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(v1.3.0.9038) prefinal 1.4.0
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<script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet">
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<script src="../extra.js"></script><meta property="og:title" content="How to conduct principal component analysis (PCA) for AMR">
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<meta property="og:description" content="AMR">
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<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg">
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<meta property="og:image" content="https://msberends.github.io/AMR/logo.png">
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<!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0</span>
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</span>
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</div>
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<span class="co"># $ PEN <rsi> R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R,…</span>
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<span class="co"># $ OXA <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
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<span class="co"># $ FLC <rsi> NA, NA, R, R, R, R, S, S, R, S, S, S, NA, NA, NA, NA,…</span>
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<span class="co"># $ AMX <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
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<span class="co"># $ AMX <rsi> NA, NA, NA, NA, NA, NA, R, R, NA, NA, NA, NA, NA, NA,…</span>
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<span class="co"># $ AMC <rsi> I, I, NA, NA, NA, NA, S, S, NA, NA, S, S, I, I, R, I,…</span>
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<span class="co"># $ AMP <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
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<span class="co"># $ AMP <rsi> NA, NA, NA, NA, NA, NA, R, R, NA, NA, NA, NA, NA, NA,…</span>
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<span class="co"># $ TZP <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
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<span class="co"># $ CZO <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
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<span class="co"># $ FEP <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
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<span class="co"># $ VAN <rsi> R, R, S, S, S, S, S, S, S, S, NA, NA, R, R, R, R, R, …</span>
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<span class="co"># $ TEC <rsi> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R…</span>
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<span class="co"># $ TCY <rsi> R, R, S, S, S, S, S, S, S, I, S, S, NA, NA, I, R, R, …</span>
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<span class="co"># $ TGC <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
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<span class="co"># $ TGC <rsi> NA, NA, S, S, S, S, S, S, S, NA, S, S, NA, NA, NA, R,…</span>
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<span class="co"># $ DOX <rsi> NA, NA, S, S, S, S, S, S, S, NA, S, S, NA, NA, NA, R,…</span>
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<span class="co"># $ ERY <rsi> R, R, R, R, R, R, S, S, R, S, S, S, R, R, R, R, R, R,…</span>
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<span class="co"># $ CLI <rsi> NA, NA, NA, NA, NA, R, NA, NA, NA, NA, NA, NA, NA, NA…</span>
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<span class="co"># $ CLI <rsi> R, R, NA, NA, NA, R, NA, NA, NA, NA, NA, NA, R, R, R,…</span>
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<span class="co"># $ AZM <rsi> R, R, R, R, R, R, S, S, R, S, S, S, R, R, R, R, R, R,…</span>
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<span class="co"># $ IPM <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S,…</span>
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<span class="co"># $ MEM <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
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<span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="kw">pca_result</span>)
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<span class="co"># Importance of components:</span>
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<span class="co"># PC1 PC2 PC3 PC4 PC5 PC6 PC7</span>
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<span class="co"># Standard deviation 2.154 1.6809 0.61305 0.33882 0.20755 0.03137 1.602e-16</span>
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<span class="co"># Proportion of Variance 0.580 0.3532 0.04698 0.01435 0.00538 0.00012 0.000e+00</span>
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<span class="co"># Cumulative Proportion 0.580 0.9332 0.98014 0.99449 0.99988 1.00000 1.000e+00</span>
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<span class="co"># Standard deviation 2.154 1.6807 0.61365 0.33902 0.20757 0.03136 1.733e-16</span>
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<span class="co"># Proportion of Variance 0.580 0.3531 0.04707 0.01437 0.00539 0.00012 0.000e+00</span>
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<span class="co"># Cumulative Proportion 0.580 0.9331 0.98012 0.99449 0.99988 1.00000 1.000e+00</span>
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</pre></div>
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<p>Good news. The first two components explain a total of 93.3% of the variance (see the PC1 and PC2 values of the <em>Proportion of Variance</em>. We can create a so-called biplot with the base R <code><a href="https://rdrr.io/r/stats/biplot.html">biplot()</a></code> function, to see which antimicrobial resistance per drug explain the difference per microorganism.</p>
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</div>
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