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(v1.2.0.9008) ab_class improvement

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dr. M.S. (Matthijs) Berends
2020-06-17 15:14:37 +02:00
parent c4d7412f36
commit ac12392da3
37 changed files with 619 additions and 362 deletions
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27
docs/reference/antibiotic_class_selectors.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">1.2.0.9007</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9008</span>
</span>
</div>
@ -235,7 +235,9 @@
<p>Use these selection helpers inside any function that allows <a href='https://tidyselect.r-lib.org/reference/language.html'>Tidyverse selections</a>, like <code><a href='https://dplyr.tidyverse.org/reference/select.html'>dplyr::select()</a></code> or <code><a href='https://tidyr.tidyverse.org/reference/pivot_longer.html'>tidyr::pivot_longer()</a></code>. They help to select the columns of antibiotics 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'>aminoglycosides</span>()
<pre class="usage"><span class='fu'>ab_class</span>(<span class='no'>ab_class</span>)
<span class='fu'>aminoglycosides</span>()
<span class='fu'>carbapenems</span>()
@ -261,6 +263,14 @@
<span class='fu'>tetracyclines</span>()</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<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>
</table>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
@ -277,11 +287,22 @@
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='fu'>carbapenems</span>())
<span class='co'># this will select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB':</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>mo</span>, <span class='fu'>aminoglycosides</span>())
<span class='co'># this will select columns 'mo' and all antimycobacterial drugs ('RIF'):</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>mo</span>, <span class='fu'>ab_class</span>(<span class='st'>"mycobact"</span>))
<span class='co'># get bug/drug combinations for only macrolides in Gram-positives:</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='fu'><a href='mo_property.html'>mo_gramstain</a></span>(<span class='no'>mo</span>) <span class='kw'>%like%</span> <span class='st'>"pos"</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>mo</span>, <span class='fu'>macrolides</span>()) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='bug_drug_combinations.html'>bug_drug_combinations</a></span>() <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://rdrr.io/r/base/format.html'>format</a></span>()
<span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(<span class='kw'>irrelevant</span> <span class='kw'>=</span> <span class='st'>"value"</span>,
<span class='kw'>J01CA01</span> <span class='kw'>=</span> <span class='st'>"S"</span>) <span class='kw'>%&gt;%</span> <span class='co'># ATC code of ampicillin</span>