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<h1>Principal Component Analysis (for AMR)</h1>
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<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/pca.R'><code>R/pca.R</code></a></small>
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<div class="hidden name"><code>pca.Rd</code></div>
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</div>
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<div class="ref-description">
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<p>Performs a principal component analysis (PCA) based on a data set with automatic determination for afterwards plotting the groups and labels, and automatic filtering on only suitable (i.e. non-empty and numeric) variables.</p>
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</div>
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<pre class="usage"><span class='fu'>pca</span><span class='op'>(</span>
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<span class='va'>x</span>,
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<span class='va'>...</span>,
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retx <span class='op'>=</span> <span class='cn'>TRUE</span>,
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center <span class='op'>=</span> <span class='cn'>TRUE</span>,
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scale. <span class='op'>=</span> <span class='cn'>TRUE</span>,
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tol <span class='op'>=</span> <span class='cn'>NULL</span>,
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rank. <span class='op'>=</span> <span class='cn'>NULL</span>
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<span class='op'>)</span></pre>
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<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
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<table class="ref-arguments">
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<colgroup><col class="name" /><col class="desc" /></colgroup>
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<tr>
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<th>x</th>
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<td><p>a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> containing <a href='https://rdrr.io/r/base/numeric.html'>numeric</a> columns</p></td>
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</tr>
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<tr>
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<th>...</th>
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<td><p>columns of <code>x</code> to be selected for PCA, can be unquoted since it supports quasiquotation.</p></td>
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</tr>
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<tr>
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<th>retx</th>
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<td><p>a logical value indicating whether the rotated variables
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should be returned.</p></td>
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</tr>
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<tr>
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<th>center</th>
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<td><p>a logical value indicating whether the variables
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should be shifted to be zero centered. Alternately, a vector of
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length equal the number of columns of <code>x</code> can be supplied.
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The value is passed to <code>scale</code>.</p></td>
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</tr>
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<tr>
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<th>scale.</th>
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<td><p>a logical value indicating whether the variables should
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be scaled to have unit variance before the analysis takes
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place. The default is <code>FALSE</code> for consistency with S, but
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in general scaling is advisable. Alternatively, a vector of length
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equal the number of columns of <code>x</code> can be supplied. The
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value is passed to <code><a href='https://rdrr.io/r/base/scale.html'>scale</a></code>.</p></td>
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</tr>
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<tr>
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<th>tol</th>
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<td><p>a value indicating the magnitude below which components
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should be omitted. (Components are omitted if their
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standard deviations are less than or equal to <code>tol</code> times the
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standard deviation of the first component.) With the default null
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setting, no components are omitted (unless <code>rank.</code> is specified
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less than <code><a href='https://rdrr.io/r/base/Extremes.html'>min(dim(x))</a></code>.). Other settings for tol could be
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<code>tol = 0</code> or <code>tol = sqrt(.Machine$double.eps)</code>, which
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would omit essentially constant components.</p></td>
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</tr>
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<tr>
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<th>rank.</th>
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<td><p>optionally, a number specifying the maximal rank, i.e.,
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maximal number of principal components to be used. Can be set as
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alternative or in addition to <code>tol</code>, useful notably when the
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desired rank is considerably smaller than the dimensions of the matrix.</p></td>
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</tr>
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</table>
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<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
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<p>An object of classes pca and <a href='https://rdrr.io/r/stats/prcomp.html'>prcomp</a></p>
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<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
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<p>The <code>pca()</code> function takes a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> as input and performs the actual PCA with the <span style="R">R</span> function <code><a href='https://rdrr.io/r/stats/prcomp.html'>prcomp()</a></code>.</p>
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<p>The result of the <code>pca()</code> function is a <a href='https://rdrr.io/r/stats/prcomp.html'>prcomp</a> object, with an additional attribute <code>non_numeric_cols</code> which is a vector with the column names of all columns that do not contain <a href='https://rdrr.io/r/base/numeric.html'>numeric</a> values. These are probably the groups and labels, and will be used by <code><a href='ggplot_pca.html'>ggplot_pca()</a></code>.</p>
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<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable Lifecycle</h2>
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<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
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The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
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<p>If the unlying code needs breaking changes, they will occur gradually. For example, a argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
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<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on Our Website!</h2>
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<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
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<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
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<pre class="examples"><span class='co'># `example_isolates` is a data set available in the AMR package.</span>
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<span class='co'># See ?example_isolates.</span>
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<span class='co'># \donttest{</span>
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<span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
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<span class='co'># calculate the resistance per group first </span>
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<span class='va'>resistance_data</span> <span class='op'><-</span> <span class='va'>example_isolates</span> <span class='op'>%>%</span>
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span><span class='op'>(</span>order <span class='op'>=</span> <span class='fu'><a href='mo_property.html'>mo_order</a></span><span class='op'>(</span><span class='va'>mo</span><span class='op'>)</span>, <span class='co'># group on anything, like order</span>
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genus <span class='op'>=</span> <span class='fu'><a href='mo_property.html'>mo_genus</a></span><span class='op'>(</span><span class='va'>mo</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%>%</span> <span class='co'># and genus as we do here;</span>
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise_all.html'>summarise_if</a></span><span class='op'>(</span><span class='va'>is.rsi</span>, <span class='va'>resistance</span><span class='op'>)</span> <span class='co'># then get resistance of all drugs</span>
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<span class='co'># now conduct PCA for certain antimicrobial agents</span>
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<span class='va'>pca_result</span> <span class='op'><-</span> <span class='va'>resistance_data</span> <span class='op'>%>%</span>
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<span class='fu'>pca</span><span class='op'>(</span><span class='va'>AMC</span>, <span class='va'>CXM</span>, <span class='va'>CTX</span>, <span class='va'>CAZ</span>, <span class='va'>GEN</span>, <span class='va'>TOB</span>, <span class='va'>TMP</span>, <span class='va'>SXT</span><span class='op'>)</span>
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<span class='va'>pca_result</span>
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<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>pca_result</span><span class='op'>)</span>
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<span class='fu'><a href='https://rdrr.io/r/stats/biplot.html'>biplot</a></span><span class='op'>(</span><span class='va'>pca_result</span><span class='op'>)</span>
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<span class='fu'><a href='ggplot_pca.html'>ggplot_pca</a></span><span class='op'>(</span><span class='va'>pca_result</span><span class='op'>)</span> <span class='co'># a new and convenient plot function</span>
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<span class='op'>}</span>
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<span class='co'># }</span>
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</pre>
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
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