \frac{ (-1)^n }{ 2n+1 } = \pi , \]</span></p>
<div class="sourceCode" id="cb20"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb20-1" title="1"><span class="kw">cumsum</span>( <span class="dv">4</span> <span class="op">*</span><span class="st"> </span>(<span class="op">-</span><span class="dv">1</span>)<span class="op">^</span>(<span class="dv">0</span><span class="op">:</span><span class="dv">20</span>) <span class="op">/</span><span class="st"> </span>(<span class="dv">2</span><span class="op">*</span>(<span class="dv">0</span><span class="op">:</span><span class="dv">20</span>)<span class="op">+</span><span class="dv">1</span>) )</a></code></pre></div>
<pre><code>## [1] 4.000000 2.666667 3.466667 2.895238 3.339683 2.976046 3.283738 3.017072 3.252366 3.041840 3.232316 3.058403 3.218403 3.070255 3.208186 3.079153 3.200366 3.086080 3.194188 3.091624 3.189185</code></pre>
</div>
</section><section class="slide level2">
<pre class="Rmd"><code> ```{r}
plot(cumsum( 4 * (-1)^(0:20) / (2*(0:20)+1) ))
abline(h=pi, col='red')
```</code></pre>
<div class="fragment">
<div class="sourceCode" id="cb23"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb23-1" title="1"><span class="kw">plot</span>(<span class="kw">cumsum</span>( <span class="dv">4</span> <span class="op">*</span><span class="st"> </span>(<span class="op">-</span><span class="dv">1</span>)<span class="op">^</span>(<span class="dv">0</span><span class="op">:</span><span class="dv">20</span>) <span class="op">/</span><span class="st"> </span>(<span class="dv">2</span><span class="op">*</span>(<span class="dv">0</span><span class="op">:</span><span class="dv">20</span>)<span class="op">+</span><span class="dv">1</span>) ))</a>
<a class="sourceLine" id="cb23-2" title="2"><span class="kw">abline</span>(<span class="dt">h=</span>pi, <span class="dt">col=</span><span class="st">'red'</span>)</a></code></pre></div>
<figure>
<img data-src="figure/using-rmarkdown/unnamed-chunk-3-1.png" alt="plot of chunk unnamed-chunk-3" /><figcaption>plot of chunk unnamed-chunk-3</figcaption>
</figure>
</div>
</section><section id="exercise" class="slide level2">
<h2>Exercise</h2>
<p>Make a short Rmarkdown document that</p>
<ul>
<li><p>checks that <span class="math display">\[1 + 2 + \cdots + n = n(n+1)/2\]</span> for every <span class="math inline">\(n\)</span> between 1 and 100</p></li>
<li><p>shows these on a plot</p></li>
<li><p>explains what’s being computed</p></li>
</ul>
<p><em>Useful:</em> <code>x = cumsum(1:100)</code> and <code>plot(x)</code> and <code>lines(y)</code>.</p>
</section><section id="whats-going-on" class="slide level2">
<h2>What’s going on</h2>
<ol type="1">
<li><p><code>knitr</code> uses a <em>regular expression</em> to find code chunks</p>
<ul>
<li>pulls these out,</li>
<li>evaluates them one at a time</li>
<li>and inserts “the results” back in</li>
</ul></li>
<li><p><code>pandoc</code> renders the resulting markdown file</p>
<ul>
<li>with various choices of styling</li>
</ul></li>
</ol>
</section><section id="chunk-options" class="slide level2">
<h2>Chunk options</h2>
<p>Name each chunk, and set <a href="http://yihui.name/knitr/options/">options</a> for <a href="http://yihui.name/knitr/demo/output/">what gets printed</a></p>
<pre class="Rmd"><code> ```{r my_chunk_name, fig.height=4, echo=FALSE}</code></pre>
<dl>
<dt><code>echo=(TRUE|FALSE)</code></dt>
<dd><p>include source code in the output?</p>
</dd>
<dt><code>results="(markup|asis)"</code></dt>
