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(v1.5.0.9006) major documentation update

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dr. M.S. (Matthijs) Berends
2021-01-18 16:57:56 +01:00
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docs/reference/pca.html
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</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">1.5.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9006</span>
</span>
</div>
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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>
<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>
<h2 class="hasAnchor" id="maturing-lifecycle"><a class="anchor" href="#maturing-lifecycle"></a>Maturing lifecycle</h2>
<h2 class="hasAnchor" id="maturing-lifecycle"><a class="anchor" href="#maturing-lifecycle"></a>Maturing Lifecycle</h2>
<p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
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. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://github.com/msberends/AMR/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
<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>
<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 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>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># `example_isolates` is a dataset available in the AMR package.</span>