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(v1.7.1.9022) rely on vctrs for ab selectors

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dr. M.S. (Matthijs) Berends
2021-07-23 21:42:11 +02:00
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docs/reference/antibiotic_class_selectors.html
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@ -55,6 +55,8 @@
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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</head>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@ -82,7 +90,7 @@
</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">1.7.1.9019</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9022</span>
</span>
</div>
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<p>These functions allow for filtering rows and selecting columns based on antibiotic test results that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations.</p>
</div>
<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'>FALSE</span>, only_treatable <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><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'>FALSE</span>, only_treatable <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
<span class='fu'>aminoglycosides</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>, only_treatable <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
@ -286,7 +294,7 @@
<span class='fu'>tetracyclines</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<span class='fu'>ureidopenicillins</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span></pre>
<span class='fu'>ureidopenicillins</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span></code></pre></div>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@ -308,7 +316,7 @@
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>These functions can be used in data set calls for selecting columns and filtering rows. They are heavily inspired by the <a href='https://tidyselect.r-lib.org/reference/language.html'>Tidyverse selection helpers</a> such as <code><a href='https://tidyselect.r-lib.org/reference/everything.html'>everything()</a></code>, but also work in base <span style="R">R</span> and not only in <code>dplyr</code> verbs. Nonetheless, they are very convenient to use with <code>dplyr</code> functions such as <code><a href='https://dplyr.tidyverse.org/reference/select.html'>select()</a></code>, <code><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter()</a></code> and <code><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise()</a></code>, see <em>Examples</em>.</p>
<p>All columns in the data in which these functions are called will be searched for known antibiotic names, abbreviations, brand names, and codes (ATC, EARS-Net, WHO, etc.) in the <a href='antibiotics.html'>antibiotics</a> data set. This means that a selector such as <code>aminoglycosides()</code> will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc. Use the <code>ab_class()</code> function to filter/select on a manually defined antibiotic class.</p>
<p>All columns in the data in which these functions are called will be searched for known antibiotic names, abbreviations, brand names, and codes (ATC, EARS-Net, WHO, etc.) according to the <a href='antibiotics.html'>antibiotics</a> data set. This means that a selector such as <code>aminoglycosides()</code> will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc. Use the <code>ab_class()</code> function to filter/select on a manually defined antibiotic class.</p>
<h2 class="hasAnchor" id="full-list-of-supported-agents"><a class="anchor" href="#full-list-of-supported-agents"></a>Full list of supported agents</h2>
@ -357,7 +365,7 @@ 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 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>.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># `example_isolates` is a data set available in the AMR package.</span>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='co'># `example_isolates` is a data set available in the AMR package.</span>
<span class='co'># See ?example_isolates.</span>
<span class='co'># base R ------------------------------------------------------------------</span>
@ -436,7 +444,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='va'>example_isolates</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span><span class='op'>(</span><span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span><span class='op'>(</span><span class='fu'>carbapenems</span><span class='op'>(</span><span class='op'>)</span>, <span class='op'>~</span><span class='va'>.x</span> <span class='op'>==</span> <span class='st'>"R"</span><span class='op'>)</span><span class='op'>)</span>
<span class='op'>}</span>
<span class='co'># }</span>
</pre>
</code></pre></div>
</div>
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@ -448,11 +456,11 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
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@ -461,6 +469,8 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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