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(v1.5.0.9014) only_rsi_columns, is.rsi.eligible improvement

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dr. M.S. (Matthijs) Berends
2021-02-02 23:57:35 +01:00
parent 20d638c193
commit 2eca8c3f01
246 changed files with 1171 additions and 965 deletions
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34
docs/reference/antibiotic_class_selectors.html
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@ -244,33 +244,33 @@
</strong></p>
</div>
<pre class="usage"><span class='fu'>ab_class</span><span class='op'>(</span><span class='va'>ab_class</span><span class='op'>)</span>
<pre class="usage"><span class='fu'>ab_class</span><span class='op'>(</span><span class='va'>ab_class</span>, only_rsi_columns <span class='op'>=</span> <span class='cn'>NULL</span><span class='op'>)</span>
<span class='fu'>aminoglycosides</span><span class='op'>(</span><span class='op'>)</span>
<span class='fu'>aminoglycosides</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>NULL</span><span class='op'>)</span>
<span class='fu'>carbapenems</span><span class='op'>(</span><span class='op'>)</span>
<span class='fu'>carbapenems</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>NULL</span><span class='op'>)</span>
<span class='fu'>cephalosporins</span><span class='op'>(</span><span class='op'>)</span>
<span class='fu'>cephalosporins</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>NULL</span><span class='op'>)</span>
<span class='fu'>cephalosporins_1st</span><span class='op'>(</span><span class='op'>)</span>
<span class='fu'>cephalosporins_1st</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>NULL</span><span class='op'>)</span>
<span class='fu'>cephalosporins_2nd</span><span class='op'>(</span><span class='op'>)</span>
<span class='fu'>cephalosporins_2nd</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>NULL</span><span class='op'>)</span>
<span class='fu'>cephalosporins_3rd</span><span class='op'>(</span><span class='op'>)</span>
<span class='fu'>cephalosporins_3rd</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>NULL</span><span class='op'>)</span>
<span class='fu'>cephalosporins_4th</span><span class='op'>(</span><span class='op'>)</span>
<span class='fu'>cephalosporins_4th</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>NULL</span><span class='op'>)</span>
<span class='fu'>cephalosporins_5th</span><span class='op'>(</span><span class='op'>)</span>
<span class='fu'>cephalosporins_5th</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>NULL</span><span class='op'>)</span>
<span class='fu'>fluoroquinolones</span><span class='op'>(</span><span class='op'>)</span>
<span class='fu'>fluoroquinolones</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>NULL</span><span class='op'>)</span>
<span class='fu'>glycopeptides</span><span class='op'>(</span><span class='op'>)</span>
<span class='fu'>glycopeptides</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>NULL</span><span class='op'>)</span>
<span class='fu'>macrolides</span><span class='op'>(</span><span class='op'>)</span>
<span class='fu'>macrolides</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>NULL</span><span class='op'>)</span>
<span class='fu'>penicillins</span><span class='op'>(</span><span class='op'>)</span>
<span class='fu'>penicillins</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>NULL</span><span class='op'>)</span>
<span class='fu'>tetracyclines</span><span class='op'>(</span><span class='op'>)</span></pre>
<span class='fu'>tetracyclines</span><span class='op'>(</span>only_rsi_columns <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">
@ -279,6 +279,10 @@
<th>ab_class</th>
<td><p>an antimicrobial class, like <code>"carbapenems"</code>. The columns <code>group</code>, <code>atc_group1</code> and <code>atc_group2</code> of the <a href='antibiotics.html'>antibiotics</a> data set will be searched (case-insensitive) for this value.</p></td>
</tr>
<tr>
<th>only_rsi_columns</th>
<td><p>a logical to indicate whether only columns of class <a href='[rsi]'><code>&lt;rsi&gt;</code></a> must be selected. If set to <code>NULL</code> (default), it will be <code>TRUE</code> if any column of the data was <a href='[rsi]'>transformed to class <code>&lt;rsi&gt;</code></a> on beforehand, and <code>FALSE</code> otherwise.</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
@ -302,7 +306,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<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>
<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 data 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="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p><code><a href='filter_ab_class.html'>filter_ab_class()</a></code> for the <code><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter()</a></code> equivalent.</p></div>