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(v1.3.0.9001) website update

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dr. M.S. (Matthijs) Berends
2020-08-10 12:46:03 +02:00
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commit 7d16bec21f
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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">1.3.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9001</span>
</span>
</div>
@ -236,13 +236,13 @@
</div>
<pre class="usage"><span class='fu'>pca</span>(
<span class='no'>x</span>,
<span class='no'>...</span>,
<span class='kw'>retx</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>center</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>scale.</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>tol</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>rank.</span> <span class='kw'>=</span> <span class='kw'>NULL</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>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
@ -315,22 +315,22 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
<pre class="examples"><span class='co'># `example_isolates` is a dataset available in the AMR package.</span>
<span class='co'># See ?example_isolates.</span>
<span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
<span class='co'>if</span> (<span class='fl'>FALSE</span>) {
<span class='co'># calculate the resistance per group first</span>
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
<span class='no'>resistance_data</span> <span class='kw'>&lt;-</span> <span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<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>
<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'>%&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='no'>is.rsi</span>, <span class='no'>resistance</span>) <span class='co'># then get resistance of all drugs</span>
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='kw'><a href='https://dplyr.tidyverse.org'>dplyr</a></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='co'># now conduct PCA for certain antimicrobial agents</span>
<span class='no'>pca_result</span> <span class='kw'>&lt;-</span> <span class='no'>resistance_data</span> <span class='kw'>%&gt;%</span>
<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>)
<span class='no'>pca_result</span>
<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>pca_result</span>)
<span class='fu'><a href='https://rdrr.io/r/stats/biplot.html'>biplot</a></span>(<span class='no'>pca_result</span>)
<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>
<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='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>
}</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
@ -347,7 +347,7 @@ 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>
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