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<h1>Module 3 exercise</h1>
<div class="sourceCode" id="cb250"><pre class="sourceCode r codeblock"><code class="sourceCode r"><span id="cb250-1"><a href="module-3-exercise.html#cb250-1" aria-hidden="true" tabindex="-1"></a><span class="fu">data</span>(BreastCancer)</span>
<span id="cb250-2"><a href="module-3-exercise.html#cb250-2" aria-hidden="true" tabindex="-1"></a>bc <span class="ot"><-</span> BreastCancer</span>
<span id="cb250-3"><a href="module-3-exercise.html#cb250-3" aria-hidden="true" tabindex="-1"></a><span class="cf">for</span> (k <span class="cf">in</span> <span class="dv">2</span><span class="sc">:</span><span class="dv">10</span>) <span class="co"># altered for current lab</span></span>
<span id="cb250-4"><a href="module-3-exercise.html#cb250-4" aria-hidden="true" tabindex="-1"></a> bc[,k] <span class="ot"><-</span> <span class="fu">as.numeric</span>(bc[,k]) </span>
<span id="cb250-5"><a href="module-3-exercise.html#cb250-5" aria-hidden="true" tabindex="-1"></a><span class="fu">head</span>(bc)</span></code></pre></div>
<p>Explore missingness:</p>
<div class="sourceCode" id="cb251"><pre class="sourceCode r codeblock"><code class="sourceCode r"><span id="cb251-1"><a href="module-3-exercise.html#cb251-1" aria-hidden="true" tabindex="-1"></a><span class="fu">suppressMessages</span>(<span class="fu">require</span>(plotrix))</span>
<span id="cb251-2"><a href="module-3-exercise.html#cb251-2" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb251-3"><a href="module-3-exercise.html#cb251-3" aria-hidden="true" tabindex="-1"></a><span class="co">#' show data missingness as a chequered matrix</span></span>
<span id="cb251-4"><a href="module-3-exercise.html#cb251-4" aria-hidden="true" tabindex="-1"></a><span class="co">#' </span></span>
<span id="cb251-5"><a href="module-3-exercise.html#cb251-5" aria-hidden="true" tabindex="-1"></a><span class="co">#' @param x (matrix) data matrix.</span></span>
<span id="cb251-6"><a href="module-3-exercise.html#cb251-6" aria-hidden="true" tabindex="-1"></a><span class="co">#' @param outFile (char) path to file for printing graph</span></span>
<span id="cb251-7"><a href="module-3-exercise.html#cb251-7" aria-hidden="true" tabindex="-1"></a><span class="co">#' @param wd (numeric) width in inches</span></span>
<span id="cb251-8"><a href="module-3-exercise.html#cb251-8" aria-hidden="true" tabindex="-1"></a><span class="co">#' @param ht (numeric) height in inches</span></span>
<span id="cb251-9"><a href="module-3-exercise.html#cb251-9" aria-hidden="true" tabindex="-1"></a><span class="co">#' @return plots missingness matrix to file</span></span>
<span id="cb251-10"><a href="module-3-exercise.html#cb251-10" aria-hidden="true" tabindex="-1"></a><span class="co">#' @import plotrix</span></span>
<span id="cb251-11"><a href="module-3-exercise.html#cb251-11" aria-hidden="true" tabindex="-1"></a><span class="co">#' @export</span></span>
<span id="cb251-12"><a href="module-3-exercise.html#cb251-12" aria-hidden="true" tabindex="-1"></a>plotMissMat <span class="ot"><-</span> <span class="cf">function</span>(x,<span class="at">xlab=</span><span class="st">"columns"</span>,</span>
<span id="cb251-13"><a href="module-3-exercise.html#cb251-13" aria-hidden="true" tabindex="-1"></a> <span class="at">ylab=</span><span class="st">"rows"</span>,<span class="at">border=</span><span class="cn">NA</span>) {</span>
<span id="cb251-14"><a href="module-3-exercise.html#cb251-14" aria-hidden="true" tabindex="-1"></a> </span>
<span id="cb251-15"><a href="module-3-exercise.html#cb251-15" aria-hidden="true" tabindex="-1"></a> x <span class="ot"><-</span> <span class="sc">!</span><span class="fu">is.na</span>(x)</span>
<span id="cb251-16"><a href="module-3-exercise.html#cb251-16" aria-hidden="true" tabindex="-1"></a> <span class="fu">class</span>(x) <span class="ot"><-</span> <span class="st">"numeric"</span></span>
<span id="cb251-17"><a href="module-3-exercise.html#cb251-17" aria-hidden="true" tabindex="-1"></a> <span class="fu">color2D.matplot</span>(x,<span class="at">show.values=</span><span class="cn">FALSE</span>,<span class="at">axes=</span><span class="cn">FALSE</span>,</span>
