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<div id="the-first-appendix" class="section level1" number="4">
<h1><span class="header-section-number">A</span> The First Appendix</h1>
<!--
If you feel it necessary to include an appendix, it goes here.
-->
<p>This first appendix includes all of the R chunks of code that were hidden throughout the document (using the <code>include = FALSE</code> chunk tag) to help with readibility and/or setup.</p>
<p><strong>In the main Rmd file</strong></p>
<div class="sourceCode" id="cb17"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb17-1"><a href="A-the-first-appendix.html#cb17-1" aria-hidden="true" tabindex="-1"></a><span class="co"># This chunk ensures that the thesisdown package is</span></span>
<span id="cb17-2"><a href="A-the-first-appendix.html#cb17-2" aria-hidden="true" tabindex="-1"></a><span class="co"># installed and loaded. This thesisdown package includes</span></span>
<span id="cb17-3"><a href="A-the-first-appendix.html#cb17-3" aria-hidden="true" tabindex="-1"></a><span class="co"># the template files for the thesis.</span></span>
<span id="cb17-4"><a href="A-the-first-appendix.html#cb17-4" aria-hidden="true" tabindex="-1"></a><span class="cf">if</span> (<span class="sc">!</span><span class="fu">require</span>(remotes)) {</span>
<span id="cb17-5"><a href="A-the-first-appendix.html#cb17-5" aria-hidden="true" tabindex="-1"></a> <span class="cf">if</span> (params<span class="sc">$</span><span class="st">`</span><span class="at">Install needed packages for {thesisdown}</span><span class="st">`</span>) {</span>
<span id="cb17-6"><a href="A-the-first-appendix.html#cb17-6" aria-hidden="true" tabindex="-1"></a> <span class="fu">install.packages</span>(<span class="st">"remotes"</span>, <span class="at">repos =</span> <span class="st">"https://cran.rstudio.com"</span>)</span>
<span id="cb17-7"><a href="A-the-first-appendix.html#cb17-7" aria-hidden="true" tabindex="-1"></a> } <span class="cf">else</span> {</span>
<span id="cb17-8"><a href="A-the-first-appendix.html#cb17-8" aria-hidden="true" tabindex="-1"></a> <span class="fu">stop</span>(</span>
<span id="cb17-9"><a href="A-the-first-appendix.html#cb17-9" aria-hidden="true" tabindex="-1"></a> <span class="fu">paste</span>(<span class="st">'You need to run install.packages("remotes")",</span></span>
<span id="cb17-10"><a href="A-the-first-appendix.html#cb17-10" aria-hidden="true" tabindex="-1"></a><span class="st"> "first in the Console.'</span>)</span>
<span id="cb17-11"><a href="A-the-first-appendix.html#cb17-11" aria-hidden="true" tabindex="-1"></a> )</span>
<span id="cb17-12"><a href="A-the-first-appendix.html#cb17-12" aria-hidden="true" tabindex="-1"></a> }</span>
<span id="cb17-13"><a href="A-the-first-appendix.html#cb17-13" aria-hidden="true" tabindex="-1"></a>}</span>
<span id="cb17-14"><a href="A-the-first-appendix.html#cb17-14" aria-hidden="true" tabindex="-1"></a><span class="cf">if</span> (<span class="sc">!</span><span class="fu">require</span>(thesisdown)) {</span>
<span id="cb17-15"><a href="A-the-first-appendix.html#cb17-15" aria-hidden="true" tabindex="-1"></a> <span class="cf">if</span> (params<span class="sc">$</span><span class="st">`</span><span class="at">Install needed packages for {thesisdown}</span><span class="st">`</span>) {</span>
