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<h1>Create Custom EUCAST Rules</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/custom_eucast_rules.R'><code>R/custom_eucast_rules.R</code></a></small>
<div class="hidden name"><code>custom_eucast_rules.Rd</code></div>
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<p>Create Custom EUCAST Rules</p>
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<pre class="usage"><span class='fu'>custom_eucast_rules</span><span class='op'>(</span><span class='va'>...</span><span class='op'>)</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>...</th>
<td><p>rules in formula notation, see <em>Examples</em></p></td>
</tr>
</table>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>This documentation page will be updated shortly. <strong>This function is experimental.</strong></p>
<h2 class="hasAnchor" id="how-it-works"><a class="anchor" href="#how-it-works"></a>How it works</h2>
<p>..</p>
<p>It is also possible to define antibiotic groups instead of single antibiotics. The following groups are allowed (case-insensitive): <code>aminoglycosides</code>, <code>aminopenicillins</code>, <code>betalactams</code>, <code>carbapenems</code>, <code>cephalosporins</code>, <code>cephalosporins_1st</code>, <code>cephalosporins_2nd</code>, <code>cephalosporins_3rd</code>, <code>cephalosporins_except_caz</code>, <code>fluoroquinolones</code>, <code>glycopeptides</code>, <code>glycopeptides_except_lipo</code>, <code>lincosamides</code>, <code>lipoglycopeptides</code>, <code>macrolides</code>, <code>oxazolidinones</code>, <code>penicillins</code>, <code>polymyxins</code>, <code>streptogramins</code>, <code>tetracyclines</code>, <code>tetracyclines_except_tgc</code> and <code>ureidopenicillins</code>.</p>
<h2 class="hasAnchor" id="experimental-lifecycle"><a class="anchor" href="#experimental-lifecycle"></a>Experimental Lifecycle</h2>
<p><img src='figures/lifecycle_experimental.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>experimental</strong>. An experimental function is in early stages of development. The unlying code might be changing frequently. Experimental functions might be removed without deprecation, so you are generally best off waiting until a function is more mature before you use it in production code. Experimental functions are only available in development versions of this <code>AMR</code> package and will thus not be included in releases that are submitted to CRAN, since such functions have not yet matured enough.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='va'>x</span> <span class='op'>&lt;-</span> <span class='fu'>custom_eucast_rules</span><span class='op'>(</span><span class='va'>AMC</span> <span class='op'>==</span> <span class='st'>"R"</span> <span class='op'>&amp;</span> <span class='va'>genus</span> <span class='op'>==</span> <span class='st'>"Klebsiella"</span> <span class='op'>~</span> <span class='va'>aminopenicillins</span> <span class='op'>==</span> <span class='st'>"R"</span>,
<span class='va'>AMC</span> <span class='op'>==</span> <span class='st'>"I"</span> <span class='op'>&amp;</span> <span class='va'>genus</span> <span class='op'>==</span> <span class='st'>"Klebsiella"</span> <span class='op'>~</span> <span class='va'>aminopenicillins</span> <span class='op'>==</span> <span class='st'>"I"</span><span class='op'>)</span>
<span class='fu'><a href='eucast_rules.html'>eucast_rules</a></span><span class='op'>(</span><span class='va'>example_isolates</span>,
rules <span class='op'>=</span> <span class='st'>"custom"</span>,
custom_rules <span class='op'>=</span> <span class='va'>x</span>,
info <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<span class='co'># combine rule sets</span>
<span class='va'>x2</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='va'>x</span>,
<span class='fu'>custom_eucast_rules</span><span class='op'>(</span><span class='va'>TZP</span> <span class='op'>==</span> <span class='st'>"R"</span> <span class='op'>~</span> <span class='va'>carbapenems</span> <span class='op'>==</span> <span class='st'>"R"</span><span class='op'>)</span><span class='op'>)</span>
<span class='va'>x2</span>
</pre>
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