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Conduct principal component analysis for AMR
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<h1>Principal Component Analysis (for AMR)</h1>
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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>(
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<span class='no'>x</span>,
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<span class='no'>...</span>,
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<span class='kw'>retx</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
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<span class='kw'>center</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
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<span class='kw'>scale.</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
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<span class='kw'>tol</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
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<span class='kw'>rank.</span> <span class='kw'>=</span> <span class='kw'>NULL</span>
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)</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 numeric 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</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 numeric 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="maturing-lifecycle"><a class="anchor" href="#maturing-lifecycle"></a>Maturing lifecycle</h2>
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<p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
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The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. We will strive to maintain backward compatibility, but the function needs wider usage and more extensive testing in order to optimise the unlying code.</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 dataset available in the AMR package.</span>
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<span class='co'># See ?example_isolates.</span>
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<span class='co'># calculate the resistance per group first</span>
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<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
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<span class='no'>resistance_data</span> <span class='kw'><-</span> <span class='no'>example_isolates</span> <span class='kw'>%>%</span>
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='kw'>order</span> <span class='kw'>=</span> <span class='fu'><a href='mo_property.html'>mo_order</a></span>(<span class='no'>mo</span>), <span class='co'># group on anything, like order</span>
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<span class='kw'>genus</span> <span class='kw'>=</span> <span class='fu'><a href='mo_property.html'>mo_genus</a></span>(<span class='no'>mo</span>)) <span class='kw'>%>%</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='no'>is.rsi</span>, <span class='no'>resistance</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='no'>pca_result</span> <span class='kw'><-</span> <span class='no'>resistance_data</span> <span class='kw'>%>%</span>
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<span class='fu'>pca</span>(<span class='no'>AMC</span>, <span class='no'>CXM</span>, <span class='no'>CTX</span>, <span class='no'>CAZ</span>, <span class='no'>GEN</span>, <span class='no'>TOB</span>, <span class='no'>TMP</span>, <span class='no'>SXT</span>)
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<span class='no'>pca_result</span>
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<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>pca_result</span>)
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<span class='fu'><a href='https://rdrr.io/r/stats/biplot.html'>biplot</a></span>(<span class='no'>pca_result</span>)
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<span class='fu'><a href='ggplot_pca.html'>ggplot_pca</a></span>(<span class='no'>pca_result</span>) <span class='co'># a new and convenient plot function</span></pre>
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<h2>Contents</h2>
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<ul class="nav nav-pills nav-stacked">
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<li><a href="#arguments">Arguments</a></li>
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<li><a href="#value">Value</a></li>
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<li><a href="#details">Details</a></li>
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<li><a href="#maturing-lifecycle">Maturing lifecycle</a></li>
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<li><a href="#examples">Examples</a></li>
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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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