CABW2018_R_training/setup.html at master · SCCWRP/CABW2018_R_training · GitHub

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<div id="set-up" class="section level1">
<h1>Set Up</h1>
<p>Thanks for your interest in learning R. For the workshop, we will be using <a href="https://www.rstudio.com/">RStudio</a> as our interface to R. In order to participate in this workshop you will need to make sure you have R and RStudio installed on your laptop.</p>
<p>Thanks to the <a href="https://owi.usgs.gov/R/training.html">USGS-R Training group</a> and <a href="https://datacarpentry.org/R-ecology-lesson/index.html">Data Carpentry</a> for making their installation materials available. The following instructions come directly from their materials, with a few minor edits to help you get all set up for the workshop.</p>
</div>
<div id="install-r-and-rstudio" class="section level1">
<h1>Install R and RStudio</h1>
<p><strong>R</strong> and <strong>RStudio</strong> are separate downloads and installations. R is the underlying statistical computing environment, but using R alone is no fun. RStudio is a graphical integrated development environment (IDE) that makes using R much easier and more interactive. <em>You need to install R before you install RStudio</em>.</p>
<div id="windows-download-and-install-r" class="section level2">
<h2><em>Windows</em>: Download and install R</h2>
<p>Go to <a href="https://cran.rstudio.com/bin/windows/base/">CRAN and download</a> the R installer for Windows. Make sure to choose the latest stable version (v3.5.1 as of Sept 2018).</p>
<p>Once the installer downloads, Right-click on it and select “Run as administrator”.</p>
<p>Type in your credentials and click yes (or if you don’t have administrator access have your IT rep install with Admin privileges).</p>
<p><img src="figure/install_open_as_admin.png#inline-img" title="run as admin" /></p>
<p>You can click next through the standard dialogs and accept most defaults. But at the destination screen, please verify that it is installing it to C:Files(version number may vary)</p>
<p><img src="figure/install_destination.png#inline-img" title="install destination screen" /></p>
<p>At the “Select Components” screen, you can accept the default and install both 32-bit and 64-bit versions.</p>
<p><img src="figure/install_arch_window.png#inline-img" title="select architecture" /></p>
<p>At this screen, uncheck ‘Create a desktop icon’ because non-admin users in Windows will be unable to delete it.</p>
<p><img src="figure/install_tasks.png#inline-img" title="uncheck desktop icon" /></p>
</div>
<div id="windows-download-and-install-rstudio" class="section level2">
<h2><em>Windows</em>: Download and install RStudio</h2>
<p><a href="https://www.rstudio.com/products/rstudio/download/"></a></p>
<p>Double-click the installer. It will ask for your administrator credentials to install (you might need to have your IT rep install again).</p>
<p>Accept all the default options for the RStudio install.</p>
<p><img src="figure/install_rstudio.png#inline-img" title="RStudio install screen" /></p>
</div>
<div id="macos-download-and-install-r" class="section level2">
<h2><em>macOS</em>: Download and install R</h2>
<ul>
<li>Download and install R from the CRAN website for Mac <a href="https://cran.r-project.org/bin/macosx/">here</a>.</li>
<li>Select the <code>.pkg</code> file for the latest R version</li>
<li>Double click on the downloaded file to install R</li>
<li>It is also a good idea to install <a href="https://www.xquartz.org/">XQuartz</a> (needed by some packages)</li>
</ul>
</div>
<div id="macos-download-and-install-rstudio" class="section level2">
<h2><em>macOS</em>: Download and install RStudio</h2>
<ul>
<li>Go to the <a href="https://www.rstudio.com/products/rstudio/download/#download">RStudio</a> download page</li>
<li>Under Installers select <strong>RStudio x.yy.zzz - Mac OS X 10.6+ (64-bit)</strong> (where x, y, and z represent version numbers)</li>