<span id="cb17-16"><a href="A-the-first-appendix.html#cb17-16" aria-hidden="true" tabindex="-1"></a> remotes<span class="sc">::</span><span class="fu">install_github</span>(<span class="st">"ismayc/thesisdown"</span>)</span>
<span id="cb17-17"><a href="A-the-first-appendix.html#cb17-17" aria-hidden="true" tabindex="-1"></a> } <span class="cf">else</span> {</span>
<span id="cb17-18"><a href="A-the-first-appendix.html#cb17-18" aria-hidden="true" tabindex="-1"></a> <span class="fu">stop</span>(</span>
<span id="cb17-19"><a href="A-the-first-appendix.html#cb17-19" aria-hidden="true" tabindex="-1"></a> <span class="fu">paste</span>(</span>
<span id="cb17-20"><a href="A-the-first-appendix.html#cb17-20" aria-hidden="true" tabindex="-1"></a> <span class="st">"You need to run"</span>,</span>
<span id="cb17-21"><a href="A-the-first-appendix.html#cb17-21" aria-hidden="true" tabindex="-1"></a> <span class="st">'remotes::install_github("ismayc/thesisdown")'</span>,</span>
<span id="cb17-22"><a href="A-the-first-appendix.html#cb17-22" aria-hidden="true" tabindex="-1"></a> <span class="st">"first in the Console."</span></span>
<span id="cb17-23"><a href="A-the-first-appendix.html#cb17-23" aria-hidden="true" tabindex="-1"></a> )</span>
<span id="cb17-24"><a href="A-the-first-appendix.html#cb17-24" aria-hidden="true" tabindex="-1"></a> )</span>
<span id="cb17-25"><a href="A-the-first-appendix.html#cb17-25" aria-hidden="true" tabindex="-1"></a> }</span>
<span id="cb17-26"><a href="A-the-first-appendix.html#cb17-26" aria-hidden="true" tabindex="-1"></a>}</span>
<span id="cb17-27"><a href="A-the-first-appendix.html#cb17-27" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(thesisdown)</span>
<span id="cb17-28"><a href="A-the-first-appendix.html#cb17-28" aria-hidden="true" tabindex="-1"></a><span class="co"># Set how wide the R output will go</span></span>
<span id="cb17-29"><a href="A-the-first-appendix.html#cb17-29" aria-hidden="true" tabindex="-1"></a><span class="fu">options</span>(<span class="at">width =</span> <span class="dv">70</span>)</span></code></pre></div>
<p><strong>In Chapter <a href="3-ref-labels.html#ref-labels">3</a>:</strong></p>
<div class="sourceCode" id="cb18"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb18-1"><a href="A-the-first-appendix.html#cb18-1" aria-hidden="true" tabindex="-1"></a><span class="co"># This chunk ensures that the thesisdown package is</span></span>
<span id="cb18-2"><a href="A-the-first-appendix.html#cb18-2" aria-hidden="true" tabindex="-1"></a><span class="co"># installed and loaded. This thesisdown package includes</span></span>
<span id="cb18-3"><a href="A-the-first-appendix.html#cb18-3" aria-hidden="true" tabindex="-1"></a><span class="co"># the template files for the thesis and also two functions</span></span>
<span id="cb18-4"><a href="A-the-first-appendix.html#cb18-4" aria-hidden="true" tabindex="-1"></a><span class="co"># used for labeling and referencing</span></span>
<span id="cb18-5"><a href="A-the-first-appendix.html#cb18-5" aria-hidden="true" tabindex="-1"></a><span class="cf">if</span> (<span class="sc">!</span><span class="fu">require</span>(remotes)) {</span>
<span id="cb18-6"><a href="A-the-first-appendix.html#cb18-6" aria-hidden="true" tabindex="-1"></a> <span class="cf">if</span> (params<span class="sc">$</span><span class="st">`</span><span class="at">Install needed packages for {thesisdown}</span><span class="st">`</span>) {</span>