<dd><p>style the output or not?</p>
</dd>
<dt><code>include=(FALSE|TRUE)</code></dt>
<dd><p>include anything in the output?</p>
</dd>
</dl>
</section><section class="slide level2">
<p>Set document defaults up top:</p>
<pre class="Rmd"><code> ```{r, include=FALSE}
fig.dim <- 5
library(knitr)
opts_chunk$set(
fig.height=fig.dim,
fig.width=2*fig.dim,
fig.align='center'
)
```</code></pre>
</section><section id="tables" class="slide level2">
<h2>Tables</h2>
<p>One option: use <code>pander</code>.</p>
<pre class="Rmd"><code> ```{r}
library(pander)
bases <- table( sample( c("A","C","G","T"), 300, replace=TRUE ) )
pander(t(bases))
```</code></pre>
<p><em>note:</em> the transpose <code>t( )</code></p>
<div class="sourceCode" id="cb27"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb27-1" title="1"> <span class="kw">library</span>(pander)</a>
<a class="sourceLine" id="cb27-2" title="2"> bases <-<span class="st"> </span><span class="kw">table</span>( <span class="kw">sample</span>( <span class="kw">c</span>(<span class="st">"A"</span>,<span class="st">"C"</span>,<span class="st">"G"</span>,<span class="st">"T"</span>), <span class="dv">300</span>, <span class="dt">replace=</span><span class="ot">TRUE</span> ) )</a>
<a class="sourceLine" id="cb27-3" title="3"> <span class="kw">pander</span>(<span class="kw">t</span>(bases))</a></code></pre></div>
<table style="width:28%;">
<colgroup>
<col style="width: 6%" />
<col style="width: 6%" />
<col style="width: 6%" />
<col style="width: 6%" />
</colgroup>
<thead>
<tr class="header">
<th style="text-align: center;">A</th>
<th style="text-align: center;">C</th>
<th style="text-align: center;">G</th>
<th style="text-align: center;">T</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td style="text-align: center;">70</td>
<td style="text-align: center;">85</td>
<td style="text-align: center;">83</td>
<td style="text-align: center;">62</td>
</tr>
</tbody>
</table>
</section><section id="inline-code" class="slide level2">
<h2>Inline code</h2>
<pre class="Rmd"><code>You can
`r paste(letters[c(9,14,19,5,18,20)],collapse='')`
code anywhere.</code></pre>
<p>You can insert code anywhere.</p>
</section><section class="slide level2">
<p>Even in the YAML header.</p>
<p>Go change yours!</p>
<pre><code>---
title: "My notes"
author: "Peter Ralph"
date: "`r date()`"
---</code></pre>
</section></section>
<section><section id="online-example" class="title-slide slide level1"><h1>Online example</h1></section><section class="slide level2">
<p><strong>Goal:</strong> Write a function that will generate all sequences of <code>A</code>/<code>C</code>/<code>G</code>/<code>T</code> of length <span class="math inline">\(n\)</span> for which no two adjacent letters are the same.</p>
<div class="fragment">
<p>Here is a <a href="examples/sequences.html">pre-written solution</a>.</p>
</div>
</section><section id="your-turn" class="slide level2">
<h2>Your turn</h2>
<p>Download the <a href="https://raw.githubusercontent.com/petrelharp/r-markdown-tutorial/master/examples/iris.tsv">iris dataset</a> to a new directory.</p>
<p>or just do</p>
<div class="sourceCode" id="cb30"><pre class="sourceCode R"><code class="sourceCode r"><a class="sourceLine" id="cb30-1" title="1"><span class="kw">data</span>(iris)</a>
<a class="sourceLine" id="cb30-2" title="2"><span class="kw">dir.create</span>(<span class="st">"examples"</span>)</a>
