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Conduct AMR Analysis
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<a class="dropdown-item" href="../reference/antibiogram.html">
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Generate Antibiogram (Trad./Syndromic/WISCA)
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Conduct Principal Component Analysis for AMR
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Get Properties of an Antibiotic Drug
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<main id="main" class="col-md-9"><div class="page-header">
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<img src="../logo.svg" class="logo" alt=""><h1>Guess Antibiotic Column</h1>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/guess_ab_col.R" class="external-link"><code>R/guess_ab_col.R</code></a></small>
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<div class="d-none name"><code>guess_ab_col.Rd</code></div>
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</div>
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<div class="ref-description section level2">
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<p>This tries to find a column name in a data set based on information from the <a href="antibiotics.html">antibiotics</a> data set. Also supports WHONET abbreviations.</p>
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</div>
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<div class="section level2">
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<h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
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<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">guess_ab_col</span><span class="op">(</span></span>
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<span> x <span class="op">=</span> <span class="cn">NULL</span>,</span>
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<span> search_string <span class="op">=</span> <span class="cn">NULL</span>,</span>
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<span> verbose <span class="op">=</span> <span class="cn">FALSE</span>,</span>
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<span> only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span></span>
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<span><span class="op">)</span></span></code></pre></div>
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</div>
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<div class="section level2">
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<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
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<dl><dt>x</dt>
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<dd><p>a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></p></dd>
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<dt>search_string</dt>
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<dd><p>a text to search <code>x</code> for, will be checked with <code><a href="as.ab.html">as.ab()</a></code> if this value is not a column in <code>x</code></p></dd>
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<dt>verbose</dt>
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<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether additional info should be printed</p></dd>
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<dt>only_sir_columns</dt>
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<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether only antibiotic columns must be detected that were transformed to class <code>sir</code> (see <code><a href="as.sir.html">as.sir()</a></code>) on beforehand (default is <code>FALSE</code>)</p></dd>
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</dl></div>
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<div class="section level2">
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<h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
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<p>A column name of <code>x</code>, or <code>NULL</code> when no result is found.</p>
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</div>
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<div class="section level2">
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<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
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<p>You can look for an antibiotic (trade) name or abbreviation and it will search <code>x</code> and the <a href="antibiotics.html">antibiotics</a> data set for any column containing a name or code of that antibiotic.</p>
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</div>
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<div class="section level2">
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<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
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<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">df</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
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<span class="r-in"><span> amox <span class="op">=</span> <span class="st">"S"</span>,</span></span>
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<span class="r-in"><span> tetr <span class="op">=</span> <span class="st">"R"</span></span></span>
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<span class="r-in"><span><span class="op">)</span></span></span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="fu">guess_ab_col</span><span class="op">(</span><span class="va">df</span>, <span class="st">"amoxicillin"</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "amox"</span>
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<span class="r-in"><span><span class="fu">guess_ab_col</span><span class="op">(</span><span class="va">df</span>, <span class="st">"J01AA07"</span><span class="op">)</span> <span class="co"># ATC code of tetracycline</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "tetr"</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="fu">guess_ab_col</span><span class="op">(</span><span class="va">df</span>, <span class="st">"J01AA07"</span>, verbose <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> Auto-guessing columns suitable for analysis</span>
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<span class="r-msg co"><span class="r-pr">#></span> ...</span>
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<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
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<span class="r-msg co"><span class="r-pr">#></span> ℹ Using column 'amox' as input for AMX (amoxicillin).</span>
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<span class="r-msg co"><span class="r-pr">#></span> ℹ Using column 'tetr' as input for TCY (tetracycline).</span>
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<span class="r-msg co"><span class="r-pr">#></span> ℹ Using column 'tetr' as input for J01AA07 (tetracycline).</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "tetr"</span>
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<span class="r-in"><span><span class="co"># NOTE: Using column 'tetr' as input for J01AA07 (tetracycline).</span></span></span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="co"># WHONET codes</span></span></span>
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<span class="r-in"><span><span class="va">df</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
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<span class="r-in"><span> AMP_ND10 <span class="op">=</span> <span class="st">"R"</span>,</span></span>
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<span class="r-in"><span> AMC_ED20 <span class="op">=</span> <span class="st">"S"</span></span></span>
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<span class="r-in"><span><span class="op">)</span></span></span>
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<span class="r-in"><span><span class="fu">guess_ab_col</span><span class="op">(</span><span class="va">df</span>, <span class="st">"ampicillin"</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "AMP_ND10"</span>
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<span class="r-in"><span><span class="fu">guess_ab_col</span><span class="op">(</span><span class="va">df</span>, <span class="st">"J01CR02"</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "AMC_ED20"</span>
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<span class="r-in"><span><span class="fu">guess_ab_col</span><span class="op">(</span><span class="va">df</span>, <span class="fu"><a href="as.ab.html">as.ab</a></span><span class="op">(</span><span class="st">"augmentin"</span><span class="op">)</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "AMC_ED20"</span>
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</code></pre></div>
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<p></p><p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p>
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