<span id="cb18-7"><a href="A-the-first-appendix.html#cb18-7" aria-hidden="true" tabindex="-1"></a> <span class="fu">install.packages</span>(<span class="st">"remotes"</span>, <span class="at">repos =</span> <span class="st">"https://cran.rstudio.com"</span>)</span>
<span id="cb18-8"><a href="A-the-first-appendix.html#cb18-8" aria-hidden="true" tabindex="-1"></a> } <span class="cf">else</span> {</span>
<span id="cb18-9"><a href="A-the-first-appendix.html#cb18-9" aria-hidden="true" tabindex="-1"></a> <span class="fu">stop</span>(</span>
<span id="cb18-10"><a href="A-the-first-appendix.html#cb18-10" aria-hidden="true" tabindex="-1"></a> <span class="fu">paste</span>(</span>
<span id="cb18-11"><a href="A-the-first-appendix.html#cb18-11" aria-hidden="true" tabindex="-1"></a> <span class="st">'You need to run install.packages("remotes")'</span>,</span>
<span id="cb18-12"><a href="A-the-first-appendix.html#cb18-12" aria-hidden="true" tabindex="-1"></a> <span class="st">"first in the Console."</span></span>
<span id="cb18-13"><a href="A-the-first-appendix.html#cb18-13" aria-hidden="true" tabindex="-1"></a> )</span>
<span id="cb18-14"><a href="A-the-first-appendix.html#cb18-14" aria-hidden="true" tabindex="-1"></a> )</span>
<span id="cb18-15"><a href="A-the-first-appendix.html#cb18-15" aria-hidden="true" tabindex="-1"></a> }</span>
<span id="cb18-16"><a href="A-the-first-appendix.html#cb18-16" aria-hidden="true" tabindex="-1"></a>}</span>
<span id="cb18-17"><a href="A-the-first-appendix.html#cb18-17" aria-hidden="true" tabindex="-1"></a><span class="cf">if</span> (<span class="sc">!</span><span class="fu">require</span>(dplyr)) {</span>
<span id="cb18-18"><a href="A-the-first-appendix.html#cb18-18" aria-hidden="true" tabindex="-1"></a> <span class="cf">if</span> (params<span class="sc">$</span><span class="st">`</span><span class="at">Install needed packages for {thesisdown}</span><span class="st">`</span>) {</span>
<span id="cb18-19"><a href="A-the-first-appendix.html#cb18-19" aria-hidden="true" tabindex="-1"></a> <span class="fu">install.packages</span>(<span class="st">"dplyr"</span>, <span class="at">repos =</span> <span class="st">"https://cran.rstudio.com"</span>)</span>
<span id="cb18-20"><a href="A-the-first-appendix.html#cb18-20" aria-hidden="true" tabindex="-1"></a> } <span class="cf">else</span> {</span>
<span id="cb18-21"><a href="A-the-first-appendix.html#cb18-21" aria-hidden="true" tabindex="-1"></a> <span class="fu">stop</span>(</span>
<span id="cb18-22"><a href="A-the-first-appendix.html#cb18-22" aria-hidden="true" tabindex="-1"></a> <span class="fu">paste</span>(</span>
<span id="cb18-23"><a href="A-the-first-appendix.html#cb18-23" aria-hidden="true" tabindex="-1"></a> <span class="st">'You need to run install.packages("dplyr")'</span>,</span>
<span id="cb18-24"><a href="A-the-first-appendix.html#cb18-24" aria-hidden="true" tabindex="-1"></a> <span class="st">"first in the Console."</span></span>
<span id="cb18-25"><a href="A-the-first-appendix.html#cb18-25" aria-hidden="true" tabindex="-1"></a> )</span>
<span id="cb18-26"><a href="A-the-first-appendix.html#cb18-26" aria-hidden="true" tabindex="-1"></a> )</span>
<span id="cb18-27"><a href="A-the-first-appendix.html#cb18-27" aria-hidden="true" tabindex="-1"></a> }</span>
<span id="cb18-28"><a href="A-the-first-appendix.html#cb18-28" aria-hidden="true" tabindex="-1"></a>}</span>