<span id="cb251-18"><a href="module-3-exercise.html#cb251-18" aria-hidden="true" tabindex="-1"></a> <span class="at">cs1=</span><span class="fu">c</span>(<span class="dv">1</span>,<span class="dv">0</span>),<span class="at">cs2=</span><span class="fu">c</span>(<span class="dv">1</span>,<span class="dv">0</span>),<span class="at">cs3=</span><span class="fu">c</span>(<span class="dv">1</span>,<span class="dv">0</span>),<span class="at">border=</span>border,</span>
<span id="cb251-19"><a href="module-3-exercise.html#cb251-19" aria-hidden="true" tabindex="-1"></a> <span class="at">cex=</span><span class="fl">0.8</span>,</span>
<span id="cb251-20"><a href="module-3-exercise.html#cb251-20" aria-hidden="true" tabindex="-1"></a> <span class="at">xlab=</span>xlab,<span class="at">ylab=</span>ylab)</span>
<span id="cb251-21"><a href="module-3-exercise.html#cb251-21" aria-hidden="true" tabindex="-1"></a>}</span></code></pre></div>
<p>Explore missingness:</p>
<div class="sourceCode" id="cb252"><pre class="sourceCode r codeblock"><code class="sourceCode r"><span id="cb252-1"><a href="module-3-exercise.html#cb252-1" aria-hidden="true" tabindex="-1"></a><span class="fu">plotMissMat</span>(bc)</span>
<span id="cb252-2"><a href="module-3-exercise.html#cb252-2" aria-hidden="true" tabindex="-1"></a><span class="fu">colSums</span>(<span class="fu">is.na</span>(bc))</span></code></pre></div>
<p>Plot relationship between variables</p>
<div class="sourceCode" id="cb253"><pre class="sourceCode r codeblock"><code class="sourceCode r"><span id="cb253-1"><a href="module-3-exercise.html#cb253-1" aria-hidden="true" tabindex="-1"></a><span class="fu">require</span>(ggplot2)</span>
<span id="cb253-2"><a href="module-3-exercise.html#cb253-2" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb253-3"><a href="module-3-exercise.html#cb253-3" aria-hidden="true" tabindex="-1"></a><span class="fu">ggplot</span>(bc,<span class="fu">aes</span>(Cell.size,Normal.nucleoli)) <span class="sc">+</span> <span class="fu">geom_point</span>()</span>
<span id="cb253-4"><a href="module-3-exercise.html#cb253-4" aria-hidden="true" tabindex="-1"></a><span class="fu">ggplot</span>(bc) <span class="sc">+</span> <span class="fu">geom_boxplot</span>(<span class="fu">aes</span>(<span class="fu">factor</span>(Class), Normal.nucleoli))</span>
<span id="cb253-5"><a href="module-3-exercise.html#cb253-5" aria-hidden="true" tabindex="-1"></a><span class="fu">ggplot</span>(bc) <span class="sc">+</span> <span class="fu">geom_boxplot</span>(<span class="fu">aes</span>(<span class="fu">factor</span>(Class), Cl.thickness))</span>
<span id="cb253-6"><a href="module-3-exercise.html#cb253-6" aria-hidden="true" tabindex="-1"></a><span class="fu">ggplot</span>(bc) <span class="sc">+</span> <span class="fu">geom_boxplot</span>(<span class="fu">aes</span>(<span class="fu">factor</span>(Class), Bare.nuclei))</span></code></pre></div>
<p>Fit a binary outcome model:</p>
<div class="sourceCode" id="cb254"><pre class="sourceCode r codeblock"><code class="sourceCode r"><span id="cb254-1"><a href="module-3-exercise.html#cb254-1" aria-hidden="true" tabindex="-1"></a>mod <span class="ot"><-</span> <span class="fu">glm</span>(</span>
<span id="cb254-2"><a href="module-3-exercise.html#cb254-2" aria-hidden="true" tabindex="-1"></a> Class <span class="sc">~</span> Cl.thickness <span class="sc">+</span> Bare.nuclei <span class="sc">+</span> Normal.nucleoli <span class="sc">+</span> Mitoses <span class="sc">+</span> Bl.cromatin, </span>
<span id="cb254-3"><a href="module-3-exercise.html#cb254-3" aria-hidden="true" tabindex="-1"></a> bc,</span>
<span id="cb254-4"><a href="module-3-exercise.html#cb254-4" aria-hidden="true" tabindex="-1"></a> <span class="at">family=</span><span class="st">"binomial"</span>)</span>
<span id="cb254-5"><a href="module-3-exercise.html#cb254-5" aria-hidden="true" tabindex="-1"></a><span class="fu">summary</span>(mod)</span></code></pre></div>
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