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<img src="../logo.svg" class="logo" alt=""><h1>Get Properties of an Antibiotic</h1>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/ab_property.R" class="external-link"><code>R/ab_property.R</code></a></small>
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<div class="d-none name"><code>ab_property.Rd</code></div>
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</div>
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<div class="ref-description section level2">
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<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>
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</div>
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<div class="section level2">
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<h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
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<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">ab_name</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, tolower <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
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<span></span>
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<span><span class="fu">ab_cid</span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span>
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<span></span>
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<span><span class="fu">ab_synonyms</span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span>
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<span></span>
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<span><span class="fu">ab_tradenames</span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span>
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<span></span>
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<span><span class="fu">ab_group</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
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<span></span>
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<span><span class="fu">ab_atc</span><span class="op">(</span><span class="va">x</span>, only_first <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
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<span></span>
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<span><span class="fu">ab_atc_group1</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
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<span></span>
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<span><span class="fu">ab_atc_group2</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
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<span></span>
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<span><span class="fu">ab_loinc</span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span>
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<span></span>
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<span><span class="fu">ab_ddd</span><span class="op">(</span><span class="va">x</span>, administration <span class="op">=</span> <span class="st">"oral"</span>, <span class="va">...</span><span class="op">)</span></span>
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<span></span>
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<span><span class="fu">ab_ddd_units</span><span class="op">(</span><span class="va">x</span>, administration <span class="op">=</span> <span class="st">"oral"</span>, <span class="va">...</span><span class="op">)</span></span>
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<span></span>
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<span><span class="fu">ab_info</span><span class="op">(</span><span class="va">x</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
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<span></span>
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<span><span class="fu">ab_url</span><span class="op">(</span><span class="va">x</span>, open <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
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<span></span>
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<span><span class="fu">ab_property</span><span class="op">(</span><span class="va">x</span>, property <span class="op">=</span> <span class="st">"name"</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
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<span></span>
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<span><span class="fu">set_ab_names</span><span class="op">(</span></span>
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<span> <span class="va">data</span>,</span>
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<span> <span class="va">...</span>,</span>
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<span> property <span class="op">=</span> <span class="st">"name"</span>,</span>
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<span> language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
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<span> snake_case <span class="op">=</span> <span class="cn">NULL</span></span>
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<span><span class="op">)</span></span></code></pre></div>
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</div>
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<div class="section level2">
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<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
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<dl><dt>x</dt>
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<dd><p>any (vector of) text that can be coerced to a valid antibiotic code with <code><a href="as.ab.html">as.ab()</a></code></p></dd>
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<dt>language</dt>
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<dd><p>language of the returned text, defaults to system language (see <code><a href="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>
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<dt>tolower</dt>
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<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether the first <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> of every output should be transformed to a lower case <a href="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>
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<dt>...</dt>
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<dd><p>in case of <code>set_ab_names()</code> and <code>data</code> is a <a href="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><a href="as.ab.html">as.ab()</a></code></p></dd>
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<dt>only_first</dt>
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<dd><p>a <a href="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>
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<dt>administration</dt>
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<dd><p>way of administration, either <code>"oral"</code> or <code>"iv"</code></p></dd>
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<dt>open</dt>
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<dd><p>browse the URL using <code><a href="https://rdrr.io/r/utils/browseURL.html" class="external-link">utils::browseURL()</a></code></p></dd>
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<dt>property</dt>
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<dd><p>one of the column names of one of the <a href="antibiotics.html">antibiotics</a> data set: <code>vector_or(colnames(antibiotics), sort = FALSE)</code>.</p></dd>
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<dt>data</dt>
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<dd><p>a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> of which the columns need to be renamed, or a <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> vector of column names</p></dd>
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<dt>snake_case</dt>
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<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether the names should be in so-called <a href="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>
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</dl></div>
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<div class="section level2">
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<h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
