<!-- Generated by pkgdown: do not edit by hand --><htmllang="en"><head><metahttp-equiv="Content-Type"content="text/html; charset=UTF-8"><metacharset="utf-8"><metahttp-equiv="X-UA-Compatible"content="IE=edge"><metaname="viewport"content="width=device-width, initial-scale=1, shrink-to-fit=no"><metaname="description"content="Use these functions to return a specific property of an antibiotic from the antibiotics data set. All input values will be evaluated internally with as.ab()."><title>Get Properties of an Antibiotic — ab_property • AMR (for R)</title><!-- favicons --><linkrel="icon"type="image/png"sizes="16x16"href="../favicon-16x16.png"><linkrel="icon"type="image/png"sizes="32x32"href="../favicon-32x32.png"><linkrel="apple-touch-icon"type="image/png"sizes="180x180"href="../apple-touch-icon.png"><linkrel="apple-touch-icon"type="image/png"sizes="120x120"href="../apple-touch-icon-120x120.png"><linkrel="apple-touch-icon"type="image/png"sizes="76x76"href="../apple-touch-icon-76x76.png"><linkrel="apple-touch-icon"type="image/png"sizes="60x60"href="../apple-touch-icon-60x60.png"><scriptsrc="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><metaname="viewport"content="width=device-width, initial-scale=1, shrink-to-fit=no"><linkhref="../deps/bootstrap-5.1.3/bootstrap.min.css"rel="stylesheet"><scriptsrc="../deps/bootstrap-5.1.3/bootstrap.bundle.min.js"></script><linkhref="../deps/Fira_Code-0.4.2/font.css"rel="stylesheet"><!-- Font Awesome icons --><linkrel="stylesheet"href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css"integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk="crossorigin="anonymous"><linkrel="stylesheet"href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css"integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw="crossorigin="anonymous"><!-- bootstrap-toc --><scriptsrc="https://cdn.rawgit.com/afeld/bootstrap-toc/v1.0.1/dist/bootstrap-toc.min.js"></script><!-- headroom.js --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js"integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0="crossorigin="anonymous"></script><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js"integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4="crossorigin="anonymous"></script><!-- clipboard.js --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js"integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI="crossorigin="anonymous"></script><!-- search --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js"integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A=="crossorigin="anonymous"></script><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js"integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg=="crossorigin="anonymous"></script><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js"integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww=="crossorigin="anonymous"></script><!-- pkgdown --><scriptsrc="../pkgdown.js"></script><linkhref="../extra.css"rel="stylesheet"><scriptsrc="../extra.js"></script><metaproperty="og:title"content="Get Properties of an Antibiotic — ab_property"><metaproperty="og:description"content="Use these functions to return a specific property of an antibiotic from the antibiotics data set. All input values will be evaluated internally with as.ab()."><metaproperty="og:image"content="https://msberends.github.io/AMR/logo.svg"><metaname="twitter:card"content="summary_large_image"><metaname="twitter:creator"content="@msberends"><metaname="twitter:site"content="@msberends"><!-- mathjax --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js"integrity="sha256-nvJJv9wWKEm88qvoQl9ek
<p>Use these functions to return a specific property of an antibiotic from the <ahref="antibiotics.html">antibiotics</a> data set. All input values will be evaluated internally with <code><ahref="as.ab.html">as.ab()</a></code>.</p>
<span><spanclass="fu">ab_group</span><spanclass="op">(</span><spanclass="va">x</span>, language <spanclass="op">=</span><spanclass="fu"><ahref="translate.html">get_AMR_locale</a></span><spanclass="op">(</span><spanclass="op">)</span>, <spanclass="va">...</span><spanclass="op">)</span></span>
<span><spanclass="fu">ab_atc_group1</span><spanclass="op">(</span><spanclass="va">x</span>, language <spanclass="op">=</span><spanclass="fu"><ahref="translate.html">get_AMR_locale</a></span><spanclass="op">(</span><spanclass="op">)</span>, <spanclass="va">...</span><spanclass="op">)</span></span>