<li>Double click the file to install RStudio</li>
<li>Once it’s installed, open RStudio to make sure it works and you don’t get any error messages.</li>
</ul>
</div>
</div>
<div id="check-install" class="section level1">
<h1>Check Install</h1>
<div id="open-rstudio" class="section level2">
<h2>Open RStudio</h2>
<p>Once installed, RStudio should be accessible from the start menu. Start up RStudio. Once running it should look something like:</p>
<p><img src="figure/rstudio.png#inline-img" title="RStudio window" /></p>
</div>
<div id="find-console-window" class="section level2">
<h2>Find “Console” window</h2>
<p>By default the console window will be on the left side of RStudio. Find that window. It will looking something like:</p>
<p><img src="figure/rstudio_console.png#inline-img" title="RStudio console" /></p>
</div>
<div id="copy-and-paste-the-code" class="section level2">
<h2>Copy and paste the code</h2>
<p>Click in the window and paste in the code from below:</p>
<pre class="r"><code>version$version.string</code></pre>
</div>
<div id="verify-your-installed-r-version" class="section level2">
<h2>Verify your installed R version</h2>
<p>Ideally you should be running the latest stable release (<code>v3.5.1</code> as of Sept 2018). If you have an older version, please install the newest version using the instructions above.</p>
<p>Here is what my R version looks like.</p>
<pre><code>## [1] &quot;R version 3.5.1 (2018-07-02)&quot;</code></pre>
</div>
</div>
<div id="add-packages" class="section level1">
<h1>Add Packages</h1>
<p>Install packages available for all R users from <a href="https://cran.r-project.org/">CRAN</a> by pasting the following code and hitting <code>ENTER</code>.</p>
<pre class="r"><code>install.packages(&quot;tidyverse&quot;)
install.packages(&quot;sf&quot;)
install.packages(&quot;mapview&quot;)
install.packages(&quot;viridis&quot;)
install.packages(&quot;USAboundaries&quot;)</code></pre>
<p>If you see</p>
<p><img src="figure/personal_library_dialog.png#inline-img" title="dialog box behind" /></p>
<p>That’s OK! There’s a dialog box hiding behind RStudio asking if you want to create a personal folder in your Documents folder. Click <em>Yes</em>. It will look something like this when done:</p>
<p><img src="figure/general_pkg_output.png#inline-img" title="console output" /></p>
</div>
<div id="grab-the-sample-datasets" class="section level1">
<h1>Grab the Sample Datasets</h1>
<p>We’ll be working with some California bioassessment data for this workshop. The bioassessment data are available as three separate csv files that describe scores for the California Stream Condition Index (CSCI), the Algal Stream Condition Index (ASCI), and a separate file for station locations. These files include scores at over 2000 locations and are a portion of the data used to develop the indices.</p>
<ul>
<li><code>ascidat.csv</code>: ASCI index data</li>
<li><code>cscidat.csv</code>: CSCI index data</li>
<li><code>latlon.csv</code>: Station location data</li>
</ul>
<p>Download the zipped file of all the data from this <a href="https://SCCWRP.github.io/CABW2018_R_training/data/datazip.zip">link</a>. Unzip the content into a folder on your computer that you can access for the workshop.</p>
<div id="exercise-1" class="section level2">
<h2>Exercise 1</h2>
<p>Just to make sure everything is working do the following:</p>
<ol style="list-style-type: decimal">
<li>Open up RStudio.</li>
<li>Find the “Console.” This is usually the left part RStudio.</li>
<li>In the “Console”, find the R Prompt.</li>
<li>Type in (copy and paste from here will also work) the following commands at the R Prompt and hit return.</li>
</ol>
<pre class="r"><code>c(&quot;tidyverse&quot;, &quot;sf&quot;, &quot;viridis&quot;, &quot;mapview&quot;, &quot;USAboundaries&quot;) %in% installed.packages()</code></pre>
<p>The end result should look something like:</p>
<p><img src="figure/install_success.jpg" /></p>
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