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<h1>Create Identifier of an Isolate</h1>
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<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>
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<div class="hidden name"><code>isolate_identifier.Rd</code></div>
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</div>
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<div class="ref-description">
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<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>
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</div>
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<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>
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<span class='co'># S3 method for isolate_identifier</span>
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<span class='fu'><a href='https://rdrr.io/r/base/all.equal.html'>all.equal</a></span><span class='op'>(</span><span class='va'>target</span>, <span class='va'>current</span>, ignore_empty_results <span class='op'>=</span> <span class='cn'>TRUE</span>, <span class='va'>...</span><span class='op'>)</span></pre>
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<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
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<table class="ref-arguments">
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<colgroup><col class="name" /><col class="desc" /></colgroup>
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<tr>
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<th>x</th>
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<td><p>data with antibiotic columns, such as <code>amox</code>, <code>AMX</code> and <code>AMC</code></p></td>
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</tr>
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<tr>
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<th>col_mo</th>
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<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>
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</tr>
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<tr>
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<th>cols_ab</th>
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<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><a href='antibiotic_class_selectors.html'>aminoglycosides()</a></code></p></td>
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</tr>
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<tr>
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<th>target</th>
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<td><p><span style="R">R</span> object.</p></td>
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</tr>
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<tr>
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<th>current</th>
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<td><p>other <span style="R">R</span> object, to be compared with <code>target</code>.</p></td>
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</tr>
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<tr>
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<th>ignore_empty_results</th>
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<td><p>a logical to indicate whether empty results must be ignored, so that only values R, S and I will be compared</p></td>
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</tr>
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<tr>
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<th>...</th>
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<td><p>column name of an antibiotic, see section <em>Antibiotics</em> below</p></td>
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</tr>
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</table>
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<h2 class="hasAnchor" id="experimental-lifecycle"><a class="anchor" href="#experimental-lifecycle"></a>Experimental Lifecycle</h2>
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<p><img src='figures/lifecycle_experimental.svg' style=margin-bottom:5px /> <br />
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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>
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<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>
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<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>. 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>
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<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
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<pre class="examples"><span class='co'># automatic selection of microorganism and antibiotics (i.e., all <rsi> columns, see ?as.rsi)</span>
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<span class='va'>x</span> <span class='op'><-</span> <span class='fu'>isolate_identifier</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>)</span>
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<span class='co'># ignore microorganism codes, only use antimicrobial results</span>
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<span class='va'>x</span> <span class='op'><-</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>
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<span class='co'># select antibiotics from certain antibiotic classes</span>
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<span class='va'>x</span> <span class='op'><-</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>
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</pre>
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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>
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