<span id="cb18-29"><a href="A-the-first-appendix.html#cb18-29" aria-hidden="true" tabindex="-1"></a><span class="cf">if</span> (<span class="sc">!</span><span class="fu">require</span>(ggplot2)) {</span>
<span id="cb18-30"><a href="A-the-first-appendix.html#cb18-30" aria-hidden="true" tabindex="-1"></a> <span class="cf">if</span> (params<span class="sc">$</span><span class="st">`</span><span class="at">Install needed packages for {thesisdown}</span><span class="st">`</span>) {</span>
<span id="cb18-31"><a href="A-the-first-appendix.html#cb18-31" aria-hidden="true" tabindex="-1"></a> <span class="fu">install.packages</span>(<span class="st">"ggplot2"</span>, <span class="at">repos =</span> <span class="st">"https://cran.rstudio.com"</span>)</span>
<span id="cb18-32"><a href="A-the-first-appendix.html#cb18-32" aria-hidden="true" tabindex="-1"></a> } <span class="cf">else</span> {</span>
<span id="cb18-33"><a href="A-the-first-appendix.html#cb18-33" aria-hidden="true" tabindex="-1"></a> <span class="fu">stop</span>(</span>
<span id="cb18-34"><a href="A-the-first-appendix.html#cb18-34" aria-hidden="true" tabindex="-1"></a> <span class="fu">paste</span>(</span>
<span id="cb18-35"><a href="A-the-first-appendix.html#cb18-35" aria-hidden="true" tabindex="-1"></a> <span class="st">'You need to run install.packages("ggplot2")'</span>,</span>
<span id="cb18-36"><a href="A-the-first-appendix.html#cb18-36" aria-hidden="true" tabindex="-1"></a> <span class="st">"first in the Console."</span></span>
<span id="cb18-37"><a href="A-the-first-appendix.html#cb18-37" aria-hidden="true" tabindex="-1"></a> )</span>
<span id="cb18-38"><a href="A-the-first-appendix.html#cb18-38" aria-hidden="true" tabindex="-1"></a> )</span>
<span id="cb18-39"><a href="A-the-first-appendix.html#cb18-39" aria-hidden="true" tabindex="-1"></a> }</span>
<span id="cb18-40"><a href="A-the-first-appendix.html#cb18-40" aria-hidden="true" tabindex="-1"></a>}</span>
<span id="cb18-41"><a href="A-the-first-appendix.html#cb18-41" aria-hidden="true" tabindex="-1"></a><span class="cf">if</span> (<span class="sc">!</span><span class="fu">require</span>(bookdown)) {</span>
<span id="cb18-42"><a href="A-the-first-appendix.html#cb18-42" aria-hidden="true" tabindex="-1"></a> <span class="cf">if</span> (params<span class="sc">$</span><span class="st">`</span><span class="at">Install needed packages for {thesisdown}</span><span class="st">`</span>) {</span>
<span id="cb18-43"><a href="A-the-first-appendix.html#cb18-43" aria-hidden="true" tabindex="-1"></a> <span class="fu">install.packages</span>(<span class="st">"bookdown"</span>, <span class="at">repos =</span> <span class="st">"https://cran.rstudio.com"</span>)</span>
<span id="cb18-44"><a href="A-the-first-appendix.html#cb18-44" aria-hidden="true" tabindex="-1"></a> } <span class="cf">else</span> {</span>
<span id="cb18-45"><a href="A-the-first-appendix.html#cb18-45" aria-hidden="true" tabindex="-1"></a> <span class="fu">stop</span>(</span>
<span id="cb18-46"><a href="A-the-first-appendix.html#cb18-46" aria-hidden="true" tabindex="-1"></a> <span class="fu">paste</span>(</span>
<span id="cb18-47"><a href="A-the-first-appendix.html#cb18-47" aria-hidden="true" tabindex="-1"></a> <span class="st">'You need to run install.packages("bookdown")'</span>,</span>
<span id="cb18-48"><a href="A-the-first-appendix.html#cb18-48" aria-hidden="true" tabindex="-1"></a> <span class="st">"first in the Console."</span></span>
