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<a href="01-intro-to-r.html">Introduction to R programming</a>
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<div id="header">
<h1 class="title toc-ignore">Introduction to R for Biologists</h1>
<h4 class="author">Author: Alexia Cardona</h4>
</div>
<p>Bioinformatics Training Facility<br />
University of Cambridge</p>
<p></br></p>
<div id="description" class="section level3">
<h3>Description</h3>
<p><strong>R</strong> is one of the leading programming languages in
<strong>Data Science</strong>. It is widely used to perform statistics,
machine learning, visualisations and data analyses. It is an open source
programming language so <strong>all the software we will use in the
course is free</strong>. This course is an introduction to R
<strong>designed for participants with no programming
experience</strong>. We will start from scratch by introducing how to
start programming in R and progress our way and learn how to read and
write to files, manipulate data and visualise it by creating different
plots - all the fundamental tasks you need to get you started analysing
your data. We will be working in <strong>RStudio</strong> which is a
software used to help you develop R code. During the course we will be
working with one of the most popular packages in R;
<strong>tidyverse</strong>, the umbrella package for
<strong>dplyr</strong> and <strong>ggplot2</strong> packages that will
allow you to manipulate your data effectively and visualise it to a
publication level standard.</p>
<p><br/></p>
</div>
<div id="target-audience" class="section level3">
<h3>Target Audience</h3>
<p>This course is designed for participants with no programming
experience.</p>
<p><br/></p>
</div>
<div id="sessions" class="section level3">
<h3>Sessions</h3>
<ol style="list-style-type: decimal">
<li><a href="00-getting-started.html">Getting started</a></li>
<li><a href="01-intro-to-r.html">Introduction to R programming</a></li>
<li><a href="02-starting-with-data.html">Starting with data</a></li>
<li><a href="03-tidyverse.html">Data manipulation and visualisation in
tidyverse</a></li>
</ol>
<p><br/></p>
</div>
<div id="data" class="section level3">
<h3>Data</h3>
<p>Data is from the paper <a
href="http://esapubs.org/archive/ecol/E090/118/">S. K. Morgan Ernest,
Thomas J. Valone, and James H. Brown. 2009. Long-term monitoring and
experimental manipulation of a Chihuahuan Desert ecosystem near Portal,
Arizona, USA. Ecology 90:1708.</a></p>
<p>A simplified version of this data, suitable for teaching is available
here which is the data we will be using in this course: <a
href="https://doi.org/10.6084/m9.figshare.1314459"
class="uri">https://doi.org/10.6084/m9.figshare.1314459</a></p>
<p>However, we will download them directly from R during the lessons
when we need them.</p>
<p><br/></p>
</div>
<div id="setup-instructions" class="section level3">
<h3>Setup instructions</h3>
<p>All the software required to run this course is installed on your
machine, so you do need to do the following sections. In case you are
working on this on another machine please follow the instructions
below:</p>
<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. You need to install R before you install RStudio.
After installing both programs, you will need to install the
<strong><code>tidyverse</code></strong> package from within RStudio.
