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(v1.0.1.9002) PCA unit tests

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dr. M.S. (Matthijs) Berends
2020-03-08 11:18:59 +01:00
parent 9fc858f208
commit 77656a676c
20 changed files with 182 additions and 135 deletions
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docs/reference/ggplot_pca.html
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@ -79,7 +79,7 @@
</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">1.0.1.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9002</span>
</span>
</div>
@ -236,14 +236,15 @@
<span class='no'>x</span>,
<span class='kw'>choices</span> <span class='kw'>=</span> <span class='fl'>1</span>:<span class='fl'>2</span>,
<span class='kw'>scale</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>pc.biplot</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>labels</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>labels_textsize</span> <span class='kw'>=</span> <span class='fl'>3</span>,
<span class='kw'>labels_text_placement</span> <span class='kw'>=</span> <span class='fl'>1.5</span>,
<span class='kw'>groups</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>ellipse</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>ellipse</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>ellipse_prob</span> <span class='kw'>=</span> <span class='fl'>0.68</span>,
<span class='kw'>ellipse_size</span> <span class='kw'>=</span> <span class='fl'>0.5</span>,
<span class='kw'>ellipse_alpha</span> <span class='kw'>=</span> <span class='fl'>0.25</span>,
<span class='kw'>ellipse_alpha</span> <span class='kw'>=</span> <span class='fl'>0.5</span>,
<span class='kw'>points_size</span> <span class='kw'>=</span> <span class='fl'>2</span>,
<span class='kw'>points_alpha</span> <span class='kw'>=</span> <span class='fl'>0.25</span>,
<span class='kw'>arrows</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
@ -275,6 +276,14 @@
<code><a href='https://rdrr.io/r/stats/princomp.html'>princomp</a></code>. Normally <code>0 &lt;= scale &lt;= 1</code>, and a warning
will be issued if the specified <code>scale</code> is outside this range.</p></td>
</tr>
<tr>
<th>pc.biplot</th>
<td><p>If true, use what Gabriel (1971) refers to as a "principal component
biplot", with <code>lambda = 1</code> and observations scaled up by sqrt(n) and
variables scaled down by sqrt(n). Then inner products between
variables approximate covariances and distances between observations
approximate Mahalanobis distance.</p></td>
</tr>
<tr>
<th>labels</th>
<td><p>an optional vector of labels for the observations. If set, the labels will be placed below their respective points. When using the <code><a href='pca.html'>pca()</a></code> function as input for <code>x</code>, this will be determined automatically based on the attribute <code>non_numeric_cols</code>, see <code><a href='pca.html'>pca()</a></code>.</p></td>
@ -352,13 +361,13 @@
<li><p>Rewritten code to remove the dependency on packages <code>plyr</code>, <code>scales</code> and <code>grid</code></p></li>
<li><p>Parametrised more options, like arrow and ellipse settings</p></li>
<li><p>Added total amount of explained variance as a caption in the plot</p></li>
<li><p>Cleaned all syntax based on the <code>lintr</code> package</p></li>
<li><p>Cleaned all syntax based on the <code>lintr</code> package and added integrity checks</p></li>
<li><p>Updated documentation</p></li>
</ol>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>The default colours for labels and points is set with <code>scale_colour_viridis_d()</code>, but these can be changed by adding another scale for colour, like <code>scale_colour_brewer()</code>.</p>
<p>The colours for labels and points can be changed by adding another scale layer for colour, like <code>scale_colour_viridis_d()</code> or <code>scale_colour_brewer()</code>.</p>
<h2 class="hasAnchor" id="maturing-lifecycle"><a class="anchor" href="#maturing-lifecycle"></a>Maturing lifecycle</h2>