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<h1>Property of an antibiotic</h1>
<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/ab_property.R'><code>R/ab_property.R</code></a></small>
<div class="hidden name"><code>ab_property.Rd</code></div>
</div>
<div class="ref-description">
<p>Use these functions to return a specific property of an antibiotic from the <a href='antibiotics.html'>antibiotics</a> data set. All input values will be evaluated internally with <code><a href='as.ab.html'>as.ab()</a></code>.</p>
</div>
<pre class="usage"><span class='fu'>ab_name</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>tolower</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)
<span class='fu'>ab_atc</span>(<span class='no'>x</span>, <span class='no'>...</span>)
<span class='fu'>ab_cid</span>(<span class='no'>x</span>, <span class='no'>...</span>)
<span class='fu'>ab_synonyms</span>(<span class='no'>x</span>, <span class='no'>...</span>)
<span class='fu'>ab_tradenames</span>(<span class='no'>x</span>, <span class='no'>...</span>)
<span class='fu'>ab_group</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
<span class='fu'>ab_atc_group1</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
<span class='fu'>ab_atc_group2</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
<span class='fu'>ab_loinc</span>(<span class='no'>x</span>, <span class='no'>...</span>)
<span class='fu'>ab_ddd</span>(<span class='no'>x</span>, <span class='kw'>administration</span> <span class='kw'>=</span> <span class='st'>"oral"</span>, <span class='kw'>units</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)
<span class='fu'>ab_info</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
<span class='fu'>ab_url</span>(<span class='no'>x</span>, <span class='kw'>open</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)
<span class='fu'>ab_property</span>(<span class='no'>x</span>, <span class='kw'>property</span> <span class='kw'>=</span> <span class='st'>"name"</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</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>x</th>
<td><p>any (vector of) text that can be coerced to a valid microorganism code with <code><a href='as.ab.html'>as.ab()</a></code></p></td>
</tr>
<tr>
<th>language</th>
<td><p>language of the returned text, defaults to system language (see <code><a href='translate.html'>get_locale()</a></code>) and can also be set with <code><a href='https://rdrr.io/r/base/options.html'>getOption("AMR_locale")</a></code>. Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></td>
</tr>
<tr>
<th>tolower</th>
<td><p>logical to indicate whether the first character of every output should be transformed to a lower case character. This will lead to e.g. "polymyxin B" and not "polymyxin b".</p></td>
</tr>
<tr>
<th>...</th>
<td><p>other parameters passed on to <code><a href='as.ab.html'>as.ab()</a></code></p></td>
</tr>
<tr>
<th>administration</th>
<td><p>way of administration, either <code>"oral"</code> or <code>"iv"</code></p></td>
</tr>
<tr>
<th>units</th>
<td><p>a logical to indicate whether the units instead of the DDDs itself must be returned, see Examples</p></td>
</tr>
<tr>
<th>open</th>
<td><p>browse the URL using <code><a href='https://rdrr.io/r/utils/browseURL.html'>utils::browseURL()</a></code></p></td>
</tr>
<tr>
<th>property</th>
<td><p>one of the column names of one of the <a href='antibiotics.html'>antibiotics</a> data set</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<ul>
<li><p>An <code><a href='https://rdrr.io/r/base/integer.html'>integer</a></code> in case of <code>ab_cid()</code></p></li>
<li><p>A named <code><a href='https://rdrr.io/r/base/list.html'>list</a></code> in case of <code>ab_info()</code> and multiple <code>ab_synonyms()</code>/<code>ab_tradenames()</code></p></li>
<li><p>A <code><a href='https://rdrr.io/r/base/double.html'>double</a></code> in case of <code>ab_ddd()</code></p></li>
<li><p>A <code><a href='https://rdrr.io/r/base/character.html'>character</a></code> in all other cases</p></li>
</ul>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>All output will be <a href='translate.html'>translate</a>d where possible.</p>
<p>The function <code>ab_url()</code> will return the direct URL to the official WHO website. A warning will be returned if the reauired ATC code is not available.</p>
<h2 class="hasAnchor" id="maturing-lifecycle"><a class="anchor" href="#maturing-lifecycle"></a>Maturing lifecycle</h2>