<span></span>
<span><spanclass="fu">ab_atc_group2</span><spanclass="op">(</span><spanclass="va">x</span>, language <spanclass="op">=</span><spanclass="fu"><ahref="translate.html">get_AMR_locale</a></span><spanclass="op">(</span><spanclass="op">)</span>, <spanclass="va">...</span><spanclass="op">)</span></span>
<span><spanclass="fu">ab_info</span><spanclass="op">(</span><spanclass="va">x</span>, language <spanclass="op">=</span><spanclass="fu"><ahref="translate.html">get_AMR_locale</a></span><spanclass="op">(</span><spanclass="op">)</span>, <spanclass="va">...</span><spanclass="op">)</span></span>
<span></span>
<span><spanclass="fu">ab_url</span><spanclass="op">(</span><spanclass="va">x</span>, open <spanclass="op">=</span><spanclass="cn">FALSE</span>, <spanclass="va">...</span><spanclass="op">)</span></span>
<span></span>
<span><spanclass="fu">ab_property</span><spanclass="op">(</span><spanclass="va">x</span>, property <spanclass="op">=</span><spanclass="st">"name"</span>, language <spanclass="op">=</span><spanclass="fu"><ahref="translate.html">get_AMR_locale</a></span><spanclass="op">(</span><spanclass="op">)</span>, <spanclass="va">...</span><spanclass="op">)</span></span>
<span> language <spanclass="op">=</span><spanclass="fu"><ahref="translate.html">get_AMR_locale</a></span><spanclass="op">(</span><spanclass="op">)</span>,</span>
<dd><p>any (vector of) text that can be coerced to a valid antibiotic code with <code><ahref="as.ab.html">as.ab()</a></code></p></dd>
<dt>language</dt>
<dd><p>language of the returned text, defaults to system language (see <code><ahref="translate.html">get_AMR_locale()</a></code>) and can also be set with <code>getOption("AMR_locale")</code>. Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></dd>
<dt>tolower</dt>
<dd><p>a <ahref="https://rdrr.io/r/base/logical.html"class="external-link">logical</a> to indicate whether the first <ahref="https://rdrr.io/r/base/character.html"class="external-link">character</a> of every output should be transformed to a lower case <ahref="https://rdrr.io/r/base/character.html"class="external-link">character</a>. This will lead to e.g. "polymyxin B" and not "polymyxin b".</p></dd>
<dt>...</dt>
<dd><p>in case of <code>set_ab_names()</code> and <code>data</code> is a <ahref="https://rdrr.io/r/base/data.frame.html"class="external-link">data.frame</a>: variables to select (supports tidy selection such as <code>column1:column4</code>), otherwise other arguments passed on to <code><ahref="as.ab.html">as.ab()</a></code></p></dd>
<dt>only_first</dt>
<dd><p>a <ahref="https://rdrr.io/r/base/logical.html"class="external-link">logical</a> to indicate whether only the first ATC code must be returned, with giving preference to J0-codes (i.e., the antimicrobial drug group)</p></dd>
<dt>administration</dt>
<dd><p>way of administration, either <code>"oral"</code> or <code>"iv"</code></p></dd>
<dt>open</dt>
<dd><p>browse the URL using <code><ahref="https://rdrr.io/r/utils/browseURL.html"class="external-link">utils::browseURL()</a></code></p></dd>
<dt>property</dt>
<dd><p>one of the column names of one of the <ahref="antibiotics.html">antibiotics</a> data set: <code>vector_or(colnames(antibiotics), sort = FALSE)</code>.</p></dd>
<dt>data</dt>
<dd><p>a <ahref="https://rdrr.io/r/base/data.frame.html"class="external-link">data.frame</a> of which the columns need to be renamed, or a <ahref="https://rdrr.io/r/base/character.html"class="external-link">character</a> vector of column names</p></dd>
<dt>snake_case</dt>
<dd><p>a <ahref="https://rdrr.io/r/base/logical.html"class="external-link">logical</a> to indicate whether the names should be in so-called <ahref="https://en.wikipedia.org/wiki/Snake_case"class="external-link">snake case</a>: in lower case and all spaces/slashes replaced with an underscore (<code>_</code>)</p></dd>
<ul><li><p>An <ahref="https://rdrr.io/r/base/integer.html"class="external-link">integer</a> in case of <code>ab_cid()</code></p></li>
<li><p>A named <ahref="https://rdrr.io/r/base/list.html"class="external-link">list</a> in case of <code>ab_info()</code> and multiple <code>ab_atc()</code>/<code>ab_synonyms()</code>/<code>ab_tradenames()</code></p></li>
<li><p>A <ahref="https://rdrr.io/r/base/double.html"class="external-link">double</a> in case of <code>ab_ddd()</code></p></li>
