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(v1.2.0.9001) filter_ab_class() update

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dr. M.S. (Matthijs) Berends
2020-06-03 11:48:00 +02:00
parent 02d07b9fb3
commit 5dc4c96b7d
18 changed files with 159 additions and 77 deletions
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13
docs/reference/filter_ab_class.html
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@ -49,7 +49,7 @@
<script src="../extra.js"></script>
<meta property="og:title" content="Filter isolates on result in antimicrobial class — filter_ab_class" />
<meta property="og:description" content="Filter isolates on results in specific antimicrobial classes. This makes it easy to filter on isolates that were tested for e.g. any aminoglycoside." />
<meta property="og:description" content="Filter isolates on results in specific antimicrobial classes. This makes it easy to filter on isolates that were tested for e.g. any aminoglycoside, or to filter on carbapenem-resistant isolates without the need to specify the drugs." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.svg" />
@ -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</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9001</span>
</span>
</div>
@ -232,7 +232,7 @@
</div>
<div class="ref-description">
<p>Filter isolates on results in specific antimicrobial classes. This makes it easy to filter on isolates that were tested for e.g. any aminoglycoside.</p>
<p>Filter isolates on results in specific antimicrobial classes. This makes it easy to filter on isolates that were tested for e.g. any aminoglycoside, or to filter on carbapenem-resistant isolates without the need to specify the drugs.</p>
</div>
<pre class="usage"><span class='fu'>filter_ab_class</span>(<span class='no'>x</span>, <span class='no'>ab_class</span>, <span class='kw'>result</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>scope</span> <span class='kw'>=</span> <span class='st'>"any"</span>, <span class='no'>...</span>)
@ -259,6 +259,8 @@
<span class='fu'>filter_macrolides</span>(<span class='no'>x</span>, <span class='kw'>result</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>scope</span> <span class='kw'>=</span> <span class='st'>"any"</span>, <span class='no'>...</span>)
<span class='fu'>filter_penicillins</span>(<span class='no'>x</span>, <span class='kw'>result</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>scope</span> <span class='kw'>=</span> <span class='st'>"any"</span>, <span class='no'>...</span>)
<span class='fu'>filter_tetracyclines</span>(<span class='no'>x</span>, <span class='kw'>result</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>scope</span> <span class='kw'>=</span> <span class='st'>"any"</span>, <span class='no'>...</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
@ -288,7 +290,7 @@
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>The <code>group</code> column in <a href='antibiotics.html'>antibiotics</a> data set will be searched for <code>ab_class</code> (case-insensitive). If no results are found, the <code>atc_group1</code> and <code>atc_group2</code> columns will be searched. Next, <code>x</code> will be checked for column names with a value in any abbreviations, codes or official names found in the <a href='antibiotics.html'>antibiotics</a> data set.</p>
<p>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 for the input given in <code>ab_class</code> (case-insensitive). Next, <code>x</code> will be checked for column names with a value in any abbreviation, code or official name found in the <a href='antibiotics.html'>antibiotics</a> data set.</p>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
@ -302,6 +304,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>dplyr</span>)
<span class='co'># filter on isolates that have any result for any aminoglycoside</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'>filter_ab_class</span>(<span class='st'>"aminoglycoside"</span>)
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'>filter_aminoglycosides</span>()
<span class='co'># this is essentially the same as (but without determination of column names):</span>
@ -311,7 +314,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='co'># filter on isolates that show resistance to ANY aminoglycoside</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'>filter_aminoglycosides</span>(<span class='st'>"R"</span>)
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'>filter_aminoglycosides</span>(<span class='st'>"R"</span>, <span class='st'>"any"</span>)
<span class='co'># filter on isolates that show resistance to ALL aminoglycosides</span>
<span class='no'>example_isolates</span> <span class='kw'>%&gt;%</span> <span class='fu'>filter_aminoglycosides</span>(<span class='st'>"R"</span>, <span class='st'>"all"</span>)

4
docs/reference/index.html
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@ -81,7 +81,7 @@
</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">1.2.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9001</span>
</span>
</div>
@ -421,7 +421,7 @@
</tr><tr>
<td>
<p><code><a href="filter_ab_class.html">filter_ab_class()</a></code> <code><a href="filter_ab_class.html">filter_aminoglycosides()</a></code> <code><a href="filter_ab_class.html">filter_carbapenems()</a></code> <code><a href="filter_ab_class.html">filter_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_1st_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_2nd_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_3rd_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_4th_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_5th_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_fluoroquinolones()</a></code> <code><a href="filter_ab_class.html">filter_glycopeptides()</a></code> <code><a href="filter_ab_class.html">filter_macrolides()</a></code> <code><a href="filter_ab_class.html">filter_tetracyclines()</a></code> </p>
<p><code><a href="filter_ab_class.html">filter_ab_class()</a></code> <code><a href="filter_ab_class.html">filter_aminoglycosides()</a></code> <code><a href="filter_ab_class.html">filter_carbapenems()</a></code> <code><a href="filter_ab_class.html">filter_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_1st_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_2nd_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_3rd_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_4th_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_5th_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_fluoroquinolones()</a></code> <code><a href="filter_ab_class.html">filter_glycopeptides()</a></code> <code><a href="filter_ab_class.html">filter_macrolides()</a></code> <code><a href="filter_ab_class.html">filter_penicillins()</a></code> <code><a href="filter_ab_class.html">filter_tetracyclines()</a></code> </p>
</td>
<td><p>Filter isolates on result in antimicrobial class</p></td>
</tr><tr>