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<h1 class="title toc-ignore">Principle components analysis</h1>
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<p>?princomp</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">data</span>(iris)
<span class="co"># log transform </span>
log.ir <-<span class="st"> </span><span class="kw">log</span>(iris[, <span class="dv">1</span>:<span class="dv">4</span>])
ir.species <-<span class="st"> </span>iris[, <span class="dv">5</span>]
<span class="co"># apply PCA - scale. = TRUE is highly </span>
<span class="co"># advisable, but default is FALSE. </span>
ir.pca <-<span class="st"> </span><span class="kw">prcomp</span>(log.ir,
<span class="dt">center =</span> <span class="ot">TRUE</span>,
<span class="dt">scale. =</span> <span class="ot">TRUE</span>) </code></pre></div>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># plot method</span>
<span class="kw">plot</span>(ir.pca, <span class="dt">type =</span> <span class="st">"l"</span>)</code></pre></div>
<p><img src="pca_files/figure-html/unnamed-chunk-2-1.png" width="384" style="display: block; margin: auto;" /></p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">biplot</span>(ir.pca)</code></pre></div>
<p><img src="pca_files/figure-html/unnamed-chunk-3-1.png" width="960" style="display: block; margin: auto;" /></p>
<div id="links" class="section level2">
<h2>Links</h2>
<p><a href="https://www.r-bloggers.com/computing-and-visualizing-pca-in-r/" class="uri">https://www.r-bloggers.com/computing-and-visualizing-pca-in-r/</a><br />
<a href="http://rcharlie.com/2017-04-13-Coachella/" class="uri">http://rcharlie.com/2017-04-13-Coachella/</a></p>
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