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<h1 class="title toc-ignore">Exercise Solutions</h1>
</div>
<p> </p>
<div id="exercise-1-getting-to-know-r-and-rstudio"
class="section level2">
<h2>Exercise 1: Getting to know R and RStudio</h2>
<p> </p>
<p>Read <a href="https://intro2r.com/chap1.html">Chapter 1</a> to help
you complete the questions in this exercise. We’ll also bounce
occasionally to <a href="https://intro2r.com/basics_r.html">Chapter
2</a> for a few questions where links will be provided.</p>
<p> </p>
<ol style="list-style-type: decimal">
<li>Start RStudio on your computer. Create a new RStudio Project (select
File –> New Project on the main menu). Create the Project in a new
directory by selecting ‘New Directory’ and then select ‘New Project’.
Give the Project a suitable name in the ‘Directory name:’ box (maybe
‘BI5009_statistics’? - see <a
href="https://intro2r.com/file_names.html">Section 1.9</a> of the
Introduction to R book for a discussion on naming files and
directories). Choose where you would like to create this Project
directory by clicking on the ‘Browse’ button. Finally create the project
by clicking on the ‘Create Project’ button. This will be your main
RStudio Project file and directory which you will use throughout this
course. If you’re confused see <a
href="https://intro2r.com/rsprojs.html">Section 1.6</a> of the
introduction to R Book which covers RStudio Projects or watch the
‘RStudio Projects’ video <a
href="https://alexd106.github.io/BI5009/howto.html#rstudio_proj-vid">here</a>.</li>
</ol>
<p> </p>
<ol start="2" style="list-style-type: decimal">
<li>Now create a new R script inside this Project by selecting File
–> New File –> R Script from the main menu (or use the shortcut
button). Before you start writing any code save this script by selecting
File –> Save from the main menu. Call this script ‘exercise_1’ or
something similar (remember, files names should not <a
href="https://intro2r.com/file_names.html">contain spaces!</a>). Click
on the ‘Files’ tab in the bottom right RStudio pane to see whether your
file has been saved in the correct location. Ok, at the top of almost
every R script (there are very few exceptions to this!) you should
include some metadata to help your collaborators (and the future you)
know who wrote the script, when it was written and what the script does
(amongst other things). Include this information at the top of your R
script making sure that you place a <code>#</code> at the beginning of
every line to let R know this is a comment. See <a
href="https://intro2r.com/proj-doc.html">Section 1.10</a> for a little
more detail.</li>
</ol>
<p> </p>
<ol start="3" style="list-style-type: decimal">
<li>Explore RStudio making sure you understand the functionality of each
of the four windows. Take a look at <a
href="https://intro2r.com/rstudio_orient.html">Section 1.3</a> of the
Introduction to R book for more details or watch this <a
href="https://alexd106.github.io/BI5009/howto.html#rstudio-vid">video</a>.
Take your time and check out each of the tabs in the windows. The
function of some of these tabs will be obvious whereas others won’t be
useful right now. In general, you will write your R code in the script
editor window (usually top left window) and then source your code into
the R console (usually bottom left) by clicking anywhere in the relevant
line of code with your mouse and then clicking on the ‘Run’ button at
the top of the script editor window. If you don’t like clicking buttons
(I don’t!) then you can use the keyboard shortcut ‘ctrl + enter’ (on
Windows) or ‘command + enter’ (on Mac OSX).</li>
</ol>
<p> </p>
<ol start="4" style="list-style-type: decimal">
<li><p>Now to practice writing code in the script editor and sourcing
this code into the R console. Let’s display the help file for the
function <code>mean</code>. In your script type
<code>help('mean')</code> and source this code into the console. Notice
that the help file is displayed in the bottom right window (if not then
click on the ‘Help’ tab). Examine the different components of the help
file (especially the examples section at the end of the help file). See
<a href="https://intro2r.com/help.html">Section 2.5</a> of the
Introduction to R book for more details on using the help functions.</p>
<div class="sourceCode" id="cb1"><pre
class="sourceCode r"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a><span class="fu">help</span>(mean) <span class="co"># different methods of using help</span></span>
<span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a>?mean</span>
<span id="cb1-3"><a href="#cb1-3" tabindex="-1"></a><span class="fu">help</span>(<span class="st">"mean"</span>)</span></code></pre></div></li>
</ol>
<p> </p>
<ol start="5" style="list-style-type: decimal">
<li><p>The content displayed in the bottom right window is context