<a class="sourceLine" id="cb30-3" title="3"><span class="kw">write.table</span>(iris,<span class="dt">file=</span><span class="st">"examples/iris.tsv"</span>,<span class="dt">sep=</span><span class="st">"</span><span class="ch">\t</span><span class="st">"</span>)</a></code></pre></div>
</section><section class="slide level2">
<ol type="1">
<li><p>Read in the data.</p></li>
<li><p>Describe the dataset: number of observations, variables, etcetera.</p>
<ul>
<li>inline <code>R</code> code (<code>`r nrow(iris)`</code>)</li>
</ul></li>
<li><p>Make a table of the number of observations for each species.</p>
<ul>
<li><code>pander()</code></li>
<li>or <code>results="asis"</code> and <code>print.xtable(xtable( ),type='html')</code></li>
</ul></li>
<li><p>Plot the flower dimensions against each other,</p>
<ul>
<li>using <code>pairs()</code>, and colored by species.</li>
</ul></li>
</ol>
</section></section>
<section><section id="templated-reports" class="title-slide slide level1"><h1>Templated reports</h1></section><section class="slide level2">
<p>Set up some fake data: each has 50 observations of two quantitative variables (<code>age</code> and <code>height</code>) and a categorical variable (<code>type</code>):</p>
<div class="sourceCode" id="cb31"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb31-1" title="1"><span class="kw">dir.create</span>(<span class="st">"examples/thedata"</span>)</a>
<a class="sourceLine" id="cb31-2" title="2">owd <-<span class="st"> </span><span class="kw">setwd</span>(<span class="st">"examples/thedata"</span>)</a>
<a class="sourceLine" id="cb31-3" title="3"><span class="cf">for</span> (samp <span class="cf">in</span> LETTERS[<span class="dv">1</span><span class="op">:</span><span class="dv">8</span>]) {</a>
<a class="sourceLine" id="cb31-4" title="4"> <span class="kw">dir.create</span>(samp)</a>
<a class="sourceLine" id="cb31-5" title="5"> xy <-<span class="st"> </span><span class="kw">data.frame</span>( </a>
<a class="sourceLine" id="cb31-6" title="6"> <span class="dt">age=</span><span class="kw">exp</span>(<span class="kw">rnorm</span>(<span class="dv">50</span>)),</a>
<a class="sourceLine" id="cb31-7" title="7"> <span class="dt">type=</span><span class="kw">sample</span>(letters[<span class="dv">1</span><span class="op">:</span><span class="dv">3</span>],<span class="dv">50</span>,<span class="dt">replace=</span><span class="ot">TRUE</span>)</a>
<a class="sourceLine" id="cb31-8" title="8"> )</a>
<a class="sourceLine" id="cb31-9" title="9"> xy<span class="op">$</span>height <-<span class="st"> </span><span class="dv">5</span> <span class="op">+</span><span class="st"> </span><span class="kw">runif</span>(<span class="dv">1</span>)<span class="op">*</span>xy<span class="op">$</span>age <span class="op">+</span><span class="st"> </span><span class="dv">3</span><span class="op">*</span><span class="kw">runif</span>(<span class="dv">1</span>)<span class="op">*</span><span class="kw">as.numeric</span>(xy<span class="op">$</span>type) <span class="op">+</span><span class="st"> </span><span class="kw">rnorm</span>(<span class="dv">50</span>)</a>
<a class="sourceLine" id="cb31-10" title="10"> <span class="kw">write.table</span>(xy,<span class="dt">file=</span><span class="kw">paste0</span>(samp,<span class="st">"/data.tsv"</span>))</a>
<a class="sourceLine" id="cb31-11" title="11">}</a>
<a class="sourceLine" id="cb31-12" title="12"><span class="kw">setwd</span>(owd)</a></code></pre></div>
</section><section class="slide level2">
