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(v1.4.0.9008) like variations

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dr. M.S. (Matthijs) Berends
2020-10-26 12:23:03 +01:00
parent f720c9ba0b
commit 760d69a3e0
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docs/reference/pca.html
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@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9008</span>
</span>
</div>
@ -242,15 +242,15 @@
<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>
</div>
<pre class="usage"><span class='fu'>pca</span>(
<span class='kw'>x</span>,
<span class='kw'>...</span>,
retx = <span class='fl'>TRUE</span>,
center = <span class='fl'>TRUE</span>,
scale. = <span class='fl'>TRUE</span>,
tol = <span class='kw'>NULL</span>,
rank. = <span class='kw'>NULL</span>
)</pre>
<pre class="usage"><span class='fu'>pca</span><span class='op'>(</span>
<span class='va'>x</span>,
<span class='va'>...</span>,
retx <span class='op'>=</span> <span class='cn'>TRUE</span>,
center <span class='op'>=</span> <span class='cn'>TRUE</span>,
scale. <span class='op'>=</span> <span class='cn'>TRUE</span>,
tol <span class='op'>=</span> <span class='cn'>NULL</span>,
rank. <span class='op'>=</span> <span class='cn'>NULL</span>
<span class='op'>)</span></pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@ -324,22 +324,22 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
<span class='co'># \donttest{</span>
<span class='co'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span>)) {
<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>
<span class='co'># calculate the resistance per group first </span>
<span class='kw'>resistance_data</span> <span class='op'>&lt;-</span> <span class='kw'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(order = <span class='fu'><a href='mo_property.html'>mo_order</a></span>(<span class='kw'>mo</span>), <span class='co'># group on anything, like order</span>
genus = <span class='fu'><a href='mo_property.html'>mo_genus</a></span>(<span class='kw'>mo</span>)) <span class='op'>%&gt;%</span> <span class='co'># and genus as we do here</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise_all.html'>summarise_if</a></span>(<span class='kw'>is.rsi</span>, <span class='kw'>resistance</span>) <span class='co'># then get resistance of all drugs</span>
<span class='va'>resistance_data</span> <span class='op'>&lt;-</span> <span class='va'>example_isolates</span> <span class='op'>%&gt;%</span>
<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>
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'>%&gt;%</span> <span class='co'># and genus as we do here</span>
<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>
<span class='co'># now conduct PCA for certain antimicrobial agents</span>
<span class='kw'>pca_result</span> <span class='op'>&lt;-</span> <span class='kw'>resistance_data</span> <span class='op'>%&gt;%</span>
<span class='fu'>pca</span>(<span class='kw'>AMC</span>, <span class='kw'>CXM</span>, <span class='kw'>CTX</span>, <span class='kw'>CAZ</span>, <span class='kw'>GEN</span>, <span class='kw'>TOB</span>, <span class='kw'>TMP</span>, <span class='kw'>SXT</span>)
<span class='va'>pca_result</span> <span class='op'>&lt;-</span> <span class='va'>resistance_data</span> <span class='op'>%&gt;%</span>
<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>
<span class='kw'>pca_result</span>
<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='kw'>pca_result</span>)
<span class='fu'><a href='https://rdrr.io/r/stats/biplot.html'>biplot</a></span>(<span class='kw'>pca_result</span>)
<span class='fu'><a href='ggplot_pca.html'>ggplot_pca</a></span>(<span class='kw'>pca_result</span>) <span class='co'># a new and convenient plot function</span>
}
<span class='va'>pca_result</span>
<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>
<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>
<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>
<span class='op'>}</span>
<span class='co'># }</span>
</pre>
</div>
@ -357,7 +357,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
</div>
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
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