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<title>1 Setup | R Crash Course for Biologists</title>
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<meta name="author" content="Robert I. Colautti" />
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<li><a href="./">@ColauttiLab</a></li>
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<li><a href="preface.html#preface" id="toc-preface">Preface<span></span></a>
<ul>
<li><a href="preface.html#advice" id="toc-advice"><span class="toc-section-number">0.1</span> Advice<span></span></a></li>
<li><a href="preface.html#learn-by-doing" id="toc-learn-by-doing"><span class="toc-section-number">0.2</span> Learn By Doing!<span></span></a></li>
<li><a href="preface.html#what-to-expect" id="toc-what-to-expect"><span class="toc-section-number">0.3</span> What to Expect<span></span></a></li>
<li><a href="preface.html#translational-coding" id="toc-translational-coding"><span class="toc-section-number">0.4</span> Translational Coding<span></span></a></li>
</ul></li>
<li><a href="setup.html#setup" id="toc-setup"><span class="toc-section-number">1</span> Setup<span></span></a>
<ul>
<li><a href="setup.html#r" id="toc-r"><span class="toc-section-number">1.1</span> R<span></span></a></li>
<li><a href="setup.html#r-studio" id="toc-r-studio"><span class="toc-section-number">1.2</span> R Studio<span></span></a></li>
<li><a href="setup.html#console" id="toc-console"><span class="toc-section-number">1.3</span> Console<span></span></a>
<ul>
<li><a href="setup.html#r-script" id="toc-r-script"><span class="toc-section-number">1.3.1</span> R Script<span></span></a></li>
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<li><a href="setup.html#packages" id="toc-packages"><span class="toc-section-number">1.4</span> Packages<span></span></a></li>
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<li><a href="https://ecoevogeno.org/" target="blank">EcoEvoGeno.org</a></li>
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<h1>
<i class="fa fa-circle-o-notch fa-spin"></i><a href="./">R Crash Course <br> for Biologists</a>
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<section class="normal" id="section-">
<div id="setup" class="section level1 hasAnchor" number="1">
<h1><span class="header-section-number">1</span> Setup<a href="setup.html#setup" class="anchor-section" aria-label="Anchor link to header"></a></h1>
<div id="r" class="section level2 hasAnchor" number="1.1">
<h2><span class="header-section-number">1.1</span> R<a href="setup.html#r" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<p>Before you begin these tutorials, you should install the latest version of R:
<a href="https://cran.r-project.org/" class="uri">https://cran.r-project.org/</a></p>
<p>Versions are available for Windows, MacOS and Linux operating systems. Immediately we can see one of the advantages of learning to code in R – we can move code across computing platforms quite easily, as long as R is installed there.</p>
</div>
<div id="r-studio" class="section level2 hasAnchor" number="1.2">
<h2><span class="header-section-number">1.2</span> R Studio<a href="setup.html#r-studio" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<p>You should also install R Studio:
<a href="https://rstudio.com/products/rstudio/download/#download" class="uri">https://rstudio.com/products/rstudio/download/#download</a></p>
<p>R Studio is an **Integrated Development Environment (IDE). Once you install and open R Studio, run the program for the first time.</p>
<p>You will see several helpful <em>tabs</em> – small windows. Several windows have more than one tab at the top, which you can click on to access. Here is a quick overview of the more useful ones (some of this will make more sense after you work through the first few chapters of the tutorial):</p>
<ul>
<li><strong>Environment</strong> keeps track of all of the objects in your programming environment. If this doesn’t make sense now, it will later.</li>
<li><strong>History</strong> keeps track of the code you have run.</li>
<li><strong>Files</strong> similar to the Finder (MacOS) or File Explorer (Windows), starting with the <em>working directory</em>.</li>
<li><strong>Plots</strong> are where your plots are created</li>
<li><strong>Packages</strong> show which packages you have installed, and which have been loaded.</li>
<li><strong>Help</strong> provides documentation for R functions</li>
<li><strong>Console</strong>…</li>
</ul>
</div>
<div id="console" class="section level2 hasAnchor" number="1.3">
<h2><span class="header-section-number">1.3</span> Console<a href="setup.html#console" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<p>One of the most important tabs is the console. It’s usually the main tab that opens on the left when you first start R Studio. You’ll see a little chevron <strong><code>></code></strong> with a cursor after it. That’s the R Console and it’s the part that actually runs the R program.</p>
<div id="r-script" class="section level3 hasAnchor" number="1.3.1">
<h3><span class="header-section-number">1.3.1</span> R Script<a href="setup.html#r-script" class="anchor-section" aria-label="Anchor link to header"></a></h3>
<p>To run an R script, you can just type functions into the console. However, it is very hard to keep track of everything you do if you only use the console. In R Studio you can click <strong><code>File-->New File-->R Script</code></strong>. This will open a new tab window called <strong>Untitled</strong>. This is called a <strong>script</strong>, but it’s really just a text file, with a <strong>.R</strong> suffix, that you can use to keep track of your R program. Try typing something into your R script – don’t worry for now if it is just some random text. Note that you can <strong>Save</strong> this file.</p>
<p>Nothing happens (yet). To run the script, you have to send the text from the script tab to the console tab. There are a few ways you could do this:</p>
<ol style="list-style-type: decimal">
<li>Copy and paste manually. This works fine, but there are more effeicient options</li>
<li>Highlight the code you want to run and click the <strong>Run</strong> button on the top-right corner of the script tab. The run button sends the highlighted text from the script to the console.</li>
<li>If you click the <strong>Run</strong> button without highlighting text, it will send whatever text is on the same <em>line</em> as your cursor</li>
<li>If you press <strong>Ctl + Enter</strong> (Windows) or <strong>Cmd + Return</strong> (Mac) it will do the same thing – this is the shortcut for the <strong>Run</strong> button</li>
<li>There are other options if you press the tiny triangle next to the <strong>Run</strong> button, including <strong>Run All</strong>. This is the equivalent of running one line at a time.</li>
<li><strong>Ctl/Cmd + Shift + Enter/Return</strong> is a shortcut for <strong>Run All</strong></li>
</ol>
</div>
</div>
<div id="packages" class="section level2 hasAnchor" number="1.4">
<h2><span class="header-section-number">1.4</span> Packages<a href="setup.html#packages" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<p>Packages in R contain functions – small programs that you can run. One really good package is called <code>tidyverse</code>. The <code>tidyverse</code> package contains a lot of useful functions for working with different types of data, including visualizations. You’ll need to make sure you are connected to the internet and that your connection to the internet won’t be interrupted during the download.</p>
<blockquote>
<p>WARNING! This may take a long time to run</p>
</blockquote>
<p>To install the packages, open R Studio and look for the <strong>Console</strong> tab. Type this into your console:</p>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb1-1"><a href="setup.html#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="fu">install.packages</span>(<span class="st">"tidyverse"</span>)</span></code></pre></div>
<p>Next, install `devtools:</p>
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb2-1"><a href="setup.html#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="fu">install.packages</span>(<span class="st">"devtools"</span>)</span></code></pre></div>
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