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<meta property="og:title" content="Create identifier of an isolate — isolate_identifier" />
<meta property="og:description" content="This function will paste the microorganism code with all antimicrobial results into one string for each row in a data set. This is useful to compare isolates, e.g. between institutions or regions, when there is no genotyping available." />
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<h1>Create identifier of an isolate</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/isolate_identifier.R'><code>R/isolate_identifier.R</code></a></small>
<div class="hidden name"><code>isolate_identifier.Rd</code></div>
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<div class="ref-description">
<p>This function will paste the microorganism code with all antimicrobial results into one string for each row in a data set. This is useful to compare isolates, e.g. between institutions or regions, when there is no genotyping available.</p>
</div>
<pre class="usage"><span class='fu'>isolate_identifier</span><span class='op'>(</span><span class='va'>x</span>, col_mo <span class='op'>=</span> <span class='cn'>NULL</span>, cols_ab <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">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>x</th>
<td><p>data with antibiotic columns, such as <code>amox</code>, <code>AMX</code> and <code>AMC</code></p></td>
</tr>
<tr>
<th>col_mo</th>
<td><p>column name of the IDs of the microorganisms (see <code><a href='as.mo.html'>as.mo()</a></code>), defaults to the first column of class <code><a href='as.mo.html'>mo</a></code>. Values will be coerced using <code><a href='as.mo.html'>as.mo()</a></code>.</p></td>
</tr>
<tr>
<th>cols_ab</th>
<td><p>a character vector of column names of <code>x</code>, or (a combination with) an <a href='[ab_class()]'>antibiotic selector function</a>, such as <code><a href='antibiotic_class_selectors.html'>carbapenems()</a></code> and <code>aminoglysides()</code></p></td>
</tr>
</table>
<h2 class="hasAnchor" id="maturing-lifecycle"><a class="anchor" href="#maturing-lifecycle"></a>Maturing lifecycle</h2>
<p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://github.com/msberends/AMR/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
<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>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># automatic selection of microorganism and antibiotics (i.e., all &lt;rsi&gt; columns, see ?as.rsi)</span>
<span class='va'>x</span> <span class='op'>&lt;-</span> <span class='fu'>isolate_identifier</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>)</span>
<span class='co'># ignore microorganism codes, only use antimicrobial results</span>
<span class='va'>x</span> <span class='op'>&lt;-</span> <span class='fu'>isolate_identifier</span><span class='op'>(</span><span class='va'>example_isolates</span>, col_mo <span class='op'>=</span> <span class='cn'>FALSE</span>, cols_ab <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"AMX"</span>, <span class='st'>"TZP"</span>, <span class='st'>"GEN"</span>, <span class='st'>"TOB"</span><span class='op'>)</span><span class='op'>)</span>
<span class='co'># select antibiotics from certain antibiotic classes</span>
<span class='va'>x</span> <span class='op'>&lt;-</span> <span class='fu'>isolate_identifier</span><span class='op'>(</span><span class='va'>example_isolates</span>, cols_ab <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fu'><a href='antibiotic_class_selectors.html'>carbapenems</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='fu'><a href='antibiotic_class_selectors.html'>aminoglycosides</a></span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>
</pre>
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