dependent. For example if we write the code <code>plot(1:10)</code> in
our script and then source it into the R console the bottom right window
will display this plot (don’t worry about understanding the R code right
now, hopefully this will become clear later on in the course!).</p>
<div class="sourceCode" id="cb2"><pre
class="sourceCode r"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1" tabindex="-1"></a><span class="fu">plot</span>(<span class="dv">1</span><span class="sc">:</span><span class="dv">10</span>) <span class="co">#dont worry about what 1:10 does just yet</span></span></code></pre></div></li>
</ol>
<p> </p>
<ol start="6" style="list-style-type: decimal">
<li><p>Next, let’s practice creating a variable and assigning a value to
this variable. Take a look at <a
href="https://intro2r.com/objects-in-r.html">Section 2.2</a> of the
Introduction to R book for further information on how to do this or if
you prefer watch the <a
href="https://alexd106.github.io/BI5009/howto.html#objs-vid">Objects in
R video</a>. Create a variable called <code>first_num</code> and assign
it the value <code>42</code>. Click on the ‘Environment’ tab in the top
right window to display the variable and value. Now create another
variable called <code>first_char</code> and assign it a value
<code>"my first character"</code>. Notice this variable is now also
displayed in the ‘Environment’ along with it’s value and class
(<code>chr</code> - short for character class).</p>
<div class="sourceCode" id="cb3"><pre
class="sourceCode r"><code class="sourceCode r"><span id="cb3-1"><a href="#cb3-1" tabindex="-1"></a>first_num <span class="ot"><-</span> <span class="dv">42</span> <span class="co"># create variable first_num and assign the value 42</span></span>
<span id="cb3-2"><a href="#cb3-2" tabindex="-1"></a>first_char <span class="ot"><-</span> <span class="st">"my first character"</span></span></code></pre></div></li>
</ol>
<p> </p>
<ol start="7" style="list-style-type: decimal">
<li><p>Remove the variable <code>first_num</code> from your environment
using the <code>rm()</code> function. Use the code
<code>rm(first_num)</code> to do this. Check out the ‘Environment’ tab
to ensure the variable has been removed. Alternatively, use the
<code>ls()</code> function to list all objects in your environment.</p>
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb4-1"><a href="#cb4-1" tabindex="-1"></a><span class="fu">rm</span>(first_num)</span>
<span id="cb4-2"><a href="#cb4-2" tabindex="-1"></a><span class="fu">ls</span>() <span class="co"># list all variables in the workspace </span></span></code></pre></div>
<p> </p></li>
<li><p>Let’s see what happens if we assign another value to an existing
variable. Assign the value <code>"my second character"</code> to the
variable <code>first_char</code> you created in Q6. Notice the value has
changed in the ‘Environment’. To display the value of
<code>first.char</code> enter the name of the variable in the console.
Don’t to forget to save your R script periodically!</p>
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb5-1"><a href="#cb5-1" tabindex="-1"></a>first_char <span class="ot"><-</span> <span class="st">"my second variable"</span></span>
<span id="cb5-2"><a href="#cb5-2" tabindex="-1"></a>first_char <span class="co"># display the value </span></span></code></pre></div>
<p> </p></li>
<li><p>OK, let’s leave RStudio for a minute. Using your favourite web
browser, navigate to the <a href="http://www.r-project.org">R-project
website</a> and explore links that catch your eye. Make sure you find
the R manuals page and the user contributed documents section. Download
any manuals that you think you might find useful (some are listed in the
course manual) and save them on your computer (or USB drive).</p></li>
</ol>
<p> </p>
<ol start="10" style="list-style-type: decimal">
<li>Click on the ‘Search’ link on the R-Project website. Use ‘Rseek’ to
search for the term ‘mixed model p values’ (this is a controversial
subject!) and explore anything that looks interesting. Also experiment
with the ‘R site search’ and ‘Nabble R Forum’ links. Learning how to
search for help when you run into a problem when using R is an acquired
skill and something you get better at over time. One note of caution,
often you will find many different solutions to solving a problem in R,
some written by experienced R users and others by people with less
experience. Whichever solution you choose make sure you understand what
the code is doing and thoroughly test it to make sure it’s doing what
you want.</li>
</ol>
<p> </p>
<ol start="11" style="list-style-type: decimal">
<li><p>OK, back to RStudio. Sometimes you may forget the exact name of a
function you want to use so it would be useful to be able to search
through all the function names. For example, you want to create a design
plot but can only remember that the name of the function has the word