Follow the instructions below for your operating system, and then follow
the instructions to install the <strong><code>tidyverse</code></strong>
package.</p>
<div id="windows" class="section level4">
<h4>Windows</h4>
<div id="if-you-already-have-r-and-rstudio-installed"
class="section level5">
<h5>If you already have R and RStudio installed</h5>
<ul>
<li>Open RStudio, and click on “Help” > “Check for updates”. If a new
version is available, quit RStudio, and download the latest version for
RStudio.</li>
<li>To check which version of R you are using, start RStudio and the
first thing that appears in the console indicates the version of R you
are running. Alternatively, you can type <code>sessionInfo()</code>,
which will also display which version of R you are running. Go on the <a
href="https://cran.r-project.org/bin/windows/base/">CRAN website</a> and
check whether a more recent version is available. If so, please download
and install it. You can <a
href="https://cran.r-project.org/bin/windows/base/rw-FAQ.html#How-do-I-UNinstall-R_003f">check
here</a> for more information on how to remove old versions from your
system if you wish to do so.</li>
</ul>
</div>
<div id="if-you-dont-have-r-and-rstudio-installed"
class="section level5">
<h5>If you don’t have R and RStudio installed</h5>
<ul>
<li>Download R from the <a
href="http://cran.r-project.org/bin/windows/base/release.htm">CRAN
website</a>. <em>OR</em> you can do this from the Rstudio page mentioned
below.</li>
<li>Run the <code>.exe</code> file that was just downloaded</li>
<li>Go to the <a
href="https://posit.co/download/rstudio-desktop/#download">RStudio
download page</a></li>
<li>Under <em>Installers</em> select <strong>RStudio x.yy.zzz - Windows
Vista/7/8/10</strong> (where x, y, and z represent version numbers)</li>
<li>Double click the file to install it</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="macos" class="section level4">
<h4>macOS</h4>
<div id="if-you-already-have-r-and-rstudio-installed-1"
class="section level5">
<h5>If you already have R and RStudio installed</h5>
<ul>
<li>Open RStudio, and click on “Help” > “Check for updates”. If a new
version is available, quit RStudio, and download the latest version for
RStudio.</li>
<li>To check the version of R you are using, start RStudio and the first
thing that appears on the terminal indicates the version of R you are
running. Alternatively, you can type <code>sessionInfo()</code>, which
will also display which version of R you are running. Go on the <a
href="https://cran.r-project.org/bin/macosx/">CRAN website</a> and check
whether a more recent version is available. If so, please download and
install it.</li>
</ul>
</div>
<div id="if-you-dont-have-r-and-rstudio-installed-1"
class="section level5">
<h5>If you don’t have R and RStudio installed</h5>
<ul>
<li>Download R from the <a
href="http://cran.r-project.org/bin/macosx/">CRAN website</a>.
<em>OR</em> you can do this from the Rstudio page mentioned below.</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>
<li>Go to the <a
href="https://posit.co/download/rstudio-desktop/#download">RStudio
download page</a></li>
<li>Under <em>Installers</em> 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="linux" class="section level4">
<h4>Linux</h4>
<ul>
<li>Follow the instructions for your distribution from <a
href="https://cloud.r-project.org/bin/linux">CRAN</a>, they provide
information to get the most recent version of R for common
distributions. For most distributions, you could use your package
manager (e.g., for Debian/Ubuntu run
<code>sudo apt-get install r-base</code>, and for Fedora
<code>sudo yum install R</code>), but we don’t recommend this approach
as the versions provided by this are usually out of date. In any case,
make sure you have at least R 3.3.1.</li>
<li>Go to the <a
href="https://posit.co/download/rstudio-desktop/#download">RStudio
download page</a></li>
<li>Under <em>Installers</em> select the version that matches your
distribution, and install it with your preferred method (e.g., with
Debian/Ubuntu <code>sudo dpkg -i rstudio-x.yy.zzz-amd64.deb</code> at
the terminal).</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 id="installing-tidyverse" class="section level4">
<h4>Installing <code>tidyverse</code></h4>
<p>After installing R and RStudio, you need to install the
<code>tidyverse</code> package.</p>
<ul>
<li><p>After starting RStudio, at the console type:
<code>install.packages("tidyverse")</code></p></li>
<li><p>You can also do this by going to Tools -> Install Packages and
typing the names of the packages separated by a comma.</p></li>
</ul>
<p><br/></p>
</div>
</div>
<div id="contributors" class="section level3">
<h3>Contributors</h3>
<p>This course has been created by Alexia Cardona by adapting and adding
new content to the <a
href="http://datacarpentry.org/R-ecology-lesson/">Data Carpentry lesson
in Ecology</a>:</p>
<p>Michonneau F, Teal T, Fournier A, Seok B, Obeng A, Pawlik AN, Conrado
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