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<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="hidden name"><code>guess_ab_col.Rd</code></div>
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</div>
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<div class="ref-description">
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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 id="ref-usage">
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<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">guess_ab_col</span><span class="op">(</span>
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x <span class="op">=</span> <span class="cn">NULL</span>,
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search_string <span class="op">=</span> <span class="cn">NULL</span>,
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verbose <span class="op">=</span> <span class="cn">FALSE</span>,
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only_rsi_columns <span class="op">=</span> <span class="cn">FALSE</span>
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<span class="op">)</span></code></pre></div>
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</div>
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<div id="arguments">
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<h2>Arguments</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_rsi_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><rsi></code> (see <code><a href="as.rsi.html">as.rsi()</a></code>) on beforehand (defaults to <code>FALSE</code>)</p></dd>
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</dl></div>
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<div id="value">
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<h2>Value</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 id="details">
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<h2>Details</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. <strong>Longer columns names take precedence over shorter column names.</strong></p>
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</div>
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<div id="stable-lifecycle">
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<h2>Stable Lifecycle</h2>
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<p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><br>
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The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
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<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
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</div>
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<div id="read-more-on-our-website-">
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<h2>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>.</p>
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</div>
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<div id="ref-examples">
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<h2>Examples</h2>
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<div class="sourceCode"><pre class="sourceCode r"><code><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>amox <span class="op">=</span> <span class="st">"S"</span>,
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tetr <span class="op">=</span> <span class="st">"R"</span><span class="op">)</span>
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<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>
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<span class="co"># [1] "amox"</span>
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<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>
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<span class="co"># [1] "tetr"</span>
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<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>
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<span class="co"># NOTE: Using column 'tetr' as input for J01AA07 (tetracycline).</span>
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<span class="co"># [1] "tetr"</span>
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<span class="co"># WHONET codes</span>
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<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>AMP_ND10 <span class="op">=</span> <span class="st">"R"</span>,
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AMC_ED20 <span class="op">=</span> <span class="st">"S"</span><span class="op">)</span>
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<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>
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<span class="co"># [1] "AMP_ND10"</span>
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<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>
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<span class="co"># [1] "AMC_ED20"</span>
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<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>
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<span class="co"># [1] "AMC_ED20"</span>
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<span class="co"># Longer names take precendence:</span>
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<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>AMP_ED2 <span class="op">=</span> <span class="st">"S"</span>,
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AMP_ED20 <span class="op">=</span> <span class="st">"S"</span><span class="op">)</span>
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<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>
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<span class="co"># [1] "AMP_ED20"</span>
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</code></pre></div>
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