<p>We now have 10 datasets, each in a file like <a href="examples/thedata/A/data.tsv"><code>A/data.tsv</code></a>. Here’s what one looks like:</p>
<div class="sourceCode" id="cb32"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb32-1" title="1">xy</a></code></pre></div>
<pre><code>## age type height
## 1 1.4796488 c 9.361211
## 2 1.0046351 b 7.809438
## 3 0.8169789 c 8.509819
## 4 0.1572326 a 5.702507
## 5 0.2543326 a 6.924387
## 6 8.1443866 b 13.790307
## 7 0.8223393 a 7.054007
## 8 6.1442730 b 13.426498
## 9 3.0191242 b 9.207488
## 10 0.7728761 c 7.260055
## 11 2.7337382 a 8.775505
## 12 4.9572850 b 10.785370
## 13 1.1893305 b 7.997365
## 14 7.4601762 a 11.033910
## 15 0.2412250 b 5.188430
## 16 1.7532513 c 9.365491
## 17 0.5922570 c 7.953115
## 18 1.1926213 b 10.210615
## 19 1.0236192 b 6.526443
## 20 5.1199085 b 8.518106
## 21 0.9541798 a 5.253971
## 22 0.3123665 b 5.506721
## 23 1.0759528 a 5.045323
## 24 1.4650504 a 6.649536
## 25 1.6650421 a 7.217283
## 26 1.1198742 b 6.362583
## 27 1.2415980 b 7.193038
## 28 2.4319417 b 8.180893
## 29 0.5862522 b 6.385537
## 30 0.8680723 b 7.183052
## 31 0.6600719 b 6.006921
## 32 0.7879503 b 6.422339
## 33 2.5323571 c 9.426129
## 34 0.2440238 c 7.841699
## 35 0.7925729 a 5.619829
## 36 3.0982004 c 9.460839
## 37 1.2647280 b 6.505928
## 38 2.3627868 a 8.699527
## 39 0.4884444 a 5.547974
## 40 0.4585299 a 6.704829
## 41 0.3537712 c 7.097977
## 42 3.4127451 b 8.615107
## 43 0.7935832 a 6.186167
## 44 0.5354499 c 6.376454
## 45 1.0126319 c 6.952713
## 46 0.3659778 c 6.663840
## 47 0.9081240 c 8.437199
## 48 0.4860253 b 6.594441
## 49 0.3530557 a 7.768926
## 50 0.5318298 a 5.175261</code></pre>
</section><section class="slide level2">
<p>We would like to <em>visualize</em> each, like this:</p>
<figure>
<img data-src="figure/using-rmarkdown/plot_one_data-1.png" alt="plot of chunk plot_one_data" /><figcaption>plot of chunk plot_one_data</figcaption>
</figure>
</section><section class="slide level2">
<p><strong>The template:</strong> <code>examples/simple-template.Rmd</code></p>
<pre class="Rmd"><code> ---
title: "Visualization for `r getwd()`"
date: "`r date()`"
---
```{r setup, echo=FALSE}
input.file <- "data.tsv"
xy <- read.table(input.file)
```
The file `r normalizePath(input.file)`
has `r nrow(xy)` observations:
```{r}
plot( height ~ age, col=type, data=xy )
legend( "topleft", pch=1, col=1:nlevels(xy$type) )
```</code></pre>
<p><strong>Input:</strong> this looks for the file <code>data.tsv</code> in the current directory.</p>
</section><section class="slide level2">
<p><strong>Render it:</strong></p>
<p><em>Option 1:</em> copy the template into each of the ten directories, and render them there.</p>
<div class="fragment">
<p><em>Option 2:</em> use my <code>templater</code> package.</p>
<div class="sourceCode" id="cb35"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb35-1" title="1"><span class="kw">library</span>(devtools)</a>
<a class="sourceLine" id="cb35-2" title="2"><span class="kw">install_github</span>(<span class="st">"petrelharp/templater"</span>)</a>
<a class="sourceLine" id="cb35-3" title="3"><span class="kw">library</span>(templater)</a>
<a class="sourceLine" id="cb35-4" title="4">dir.names <-<span class="st"> </span><span class="kw">file.path</span>(<span class="st">"examples/thedata"</span>, LETTERS[<span class="dv">1</span><span class="op">:</span><span class="dv">8</span>])</a>
