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Built site for AMR: 1.8.1.9046@fbd5d32

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2022-08-29 08:05:13 +00:00
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21
reference/guess_ab_col.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9046</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -167,7 +167,7 @@
</div>
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<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>
<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>
</div>
<div class="section level2">
@ -179,10 +179,8 @@
<span class="r-in"><span></span></span>
<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>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "amox"</span>
<span class="r-in"><span><span class="co"># [1] "amox"</span></span></span>
<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>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "tetr"</span>
<span class="r-in"><span><span class="co"># [1] "tetr"</span></span></span>
<span class="r-in"><span></span></span>
<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>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Auto-guessing columns suitable for analysis</span>
@ -193,7 +191,6 @@
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Using column 'tetr' as input for J01AA07 (tetracycline).</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "tetr"</span>
<span class="r-in"><span><span class="co"># NOTE: Using column 'tetr' as input for J01AA07 (tetracycline).</span></span></span>
<span class="r-in"><span><span class="co"># [1] "tetr"</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># WHONET codes</span></span></span>
<span class="r-in"><span><span class="va">df</span> <span class="op">&lt;-</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>
@ -202,22 +199,10 @@
<span class="r-in"><span><span class="op">)</span></span></span>
<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>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "AMP_ND10"</span>
<span class="r-in"><span><span class="co"># [1] "AMP_ND10"</span></span></span>
<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>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "AMC_ED20"</span>
<span class="r-in"><span><span class="co"># [1] "AMC_ED20"</span></span></span>
<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>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "AMC_ED20"</span>
<span class="r-in"><span><span class="co"># [1] "AMC_ED20"</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># Longer names take precendence:</span></span></span>
<span class="r-in"><span><span class="va">df</span> <span class="op">&lt;-</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>
<span class="r-in"><span> AMP_ED2 <span class="op">=</span> <span class="st">"S"</span>,</span></span>
<span class="r-in"><span> AMP_ED20 <span class="op">=</span> <span class="st">"S"</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<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>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "AMP_ED2"</span>
<span class="r-in"><span><span class="co"># [1] "AMP_ED20"</span></span></span>
</code></pre></div>
</div>
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
@ -229,7 +214,7 @@
</div>
<div class="pkgdown-footer-right">
<p></p><p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_rug.png" style="max-width: 200px;"></a></p>
<p></p><p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_rug.svg" style="max-width: 200px;"></a></p>
</div>
</footer></div>