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<h1>Transform to antibiotic ID</h1>
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<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/ab.R'><code>R/ab.R</code></a></small>
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<div class="hidden name"><code>as.ab.Rd</code></div>
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<div class="ref-description">
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<p>Use this function to determine the antibiotic code of one or more antibiotics. The data set <a href='antibiotics.html'>antibiotics</a> will be searched for abbreviations, official names and synonyms (brand names).</p>
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<pre class="usage"><span class='fu'>as.ab</span>(<span class='kw'>x</span>, flag_multiple_results = <span class='fl'>TRUE</span>, info = <span class='fl'>TRUE</span>, <span class='kw'>...</span>)
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<span class='fu'>is.ab</span>(<span class='kw'>x</span>)</pre>
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<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
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<table class="ref-arguments">
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<colgroup><col class="name" /><col class="desc" /></colgroup>
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<tr>
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<th>x</th>
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<td><p>character vector to determine to antibiotic ID</p></td>
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</tr>
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<tr>
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<th>flag_multiple_results</th>
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<td><p>logical to indicate whether a note should be printed to the console that probably more than one antibiotic code or name can be retrieved from a single input value.</p></td>
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</tr>
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<tr>
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<th>info</th>
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<td><p>logical to indicate whether a progress bar should be printed</p></td>
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</tr>
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<tr>
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<th>...</th>
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<td><p>arguments passed on to internal functions</p></td>
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</tr>
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</table>
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<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
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<p>Character (vector) with class <code>ab</code>. Unknown values will return <code>NA</code>.</p>
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<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
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<p>All entries in the <a href='antibiotics.html'>antibiotics</a> data set have three different identifiers: a human readable EARS-Net code (column <code>ab</code>, used by ECDC and WHONET), an ATC code (column <code>atc</code>, used by WHO), and a CID code (column <code>cid</code>, Compound ID, used by PubChem). The data set contains more than 5,000 official brand names from many different countries, as found in PubChem.</p>
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<p>All these properties will be searched for the user input. The <code>as.ab()</code> can correct for different forms of misspelling:</p><ul>
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<li><p>Wrong spelling of drug names (like "tobramicin" or "gentamycin"), which corrects for most audible similarities such as f/ph, x/ks, c/z/s, t/th, etc.</p></li>
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<li><p>Too few or too many vowels or consonants</p></li>
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<li><p>Switching two characters (like "mreopenem", often the case in clinical data, when doctors typed too fast)</p></li>
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<li><p>Digitalised paper records, leaving artefacts like 0/o/O (zero and O's), B/8, n/r, etc.</p></li>
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</ul>
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<p>Use the <code><a href='ab_property.html'>ab_property()</a></code> functions to get properties based on the returned antibiotic ID, see Examples.</p>
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<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
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<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>
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<p>WHONET 2019 software: <a href='http://www.whonet.org/software.html'>http://www.whonet.org/software.html</a></p>
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<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>
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<h2 class="hasAnchor" id="maturing-lifecycle"><a class="anchor" href="#maturing-lifecycle"></a>Maturing lifecycle</h2>
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<p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
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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. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://github.com/msberends/AMR/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
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<h2 class="hasAnchor" id="whocc"><a class="anchor" href="#whocc"></a>WHOCC</h2>
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<p><img src='figures/logo_who.png' height=60px style=margin-bottom:5px /> <br />
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This package contains <strong>all ~550 antibiotic, antimycotic and antiviral drugs</strong> and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, <a href='https://www.whocc.no'>https://www.whocc.no</a>) and the Pharmaceuticals Community Register of the European Commission (<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>
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<p>These have become the gold standard for international drug utilisation monitoring and research.</p>
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<p>The WHOCC is located in Oslo at the Norwegian Institute of Public Health and funded by the Norwegian government. The European Commission is the executive of the European Union and promotes its general interest.</p>
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<p><strong>NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package.</strong> See <a href='https://www.whocc.no/copyright_disclaimer/.'>https://www.whocc.no/copyright_disclaimer/.</a></p>
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<h2 class="hasAnchor" id="reference-data-publicly-available"><a class="anchor" href="#reference-data-publicly-available"></a>Reference data publicly available</h2>
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<p>All reference data sets (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find <a href='https://msberends.github.io/AMR/articles/datasets.html'>all download links on our website</a>, which is automatically updated with every code change.</p>
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<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>
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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 analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
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<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
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<div class='dont-index'>
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<ul>
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<li><p><a href='antibiotics.html'>antibiotics</a> for the dataframe that is being used to determine ATCs</p></li>
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<li><p><code><a href='ab_from_text.html'>ab_from_text()</a></code> for a function to retrieve antimicrobial drugs from clinical text (from health care records)</p></li>
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</ul>
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</div>
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<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
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<pre class="examples"><span class='co'># these examples all return "ERY", the ID of erythromycin:</span>
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<span class='fu'>as.ab</span>(<span class='st'>"J01FA01"</span>)
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<span class='fu'>as.ab</span>(<span class='st'>"J 01 FA 01"</span>)
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<span class='fu'>as.ab</span>(<span class='st'>"Erythromycin"</span>)
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<span class='fu'>as.ab</span>(<span class='st'>"eryt"</span>)
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<span class='fu'>as.ab</span>(<span class='st'>" eryt 123"</span>)
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<span class='fu'>as.ab</span>(<span class='st'>"ERYT"</span>)
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<span class='fu'>as.ab</span>(<span class='st'>"ERY"</span>)
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<span class='fu'>as.ab</span>(<span class='st'>"eritromicine"</span>) <span class='co'># spelled wrong, yet works</span>
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<span class='fu'>as.ab</span>(<span class='st'>"Erythrocin"</span>) <span class='co'># trade name</span>
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<span class='fu'>as.ab</span>(<span class='st'>"Romycin"</span>) <span class='co'># trade name</span>
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<span class='co'># spelling from different languages and dyslexia are no problem</span>
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<span class='fu'><a href='ab_property.html'>ab_atc</a></span>(<span class='st'>"ceftriaxon"</span>)
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<span class='fu'><a href='ab_property.html'>ab_atc</a></span>(<span class='st'>"cephtriaxone"</span>) <span class='co'># small spelling error</span>
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<span class='fu'><a href='ab_property.html'>ab_atc</a></span>(<span class='st'>"cephthriaxone"</span>) <span class='co'># or a bit more severe</span>
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<span class='fu'><a href='ab_property.html'>ab_atc</a></span>(<span class='st'>"seephthriaaksone"</span>) <span class='co'># and even this works</span>
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<span class='co'># use ab_* functions to get a specific properties (see ?ab_property);</span>
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<span class='co'># they use as.ab() internally:</span>
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<span class='fu'><a href='ab_property.html'>ab_name</a></span>(<span class='st'>"J01FA01"</span>) <span class='co'># "Erythromycin"</span>
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<span class='fu'><a href='ab_property.html'>ab_name</a></span>(<span class='st'>"eryt"</span>) <span class='co'># "Erythromycin"</span></pre>
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