<a class="sourceLine" id="cb35-5" title="5"><span class="cf">for</span> (input.dir <span class="cf">in</span> dir.names) {</a>
<a class="sourceLine" id="cb35-6" title="6"> output.file <-<span class="st"> </span><span class="kw">file.path</span>(input.dir, <span class="st">"visualization.html"</span>)</a>
<a class="sourceLine" id="cb35-7" title="7"> <span class="kw">render_template</span>(<span class="st">"examples/simple-template.Rmd"</span>, <span class="dt">output=</span>output.file, </a>
<a class="sourceLine" id="cb35-8" title="8"> <span class="dt">change.rootdir=</span><span class="ot">TRUE</span>, <span class="dt">quiet=</span><span class="ot">TRUE</span>)</a>
<a class="sourceLine" id="cb35-9" title="9">}</a></code></pre></div>
</div>
</section><section class="slide level2">
<p><strong>Look at them:</strong></p>
<pre class="Rmd"><code> ```{r make_links, results="asis"}
output.files <- file.path("examples/thedata", LETTERS[1:8], "visualization.html")
links <- paste("[",dir.names,"](",output.files,")",sep='')
cat( paste("- ", links, "\n"), "\n" )
```</code></pre>
<ul>
<li><a href="examples/thedata/A/visualization.html">examples/thedata/A</a></li>
<li><a href="examples/thedata/B/visualization.html">examples/thedata/B</a></li>
<li><a href="examples/thedata/C/visualization.html">examples/thedata/C</a></li>
<li><a href="examples/thedata/D/visualization.html">examples/thedata/D</a></li>
<li><a href="examples/thedata/E/visualization.html">examples/thedata/E</a></li>
<li><a href="examples/thedata/F/visualization.html">examples/thedata/F</a></li>
<li><a href="examples/thedata/G/visualization.html">examples/thedata/G</a></li>
<li><a href="examples/thedata/H/visualization.html">examples/thedata/H</a></li>
</ul>
</section><section id="another-exercise" class="slide level2">
<h2>Another exercise</h2>
<p><strong>Goal:</strong> Compare different <span class="math inline">\(k\)</span> with <span class="math inline">\(k\)</span>-means on the <code>iris</code> dataset.</p>
<ol type="1">
<li>Make subdirectories, called <code>iris/k</code>, for <span class="math inline">\(1 \le k \le 5\)</span>,</li>
<li>and in each runs <code>kmeans</code> with the appropriate <code>k</code>.</li>
</ol>
<p>Example:</p>
<div class="sourceCode" id="cb37"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb37-1" title="1"><span class="kw">data</span>(iris)</a>
<a class="sourceLine" id="cb37-2" title="2">km <-<span class="st"> </span><span class="kw">kmeans</span>(iris[,<span class="dv">1</span><span class="op">:</span><span class="dv">4</span>], <span class="dt">centers=</span><span class="dv">3</span>)</a>
<a class="sourceLine" id="cb37-3" title="3"><span class="kw">pairs</span>(iris, <span class="dt">col=</span>km<span class="op">$</span>cluster)</a></code></pre></div>
</section></section>
<section><section id="other-resources" class="title-slide slide level1"><h1>Other resources</h1></section><section class="slide level2">
<ul>
<li><a href="http://kbroman.org/knitr_knutshell/pages/Rmarkdown.html">Karl Broman’s</a> intro to Rmarkdown</li>
<li>the extensive, excellent <a href="http://pandoc.org/README.html">documentation for pandoc</a></li>
<li><a href="http://stackoverflow.com/questions/tagged/rmarkdown">Stack</a><a href="http://stackoverflow.com/questions/tagged/knitr">Overflow</a></li>
<li>my <a href="technical-notes.html">technical notes</a> I made while writing this up</li>
</ul>
</section></section>
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