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<ul><li><p>An <a href="https://rdrr.io/r/base/integer.html" class="external-link">integer</a> in case of <code>ab_cid()</code></p></li>
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<li><p>A named <a href="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>
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<li><p>A <a href="https://rdrr.io/r/base/double.html" class="external-link">double</a> in case of <code>ab_ddd()</code></p></li>
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<li><p>A <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> in case of <code>set_ab_names()</code></p></li>
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<li><p>A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> in all other cases</p></li>
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</ul></div>
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<div class="section level2">
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<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
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<p>All output <a href="translate.html">will be translated</a> where possible.</p>
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<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>
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<p>The function <code>set_ab_names()</code> is a special column renaming function for <a href="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>
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</div>
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<div class="section level2">
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<h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></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/" class="external-link">https://www.whocc.no/atc_ddd_index/</a></p>
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<p>European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: <a href="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>
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</div>
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<div class="section level2">
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<h2 id="reference-data-publicly-available">Reference Data Publicly Available<a class="anchor" aria-label="anchor" href="#reference-data-publicly-available"></a></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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</div>
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<div class="section level2">
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<h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
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<div class="dont-index"><p><a href="antibiotics.html">antibiotics</a></p></div>
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</div>
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<div class="section level2">
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<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
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<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># all properties:</span></span></span>
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<span class="r-in"><span><span class="fu">ab_name</span><span class="op">(</span><span class="st">"AMX"</span><span class="op">)</span> <span class="co"># "Amoxicillin"</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "Amoxicillin"</span>
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<span class="r-in"><span><span class="fu">ab_atc</span><span class="op">(</span><span class="st">"AMX"</span><span class="op">)</span> <span class="co"># "J01CA04" (ATC code from the WHO)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "J01CA04"</span>
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<span class="r-in"><span><span class="fu">ab_cid</span><span class="op">(</span><span class="st">"AMX"</span><span class="op">)</span> <span class="co"># 33613 (Compound ID from PubChem)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 33613</span>
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<span class="r-in"><span><span class="fu">ab_synonyms</span><span class="op">(</span><span class="st">"AMX"</span><span class="op">)</span> <span class="co"># a list with brand names of amoxicillin</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "actimoxi" "amoclen" "amolin" </span>
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<span class="r-out co"><span class="r-pr">#></span> [4] "amopen" "amopenixin" "amoxibiotic" </span>
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<span class="r-out co"><span class="r-pr">#></span> [7] "amoxicaps" "amoxicilina" "amoxicillin" </span>
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<span class="r-out co"><span class="r-pr">#></span> [10] "amoxicilline" "amoxicillinum" "amoxiden" </span>
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<span class="r-out co"><span class="r-pr">#></span> [13] "amoxil" "amoxivet" "amoxy" </span>
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<span class="r-out co"><span class="r-pr">#></span> [16] "amoxycillin" "anemolin" "aspenil" </span>
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<span class="r-out co"><span class="r-pr">#></span> [19] "biomox" "bristamox" "cemoxin" </span>
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<span class="r-out co"><span class="r-pr">#></span> [22] "clamoxyl" "delacillin" "dispermox" </span>
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<span class="r-out co"><span class="r-pr">#></span> [25] "efpenix" "flemoxin" "hiconcil" </span>
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<span class="r-out co"><span class="r-pr">#></span> [28] "histocillin" "hydroxyampicillin" "ibiamox" </span>
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<span class="r-out co"><span class="r-pr">#></span> [31] "imacillin" "lamoxy" "metafarma capsules"</span>
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<span class="r-out co"><span class="r-pr">#></span> [34] "metifarma capsules" "moxacin" "moxatag" </span>
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<span class="r-out co"><span class="r-pr">#></span> [37] "ospamox" "pamoxicillin" "piramox" </span>
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<span class="r-out co"><span class="r-pr">#></span> [40] "robamox" "sawamox pm" "tolodina" </span>
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<span class="r-out co"><span class="r-pr">#></span> [43] "unicillin" "utimox" "vetramox" </span>
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<span class="r-in"><span><span class="fu">ab_tradenames</span><span class="op">(</span><span class="st">"AMX"</span><span class="op">)</span> <span class="co"># same</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "actimoxi" "amoclen" "amolin" </span>
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<span class="r-out co"><span class="r-pr">#></span> [4] "amopen" "amopenixin" "amoxibiotic" </span>
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<span class="r-out co"><span class="r-pr">#></span> [7] "amoxicaps" "amoxicilina" "amoxicillin" </span>
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<span class="r-out co"><span class="r-pr">#></span> [10] "amoxicilline" "amoxicillinum" "amoxiden" </span>
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<span class="r-out co"><span class="r-pr">#></span> [13] "amoxil" "amoxivet" "amoxy" </span>
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<span class="r-out co"><span class="r-pr">#></span> [16] "amoxycillin" "anemolin" "aspenil" </span>
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<span class="r-out co"><span class="r-pr">#></span> [19] "biomox" "bristamox" "cemoxin" </span>
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<span class="r-out co"><span class="r-pr">#></span> [22] "clamoxyl" "delacillin" "dispermox" </span>
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|
<span class="r-out co"><span class="r-pr">#></span> [25] "efpenix" "flemoxin" "hiconcil" </span>
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|
<span class="r-out co"><span class="r-pr">#></span> [28] "histocillin" "hydroxyampicillin" "ibiamox" </span>
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<span class="r-out co"><span class="r-pr">#></span> [31] "imacillin" "lamoxy" "metafarma capsules"</span>
