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<h1 class="title toc-ignore">Installing software</h1>

</div>


<div id="background" class="section level2">
<h2>Background</h2>
<p>This course will cover basics of reproducible research using R. We
will also make use of the R Studio IDE, git, GitHub, and Docker. The
code used in the course will also rely on several R packages.</p>
<p>Prior to the start of the course, we ask that you do your best to
have:</p>
<ul>
<li>working version of R Studio installed</li>
<li>working version of R &gt;4.0 installed (version is suggested, but
not required)</li>
<li>R packages listed below installed</li>
<li>git installed and configured</li>
<li>a registered GitHub account</li>
<li>docker installed</li>
<li>a registered DockerHub account</li>
</ul>
<p>This page contains some instructions that may be helpful on
installing the required software and packages. The videos below were
created for the DATA 550 course at Emory University RSPH and are
reproduced here out of context of that course. Thus, there may be some
irrelevant or nonsensical commentary related to other contents of that
course. Nevertheless, we hope that these videos are useful for you in
preparing for the short course.</p>
</div>
<div id="installing-r-r-studio-and-git" class="section level2">
<h2>Installing R, R Studio, and git</h2>
<p>The videos below will walk you through installation of R and R
Studio. If you already have a working version of R Studio, you can
ignore these parts of the videos. However, do be sure to also install
git.</p>
<p>There is no need to make sure your version of R matches what is
installed in the videos. In general, any version of R after R 4.0 should
be sufficient. If you are working in R version 3.X, then some of the
code may not run for you (and it may be time to make the jump to version
4 anyway…).</p>
<div id="mac-instructions" class="section level3">
<h3>Mac instructions</h3>
<p>The following instructions pertain to installing software on a Mac.
You can skip this section if you are a Windows user.</p>
<div id="installing-r-and-r-studio" class="section level4">
<h4>Installing R and R Studio</h4>
<p>In this video, we describe:</p>
<ul>
<li>how to install R and R Studio on a Mac</li>
<li>how to check which version of R should be installed based on the
chip in your Mac</li>
</ul>
<p>You will see that the videos are slightly dated. For example, Mac has
now released an M2 + M3 chips (not just Intel + M1 chips as described in
the video). Just be sure to select the right version of R to install
based on the chip in your computer.</p>
<div style="padding:5px 0px 20px 0px;">
<iframe width="560px" height="320px" allowfullscreen="true" allow="autoplay *" title="mac_install_r_rstudio" src="https://emory.instructuremedia.com/embed/69db8e47-36c4-448c-9e16-1a687fd5ddc4" frameborder="0" data-external="1">
</iframe>
</div>
</div>
<div id="installing-git" class="section level4">
<h4>Installing git</h4>
<p>In this video, we describe:</p>
<ul>
<li>how to install <code>homebrew</code> on a Mac</li>
<li>how to install <code>git</code> via <code>homebrew</code> on a
Mac</li>
</ul>
<div style="padding:5px 0px 20px 0px;">
<iframe width="560px" height="320px" allowfullscreen="true" allow="autoplay *" title="mac_install_homebrew_git" src="https://emory.instructuremedia.com/embed/7b4b98eb-9bfa-4b1c-9e59-2a857cead105" frameborder="0" data-external="1">
</iframe>
</div>
</div>
<div id="configuring-git" class="section level4">
<h4>Configuring git</h4>
<p>In this video, we describe:</p>
<ul>
<li>how to configure basic settings in <code>git</code></li>
</ul>
<div style="padding:5px 0px 20px 0px;">
<iframe width="560px" height="320px" allowfullscreen="true" allow="autoplay *" title="mac_configure_git" src="https://emory.instructuremedia.com/embed/0497ac78-a886-4211-b6d0-e0a7eb2fe03a" frameborder="0" data-external="1">
</iframe>
</div>
</div>
<div id="installing-bash" class="section level4">
<h4>Installing bash</h4>
<p>In this video, we describe:</p>
<ul>
<li>how to install the most recent version of <code>bash</code> via
homebrew</li>
<li>how to set your Terminal to use <code>bash</code> instead of
<code>zsh</code> (the default in recent Mac OS’s)</li>
</ul>
<p>This video is not strictly necessary. <code>zsh</code> and
<code>bash</code> share many elements of syntax and more than likely you
will be able to follow all materials in this course without using
<code>bash</code>. I will also note that different Mac OS’s and