<li><p>A <ahref="https://rdrr.io/r/base/data.frame.html"class="external-link">data.frame</a> in case of <code>set_ab_names()</code></p></li>
<li><p>A <ahref="https://rdrr.io/r/base/character.html"class="external-link">character</a> in all other cases</p></li>
<p>All output <ahref="translate.html">will be translated</a> 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 required ATC code is not available.</p>
<p>The function <code>set_ab_names()</code> is a special column renaming function for <ahref="https://rdrr.io/r/base/data.frame.html"class="external-link">data.frame</a>s. It renames columns names that resemble antimicrobial drugs. It always makes sure that the new column names are unique. If <code>property = "atc"</code> is set, preference is given to ATC codes from the J-group.</p>
<p>World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: <ahref="https://www.whocc.no/atc_ddd_index/"class="external-link">https://www.whocc.no/atc_ddd_index/</a></p>
<p>European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: <ahref="https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm"class="external-link">https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm</a></p>
</div>
<divclass="section level2">
<h2id="reference-data-publicly-available">Reference Data Publicly Available<aclass="anchor"aria-label="anchor"href="#reference-data-publicly-available"></a></h2>
<p>All data sets in this <code>AMR</code> package (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please visit <ahref="https://msberends.github.io/AMR/articles/datasets.html">our website for the download links</a>. The actual files are of course available on <ahref="https://github.com/msberends/AMR/tree/main/data-raw"class="external-link">our GitHub repository</a>.</p>
<spanclass="r-in"><span><spanclass="fu">ab_atc</span><spanclass="op">(</span><spanclass="st">"AMX"</span><spanclass="op">)</span><spanclass="co"># "J01CA04" (ATC code from the WHO)</span></span></span>
<spanclass="r-in"><span><spanclass="fu">ab_cid</span><spanclass="op">(</span><spanclass="st">"AMX"</span><spanclass="op">)</span><spanclass="co"># 33613 (Compound ID from PubChem)</span></span></span>
<spanclass="r-in"><span><spanclass="fu">ab_synonyms</span><spanclass="op">(</span><spanclass="st">"AMX"</span><spanclass="op">)</span><spanclass="co"># a list with brand names of amoxicillin</span></span></span>
<spanclass="r-in"><span><spanclass="fu">ab_atc_group2</span><spanclass="op">(</span><spanclass="st">"AMX"</span><spanclass="op">)</span><spanclass="co"># "Penicillins with extended spectrum"</span></span></span>
<spanclass="r-out co"><spanclass="r-pr">#></span> [1] "Penicillins with extended spectrum"</span>
<spanclass="r-in"><span><spanclass="fu">ab_url</span><spanclass="op">(</span><spanclass="st">"AMX"</span><spanclass="op">)</span><spanclass="co"># link to the official WHO page</span></span></span>
<spanclass="r-in"><span> x <spanclass="op">=</span><spanclass="fu"><ahref="https://rdrr.io/r/base/c.html"class="external-link">c</a></span><spanclass="op">(</span><spanclass="st">"AMC"</span>, <spanclass="st">"PLB"</span><spanclass="op">)</span>,</span></span>
<spanclass="r-in"><span><spanclass="fu">ab_info</span><spanclass="op">(</span><spanclass="st">"AMX"</span><spanclass="op">)</span><spanclass="co"># all properties as a list</span></span></span>
<spanclass="r-in"><span><spanclass="fu">ab_group</span><spanclass="op">(</span><spanclass="st">"J01CA01"</span><spanclass="op">)</span><spanclass="co"># Drug group of ampicillins ATC code</span></span></span>
<spanclass="r-in"><span><spanclass="fu">ab_loinc</span><spanclass="op">(</span><spanclass="st">"ampicillin"</span><spanclass="op">)</span><spanclass="co"># LOINC codes of ampicillin</span></span></span>
</main><asideclass="col-md-3"><navid="toc"><h2>On this page</h2>
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<p></p><p><code>AMR</code> (for R). Developed at the <atarget="_blank"href="https://www.rug.nl"class="external-link">University of Groningen</a> in collaboration with non-profit organisations<br><atarget="_blank"href="https://www.certe.nl"class="external-link">Certe Medical Diagnostics and Advice Foundation</a> and <atarget="_blank"href="https://www.umcg.nl"class="external-link">University Medical Center Groningen</a>.</p>