<p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. This function needs wider usage and more extensive testing in order to optimise the unlying code.</p>
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
<p>World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: <a href='https://www.whocc.no/atc_ddd_index/'>https://www.whocc.no/atc_ddd_index/</a></p>
<p>WHONET 2019 software: <a href='http://www.whonet.org/software.html'>http://www.whonet.org/software.html</a></p>
<p>European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: <a href='http://ec.europa.eu/health/documents/community-register/html/atc.htm'>http://ec.europa.eu/health/documents/community-register/html/atc.htm</a></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>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 comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p><a href='antibiotics.html'>antibiotics</a></p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># all properties:</span>
<span class='fu'>ab_name</span>(<span class='st'>"AMX"</span>) <span class='co'># "Amoxicillin"</span>
<span class='fu'>ab_atc</span>(<span class='st'>"AMX"</span>) <span class='co'># J01CA04 (ATC code from the WHO)</span>
<span class='fu'>ab_cid</span>(<span class='st'>"AMX"</span>) <span class='co'># 33613 (Compound ID from PubChem)</span>
<span class='fu'>ab_synonyms</span>(<span class='st'>"AMX"</span>) <span class='co'># a list with brand names of amoxicillin</span>
<span class='fu'>ab_tradenames</span>(<span class='st'>"AMX"</span>) <span class='co'># same</span>
<span class='fu'>ab_group</span>(<span class='st'>"AMX"</span>) <span class='co'># "Beta-lactams/penicillins"</span>
<span class='fu'>ab_atc_group1</span>(<span class='st'>"AMX"</span>) <span class='co'># "Beta-lactam antibacterials, penicillins"</span>
<span class='fu'>ab_atc_group2</span>(<span class='st'>"AMX"</span>) <span class='co'># "Penicillins with extended spectrum"</span>
<span class='fu'>ab_url</span>(<span class='st'>"AMX"</span>) <span class='co'># link to the official WHO page</span>
<span class='co'># smart lowercase tranformation</span>
<span class='fu'>ab_name</span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"AMC"</span>, <span class='st'>"PLB"</span>)) <span class='co'># "Amoxicillin/clavulanic acid" "Polymyxin B"</span>
<span class='fu'>ab_name</span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"AMC"</span>, <span class='st'>"PLB"</span>),
<span class='kw'>tolower</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='co'># "amoxicillin/clavulanic acid" "polymyxin B"</span>
<span class='co'># defined daily doses (DDD)</span>
<span class='fu'>ab_ddd</span>(<span class='st'>"AMX"</span>, <span class='st'>"oral"</span>) <span class='co'># 1</span>
<span class='fu'>ab_ddd</span>(<span class='st'>"AMX"</span>, <span class='st'>"oral"</span>, <span class='kw'>units</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='co'># "g"</span>
<span class='fu'>ab_ddd</span>(<span class='st'>"AMX"</span>, <span class='st'>"iv"</span>) <span class='co'># 1</span>
<span class='fu'>ab_ddd</span>(<span class='st'>"AMX"</span>, <span class='st'>"iv"</span>, <span class='kw'>units</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='co'># "g"</span>
<span class='fu'>ab_info</span>(<span class='st'>"AMX"</span>) <span class='co'># all properties as a list</span>
<span class='co'># all ab_* functions use as.ab() internally, so you can go from 'any' to 'any':</span>
<span class='fu'>ab_atc</span>(<span class='st'>"AMP"</span>) <span class='co'># ATC code of AMP (ampicillin)</span>
<span class='fu'>ab_group</span>(<span class='st'>"J01CA01"</span>) <span class='co'># Drug group of ampicillins ATC code</span>
<span class='fu'>ab_loinc</span>(<span class='st'>"ampicillin"</span>) <span class='co'># LOINC codes of ampicillin</span>
<span class='fu'>ab_name</span>(<span class='st'>"21066-6"</span>) <span class='co'># "Ampicillin" (using LOINC)</span>
<span class='fu'>ab_name</span>(<span class='fl'>6249</span>) <span class='co'># "Ampicillin" (using CID)</span>
<span class='fu'>ab_name</span>(<span class='st'>"J01CA01"</span>) <span class='co'># "Ampicillin" (using ATC)</span>
<span class='co'># spelling from different languages and dyslexia are no problem</span>
<span class='fu'>ab_atc</span>(<span class='st'>"ceftriaxon"</span>)
<span class='fu'>ab_atc</span>(<span class='st'>"cephtriaxone"</span>)
<span class='fu'>ab_atc</span>(<span class='st'>"cephthriaxone"</span>)
<span class='fu'>ab_atc</span>(<span class='st'>"seephthriaaksone"</span>)</pre>
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