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<h1>Name of an antibiotic</h1>
<div class="hidden name"><code>abname.Rd</code></div>
</div>
<div class="ref-description">
<p>Convert antibiotic codes to a (trivial) antibiotic name or ATC code, or vice versa. This uses the data from <code><a href='antibiotics.html'>antibiotics</a></code>.</p>
</div>
<pre class="usage"><span class='fu'>abname</span>(<span class='no'>abcode</span>, <span class='kw'>from</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"guess"</span>, <span class='st'>"atc"</span>, <span class='st'>"certe"</span>, <span class='st'>"umcg"</span>),
<span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"official"</span>, <span class='kw'>textbetween</span> <span class='kw'>=</span> <span class='st'>" + "</span>, <span class='kw'>tolower</span> <span class='kw'>=</span> <span class='fl'>FALSE</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>abcode</th>
<td><p>a code or name, like <code>"AMOX"</code>, <code>"AMCL"</code> or <code>"J01CA04"</code></p></td>
</tr>
<tr>
<th>from, to</th>
<td><p>type to transform from and to. See <code><a href='antibiotics.html'>antibiotics</a></code> for its column names. WIth <code>from = "guess"</code> the from will be guessed from <code>"atc"</code>, <code>"certe"</code> and <code>"umcg"</code>. When using <code>to = "atc"</code>, the ATC code will be searched using <code><a href='as.atc.html'>as.atc</a></code>.</p></td>
</tr>
<tr>
<th>textbetween</th>
<td><p>text to put between multiple returned texts</p></td>
</tr>
<tr>
<th>tolower</th>
<td><p>return output as lower case with function <code><a href='https://www.rdocumentation.org/packages/base/topics/chartr'>tolower</a></code>.</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
<p><code><a href='antibiotics.html'>antibiotics</a></code></p>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p><strong>The <code><a href='ab_property.html'>ab_property</a></code> functions are faster and more concise</strong>, but do not support concatenated strings, like <code>abname("AMCL+GENT"</code>.</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><img src='figures/logo.png' height=40px style=margin-bottom:5px /> <br />
On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a omprehensive tutorial</a> about how to conduct AMR analysis and find <a href='https://msberends.gitlab.io/AMR/reference'>the complete documentation of all functions</a>, which reads a lot easier than in R.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># NOT RUN {</span>
<span class='fu'>abname</span>(<span class='st'>"AMCL"</span>)
<span class='co'># "Amoxicillin and beta-lactamase inhibitor"</span>
<span class='co'># It is quite flexible at default (having `from = "guess"`)</span>
<span class='fu'>abname</span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"amox"</span>, <span class='st'>"J01CA04"</span>, <span class='st'>"Trimox"</span>, <span class='st'>"dispermox"</span>, <span class='st'>"Amoxil"</span>))
<span class='co'># "Amoxicillin" "Amoxicillin" "Amoxicillin" "Amoxicillin" "Amoxicillin"</span>
<span class='co'># Multiple antibiotics can be combined with "+".</span>
<span class='co'># The second antibiotic will be set to lower case when `tolower` was not set:</span>
<span class='fu'>abname</span>(<span class='st'>"AMCL+GENT"</span>, <span class='kw'>textbetween</span> <span class='kw'>=</span> <span class='st'>"/"</span>)
<span class='co'># "amoxicillin and enzyme inhibitor/gentamicin"</span>
<span class='fu'>abname</span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"AMCL"</span>, <span class='st'>"GENT"</span>))
<span class='co'># "Amoxicillin and beta-lactamase inhibitor" "Gentamicin"</span>
<span class='fu'>abname</span>(<span class='st'>"AMCL"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"trivial_nl"</span>)
<span class='co'># "Amoxicilline/clavulaanzuur"</span>
<span class='fu'>abname</span>(<span class='st'>"AMCL"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"atc"</span>)
<span class='co'># "J01CR02"</span>
<span class='co'># specific codes for University Medical Center Groningen (UMCG):</span>
<span class='fu'>abname</span>(<span class='st'>"J01CR02"</span>, <span class='kw'>from</span> <span class='kw'>=</span> <span class='st'>"atc"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"umcg"</span>)
<span class='co'># "AMCL"</span>
<span class='co'># specific codes for Certe:</span>
<span class='fu'>abname</span>(<span class='st'>"J01CR02"</span>, <span class='kw'>from</span> <span class='kw'>=</span> <span class='st'>"atc"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"certe"</span>)
<span class='co'># "amcl"</span>
<span class='co'># }</span></pre>
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<h2>Contents</h2>
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<li><a href="#arguments">Arguments</a></li>
<li><a href="#source">Source</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#examples">Examples</a></li>
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