different user set ups on Macs lead to different behavior of the default
shell in Terminal so I cannot guarantee that these instructions will
work for everyone. If you are determined to install <code>bash</code>,
but are having difficult, you should be able to google alternative
instructions.</p>
<div style="padding:5px 0px 20px 0px;">
<iframe width="560px" height="320px" allowfullscreen="true" allow="autoplay *" title="mac_install_bash" src="https://emory.instructuremedia.com/embed/1b67e47d-b7d8-4cde-a474-a948e363d8c4" frameborder="0" data-external="1">
</iframe>
</div>
</div>
<div id="more-about-homebrew" class="section level4">
<h4>More about homebrew</h4>
<p>In this video, we describe:</p>
<ul>
<li>what <code>homebrew</code> is in greater detail</li>
<li>where <code>homebrew</code> stores files on your Mac</li>
</ul>
<p>This video is not strictly necessary to watch. Only needed if you are
curious to learn more about homebrew and how it works.</p>
<div style="padding:5px 0px 20px 0px;">
<iframe width="560px" height="320px" allowfullscreen="true" allow="autoplay *" title="mac_more_on_homebrew" src="https://emory.instructuremedia.com/embed/7fa68cb6-bd4d-4ab4-8cc2-3c1f31701495" frameborder="0" data-external="1">
</iframe>
</div>
</div>
</div>
<div id="windows-instructions" class="section level3">
<h3>Windows instructions</h3>
<p>The following instructions pertain to installing software on Windows.
You can skip this section if you are a Mac or Linux user.</p>
<div id="installing-r-r-studio-and-git-1" class="section level4">
<h4>Installing R, R studio, and git</h4>
<p>In this video, we describe:</p>
<ul>
<li>how to install R, R studio and git on a Windows machine</li>
<li>what to select for the various options available during
<code>git</code> installation</li>
</ul>
<div style="padding:5px 0px 20px 0px;">
<iframe width="560px" height="320px" allowfullscreen="true" allow="autoplay *" title="windows_install_R_Rstudio_git" src="https://emory.instructuremedia.com/embed/8e92e09b-2777-4c08-a4a4-964ea984413a" frameborder="0" data-external="1">
</iframe>
</div>
</div>
<div id="configuring-git-bash-with-r-studio" class="section level4">
<h4>Configuring git bash with R Studio</h4>
<p>In this video, we describe:</p>
<ul>
<li>how to configure R Studio to use <code>git bash</code> in the
Terminal console</li>
</ul>
<p><strong>This video is important for following along with the command
line lecture!</strong></p>
<div style="padding:5px 0px 20px 0px;">
<iframe width="560px" height="320px" allowfullscreen="true" allow="autoplay *" title="windows_rstudio_configure_gitbash" src="https://emory.instructuremedia.com/embed/141a7cf0-010d-4f31-a2c7-56ffe7934d95" frameborder="0" data-external="1">
</iframe>
</div>
</div>
</div>
</div>
<div id="register-for-a-github-account" class="section level2">
<h2>Register for a GitHub account</h2>
<p>In the course, we will make use of GitHub to practice collaborating
on code. If you do not have a GitHub account, please <a
href="https://github.com/">sign up for one</a>. The service is free and
should only require a couple minutes to complete sign up.</p>
</div>
<div id="r-packages" class="section level2">
<h2>R packages</h2>
<p>Several R packages are used in this course and ideally should be
installed prior to the start of the class. The following code chunk can
be used to install the necessary packages.</p>
<pre class="r"><code>install.packages(c(
  &quot;tidyverse&quot;, &quot;devtools&quot;, &quot;gtsummary&quot;, &quot;here&quot;, &quot;RSocrata&quot;, &quot;forcats&quot;
))</code></pre>
<p>If you have any difficulties installing these packages, please reach
out to us via Slack.</p>
</div>
<div id="installing-docker" class="section level2">
<h2>Installing Docker</h2>
<p>Docker can be challenging to install depending on how your computer
is configured. Please read through <a
href="https://docs.docker.com/engine/install/">the installation
instructions</a> and attempt to install Docker prior to the start of the
class. If you run into difficulties, please reach out to us on Slack. We
will also be available during breaks on the first two days of the class
to help trouble shoot.</p>
</div>
<div id="dockerhub-account" class="section level2">
<h2>Dockerhub account</h2>
<p>In this course, we will make use of Docker Hub repositories, which
are free to access but require an account. Please <a
href="https://hub.docker.com/">register for an account</a> prior to the
start of the course.</p>
</div>


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