‘plot’ in it. Use the <code>apropos()</code> function to list all the
functions with the word plot in their name (see <a
href="https://intro2r.com/help.html#help">Section 2.5.1</a> of the
Introduction to R book). Look through the list and once you have figured
what the correct function is then bring up the help file for this
function (Hint: the function name probably has the words ‘plot’ and
‘design’ in it!).</p>
<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb6-1"><a href="#cb6-1" tabindex="-1"></a><span class="fu">apropos</span>(<span class="st">"plot"</span>)</span>
<span id="cb6-2"><a href="#cb6-2" tabindex="-1"></a><span class="fu">help</span>(<span class="st">'plot.design'</span>)</span></code></pre></div>
<p> </p></li>
<li><p>Another strategy would be to use the <code>help.search()</code>
function to search through R’s help files. Search the R help system for
instances of the character string ‘plot’. Take a look at <a
href="https://intro2r.com/help.html#r-help">Section 2.5.1</a> for more
information. Also, see if you can figure out how to narrow your search
by only searching for ‘plot’ in the <code>nlme</code> package (hint: see
the help page for <code>help.search()</code>).</p>
<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb7-1"><a href="#cb7-1" tabindex="-1"></a><span class="fu">help.search</span>(<span class="st">"plot"</span>)</span>
<span id="cb7-2"><a href="#cb7-2" tabindex="-1"></a>??plot <span class="co"># shortcut for help.search function</span></span>
<span id="cb7-3"><a href="#cb7-3" tabindex="-1"></a></span>
<span id="cb7-4"><a href="#cb7-4" tabindex="-1"></a><span class="fu">help.search</span>(<span class="st">"plot"</span>, <span class="at">package =</span> <span class="st">"nlme"</span>)</span></code></pre></div>
<p> </p></li>
<li><p>R’s working directory is the default location of any files you
read into R, or export from R. Although you won’t be importing or
exporting files just yet (that’s tomorrows job) it’s useful to be able
to determine what your current working directory is. So, read <a
href="https://intro2r.com/work-d.html">Section 1.7</a> of the
Introduction to R book to introduce yourself to working directories and
figure out how to display your current working directory.</p>
<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb8-1"><a href="#cb8-1" tabindex="-1"></a><span class="fu">getwd</span>() <span class="co"># displays the current working directory </span></span></code></pre></div>
<p> </p></li>
<li><p>Let’s finish up by creating some additional useful directories in
your Project directory. If you’ve followed the <strong>Data
<i class="fa fa-download" aria-hidden="true"></i></strong> instructions
when downloading datasets for this course you will already have a
directory called <code>data</code> in your Project (if you didn’t then
take a look at the instructions under <strong>Data
<i class="fa fa-download" aria-hidden="true"></i></strong> to create
this directory). Now let’s create another directory called
<code>output</code> where you’ll save data files and plots you generate
later on during this course. This time, instead of clicking on the ‘New
Folder’ icon in RStudio we’ll create a new directory using R code
directly in the R console (you can also interact with your computer’s
operating system in all sorts of useful ways). To do this use the
<code>dir.create()</code> function to create a directory called
<code>output</code> (See <a
href="https://intro2r.com/dir-struct.html">Section 1.8</a> of the
Introduction to R book for more details). If you fancy it, you can also
create a subdirectory in your <code>output</code> directory called
<code>figures</code> to store all your fancy R plots for your thesis.
You can list all the files in your directories using the
<code>list.files()</code> function. Can you figure out how to list the
directories as well? (hint: see <code>?listfiles</code> or <a
href="https://intro2r.com/dir-struct.html">Section 1.8</a> of the course
book).</p>
<div class="sourceCode" id="cb9"><pre
class="sourceCode r"><code class="sourceCode r"><span id="cb9-1"><a href="#cb9-1" tabindex="-1"></a><span class="fu">dir.create</span>(<span class="at">path =</span> <span class="st">'data'</span>)</span>
<span id="cb9-2"><a href="#cb9-2" tabindex="-1"></a><span class="fu">dir.create</span>(<span class="at">path =</span> <span class="st">'output'</span>)</span>
<span id="cb9-3"><a href="#cb9-3" tabindex="-1"></a><span class="fu">list.files</span>(<span class="at">include.dirs =</span> <span class="cn">TRUE</span>)</span></code></pre></div></li>
</ol>
<p> </p>
<ol start="15" style="list-style-type: decimal">
<li>Don’t to forget to save your R script. Close your Project by
selecting File –> Close Project on the main menu.</li>
</ol>
<p> </p>
<p>End of Exercise 1</p>
</div>
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