<span id="cb18-49"><a href="A-the-first-appendix.html#cb18-49" aria-hidden="true" tabindex="-1"></a> )</span>
<span id="cb18-50"><a href="A-the-first-appendix.html#cb18-50" aria-hidden="true" tabindex="-1"></a> )</span>
<span id="cb18-51"><a href="A-the-first-appendix.html#cb18-51" aria-hidden="true" tabindex="-1"></a> }</span>
<span id="cb18-52"><a href="A-the-first-appendix.html#cb18-52" aria-hidden="true" tabindex="-1"></a>}</span>
<span id="cb18-53"><a href="A-the-first-appendix.html#cb18-53" aria-hidden="true" tabindex="-1"></a><span class="cf">if</span> (<span class="sc">!</span><span class="fu">require</span>(thesisdown)) {</span>
<span id="cb18-54"><a href="A-the-first-appendix.html#cb18-54" aria-hidden="true" tabindex="-1"></a> <span class="cf">if</span> (params<span class="sc">$</span><span class="st">`</span><span class="at">Install needed packages for {thesisdown}</span><span class="st">`</span>) {</span>
<span id="cb18-55"><a href="A-the-first-appendix.html#cb18-55" aria-hidden="true" tabindex="-1"></a> remotes<span class="sc">::</span><span class="fu">install_github</span>(<span class="st">"ismayc/thesisdown"</span>)</span>
<span id="cb18-56"><a href="A-the-first-appendix.html#cb18-56" aria-hidden="true" tabindex="-1"></a> } <span class="cf">else</span> {</span>
<span id="cb18-57"><a href="A-the-first-appendix.html#cb18-57" aria-hidden="true" tabindex="-1"></a> <span class="fu">stop</span>(</span>
<span id="cb18-58"><a href="A-the-first-appendix.html#cb18-58" aria-hidden="true" tabindex="-1"></a> <span class="fu">paste</span>(</span>
<span id="cb18-59"><a href="A-the-first-appendix.html#cb18-59" aria-hidden="true" tabindex="-1"></a> <span class="st">"You need to run"</span>,</span>
<span id="cb18-60"><a href="A-the-first-appendix.html#cb18-60" aria-hidden="true" tabindex="-1"></a> <span class="st">'remotes::install_github("ismayc/thesisdown")'</span>,</span>
<span id="cb18-61"><a href="A-the-first-appendix.html#cb18-61" aria-hidden="true" tabindex="-1"></a> <span class="st">"first in the Console."</span></span>
<span id="cb18-62"><a href="A-the-first-appendix.html#cb18-62" aria-hidden="true" tabindex="-1"></a> )</span>
<span id="cb18-63"><a href="A-the-first-appendix.html#cb18-63" aria-hidden="true" tabindex="-1"></a> )</span>
<span id="cb18-64"><a href="A-the-first-appendix.html#cb18-64" aria-hidden="true" tabindex="-1"></a> }</span>
<span id="cb18-65"><a href="A-the-first-appendix.html#cb18-65" aria-hidden="true" tabindex="-1"></a>}</span>
<span id="cb18-66"><a href="A-the-first-appendix.html#cb18-66" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(thesisdown)</span>
<span id="cb18-67"><a href="A-the-first-appendix.html#cb18-67" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(dplyr)</span>
<span id="cb18-68"><a href="A-the-first-appendix.html#cb18-68" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(ggplot2)</span>
<span id="cb18-69"><a href="A-the-first-appendix.html#cb18-69" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(knitr)</span>
<span id="cb18-70"><a href="A-the-first-appendix.html#cb18-70" aria-hidden="true" tabindex="-1"></a>flights <span class="ot"><-</span> <span class="fu">read.csv</span>(<span class="st">"data/flights.csv"</span>, <span class="at">stringsAsFactors =</span> <span class="cn">FALSE</span>)</span></code></pre></div>
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