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<h1 class="title toc-ignore">Background functions</h1>
<h4 class="author">Brian J. Knaus</h4>
<h4 class="date">June 25, 2018</h4>

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<div id="background-functions" class="section level2">
<h2>Background functions</h2>
<p>Some R functions may be used frequently throughout analyses yet to new users some of them may appear non-intuitive. Here we attempt to identify some of these functions and illustrate their use.</p>
</div>
<div id="apply" class="section level2">
<h2>apply()</h2>
<p>One of R’s shortcomings is that <code>for()</code> loops are relatvely slow. Historically this was a greater problem and recent versions of R have improved the performance of these loops. Because of the performance cost associated with <code>for</code> loops it is generally recommended to avoid them in your R code, particularly when performance is an issue. If you have a task that requires iteration and you want performance that is greater than a <code>for()</code> loop will provide, you should consider <code>apply()</code>. We’ll create a matrix to illustrate its use.</p>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1"></a>tmp &lt;-<span class="st"> </span><span class="kw">matrix</span>(<span class="kw">rep</span>(<span class="dv">1</span><span class="op">:</span><span class="dv">3</span>, <span class="dt">times =</span> <span class="dv">3</span>), <span class="dt">ncol =</span> <span class="dv">3</span>)</span>
<span id="cb1-2"><a href="#cb1-2"></a>tmp</span></code></pre></div>
<pre><code>##      [,1] [,2] [,3]
## [1,]    1    1    1
## [2,]    2    2    2
## [3,]    3    3    3</code></pre>
<p>The function <code>apply()</code> will ‘apply’ a function over the rows or columns of a matrix. Here we’ll use the function <code>sum()</code> to illustrate this.</p>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb3-1"><a href="#cb3-1"></a><span class="kw">apply</span>(tmp, <span class="dt">MARGIN =</span> <span class="dv">1</span>, sum)</span></code></pre></div>
<pre><code>## [1] 3 6 9</code></pre>
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb5-1"><a href="#cb5-1"></a><span class="kw">apply</span>(tmp, <span class="dt">MARGIN =</span> <span class="dv">2</span>, sum)</span></code></pre></div>
<pre><code>## [1] 6 6 6</code></pre>
<p>The <code>MARGIN</code> parameter specifies whether to operate on rows or columns. I remember how 1 and 2 behave by remembering that when we specify the rows of a matrix with the square brackets (<code>[]</code>) we use the first position before the comma. To specify the columns we use the second position or after the comma.</p>
<p>More information on <code>apply()</code> can be found by consulting it’s manual page.</p>
<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb7-1"><a href="#cb7-1"></a>?apply</span></code></pre></div>
</div>
<div id="sweep" class="section level2">
<h2>sweep()</h2>
<p>The function <code>sweep()</code> is similar to <code>apply()</code> in that it iterates over the rows or columns of a matrix. However, it takes the additional parameters <code>STATS</code> and <code>FUN</code>. The parameter <code>FUN</code> is a function to be used. This may be an R function or a custom function you’ve created. The parameter <code>STATS</code> is a vector of data to be used by the function. Here we use <code>apply()</code> to create a mean for each column and then use <code>sweep()</code> to divide the values in the matrix by their column mean.</p>
<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb8-1"><a href="#cb8-1"></a>my_means &lt;-<span class="st"> </span><span class="kw">apply</span>(tmp, <span class="dt">MARGIN =</span> <span class="dv">2</span>, sum) <span class="op">/</span><span class="st"> </span><span class="kw">nrow</span>(tmp)</span>
<span id="cb8-2"><a href="#cb8-2"></a><span class="kw">sweep</span>(tmp, <span class="dt">MARGIN =</span> <span class="dv">2</span>, <span class="dt">STATS =</span> my_means, <span class="dt">FUN =</span> <span class="st">&quot;/&quot;</span>)</span></code></pre></div>
<pre><code>##      [,1] [,2] [,3]
## [1,]  0.5  0.5  0.5
## [2,]  1.0  1.0  1.0
## [3,]  1.5  1.5  1.5</code></pre>
<p>More information on <code>sweep()</code> can be found by consulting it’s manual page.</p>
<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb10-1"><a href="#cb10-1"></a>?sweep</span></code></pre></div>
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