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<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8">
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<title>Software Carpentry: R for reproducible scientific analysis</title>
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<a href="http://software-carpentry.org" title="Software Carpentry">
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<div class="span10 offset1">
<h1 class="title">R for reproducible scientific analysis</h1>
<h2 class="subtitle">Wrapping up</h2>
<div id="learning-objectives" class="objectives">
<h3>Learning Objectives</h3>
<ul>
<li>To be able to bundle up a project using packrat</li>
<li>To review the best practices for using R for scientific analysis.</li>
</ul>
</div>
<h3 id="wrapping-up-a-project">Wrapping up a project</h3>
<p>To finish up, let's use <code>packrat</code> to bundle up what we've done so far so you can take it home with you.</p>
<pre class="sourceCode r"><code class="sourceCode r"><span class="kw">library</span>(packrat)
packrat::<span class="kw">bundle</span>(
<span class="dt">file=</span><span class="st">"R-intro-workshop.tar.gz"</span>,
<span class="dt">include.vcs.history=</span><span class="ot">TRUE</span>
)</code></pre>
<p>Now everything we've done, including our version history, is stored in the <code>R-intro-workshop.tar.gz</code> file. You can download this and take it with you.</p>
<div id="challenge" class="challenge">
<h4>Challenge</h4>
<p>Use <code>packrat::bundle</code> to bundle up your project into a single portable file.</p>
</div>
<h3 id="best-practices-for-writing-nice-code">Best practices for writing nice code</h3>
<h4 id="make-code-readable">Make code readable</h4>
<p>The most important part of writing code is making it readable and understandable. You want someone else to be able to pick up your code and be able to understand what it does: more often than not this someone will be you 6 months down the line, who will otherwise be cursing past-self.</p>
<h4 id="documentation-tell-us-what-and-why-not-how">Documentation: tell us what and why, not how</h4>
<p>When you first start out, your comments will often describe what a command does, since you're still learning yourself and it can help to clarify concepts and remind you later. However, these comments aren't particularly useful later on when you don't remember what problem your code is trying to solve. Try to also include comments that tell you <em>why</em> you're solving a problem, and <em>what</em> problem that is. The <em>how</em> can come after that: it's an implementation detail you ideally shouldn't have to worry about.</p>
<h4 id="keep-your-code-modular">Keep your code modular</h4>
<p>Our recommendation is that you should separate your functions from your analysis scripts, and store them in a separate file that you <code>source</code> when you open the R session in your project. This approach is nice because it leaves you with an uncluttered analysis script, and a repository of useful functions that can be loaded into any analysis script in your project. It also lets you group related functions together easily.</p>
<h4 id="break-down-problem-into-bite-size-pieces">Break down problem into bite size pieces</h4>
<p>When you first start out, problem solving and function writing can be daunting tasks, and hard to separate from code inexperience. Try to break down your problem into digestable chunks and worry about the implementation details later: keep breaking down the problem into smaller and smaller functions until you reach a point where you can code a solution, and build back up from there.</p>
<h4 id="know-that-your-code-is-doing-the-right-thing">Know that your code is doing the right thing</h4>
<p>Make sure to test your functions!</p>
<h4 id="dont-repeat-yourself">Don't repeat yourself</h4>
<p>Functions enable easy reuse within a project. If you see blocks of similar lines of code through your project, those are usually candidates for being moved into functions.</p>
<p>If your calculations are performed through a series of functions, then the project becomes more modular and easier to change. This is especially the case for which a particular input always gives a particular output.</p>
<h4 id="remember-to-be-stylish">Remember to be stylish</h4>
<p>Apply consistent style to your code.</p>
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