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|
<span class="r-out co"><span class="r-pr">#></span> [34] "metifarma capsules" "moxacin" "moxatag" </span>
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|
<span class="r-out co"><span class="r-pr">#></span> [37] "ospamox" "pamoxicillin" "piramox" </span>
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<span class="r-out co"><span class="r-pr">#></span> [40] "robamox" "sawamox pm" "tolodina" </span>
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<span class="r-out co"><span class="r-pr">#></span> [43] "unicillin" "utimox" "vetramox" </span>
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<span class="r-in"><span><span class="fu">ab_group</span><span class="op">(</span><span class="st">"AMX"</span><span class="op">)</span> <span class="co"># "Beta-lactams/penicillins"</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "Beta-lactams/penicillins"</span>
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<span class="r-in"><span><span class="fu">ab_atc_group1</span><span class="op">(</span><span class="st">"AMX"</span><span class="op">)</span> <span class="co"># "Beta-lactam antibacterials, penicillins"</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "Beta-lactam antibacterials, penicillins"</span>
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<span class="r-in"><span><span class="fu">ab_atc_group2</span><span class="op">(</span><span class="st">"AMX"</span><span class="op">)</span> <span class="co"># "Penicillins with extended spectrum"</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "Penicillins with extended spectrum"</span>
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<span class="r-in"><span><span class="fu">ab_url</span><span class="op">(</span><span class="st">"AMX"</span><span class="op">)</span> <span class="co"># link to the official WHO page</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> Amoxicillin </span>
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<span class="r-out co"><span class="r-pr">#></span> "https://www.whocc.no/atc_ddd_index/?code=J01CA04&showdescription=no" </span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="co"># smart lowercase tranformation</span></span></span>
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<span class="r-in"><span><span class="fu">ab_name</span><span class="op">(</span>x <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"AMC"</span>, <span class="st">"PLB"</span><span class="op">)</span><span class="op">)</span> <span class="co"># "Amoxicillin/clavulanic acid" "Polymyxin B"</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "Amoxicillin/clavulanic acid" "Polymyxin B" </span>
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<span class="r-in"><span><span class="fu">ab_name</span><span class="op">(</span>x <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"AMC"</span>, <span class="st">"PLB"</span><span class="op">)</span>,</span></span>
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<span class="r-in"><span> tolower <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="co"># "amoxicillin/clavulanic acid" "polymyxin B"</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "amoxicillin/clavulanic acid" "polymyxin B" </span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="co"># defined daily doses (DDD)</span></span></span>
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<span class="r-in"><span><span class="fu">ab_ddd</span><span class="op">(</span><span class="st">"AMX"</span>, <span class="st">"oral"</span><span class="op">)</span> <span class="co"># 1.5</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 1.5</span>
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<span class="r-in"><span><span class="fu">ab_ddd_units</span><span class="op">(</span><span class="st">"AMX"</span>, <span class="st">"oral"</span><span class="op">)</span> <span class="co"># "g"</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "g"</span>
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<span class="r-in"><span><span class="fu">ab_ddd</span><span class="op">(</span><span class="st">"AMX"</span>, <span class="st">"iv"</span><span class="op">)</span> <span class="co"># 3</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 3</span>
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<span class="r-in"><span><span class="fu">ab_ddd_units</span><span class="op">(</span><span class="st">"AMX"</span>, <span class="st">"iv"</span><span class="op">)</span> <span class="co"># "g"</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "g"</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="fu">ab_info</span><span class="op">(</span><span class="st">"AMX"</span><span class="op">)</span> <span class="co"># all properties as a list</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> $ab</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "AMX"</span>
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<span class="r-out co"><span class="r-pr">#></span> </span>
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<span class="r-out co"><span class="r-pr">#></span> $cid</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 33613</span>
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<span class="r-out co"><span class="r-pr">#></span> </span>
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<span class="r-out co"><span class="r-pr">#></span> $name</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "Amoxicillin"</span>
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<span class="r-out co"><span class="r-pr">#></span> </span>
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<span class="r-out co"><span class="r-pr">#></span> $group</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "Beta-lactams/penicillins"</span>
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<span class="r-out co"><span class="r-pr">#></span> </span>
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<span class="r-out co"><span class="r-pr">#></span> $atc</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "J01CA04"</span>
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<span class="r-out co"><span class="r-pr">#></span> </span>
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<span class="r-out co"><span class="r-pr">#></span> $atc_group1</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "Beta-lactam antibacterials, penicillins"</span>
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<span class="r-out co"><span class="r-pr">#></span> </span>
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<span class="r-out co"><span class="r-pr">#></span> $atc_group2</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "Penicillins with extended spectrum"</span>
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<span class="r-out co"><span class="r-pr">#></span> </span>
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<span class="r-out co"><span class="r-pr">#></span> $tradenames</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "actimoxi" "amoclen" "amolin" </span>
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<span class="r-out co"><span class="r-pr">#></span> [4] "amopen" "amopenixin" "amoxibiotic" </span>
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<span class="r-out co"><span class="r-pr">#></span> [7] "amoxicaps" "amoxicilina" "amoxicillin" </span>
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<span class="r-out co"><span class="r-pr">#></span> [10] "amoxicilline" "amoxicillinum" "amoxiden" </span>
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<span class="r-out co"><span class="r-pr">#></span> [13] "amoxil" "amoxivet" "amoxy" </span>
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<span class="r-out co"><span class="r-pr">#></span> [16] "amoxycillin" "anemolin" "aspenil" </span>
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<span class="r-out co"><span class="r-pr">#></span> [19] "biomox" "bristamox" "cemoxin" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [22] "clamoxyl" "delacillin" "dispermox" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [25] "efpenix" "flemoxin" "hiconcil" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [28] "histocillin" "hydroxyampicillin" "ibiamox" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [31] "imacillin" "lamoxy" "metafarma capsules"</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [34] "metifarma capsules" "moxacin" "moxatag" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [37] "ospamox" "pamoxicillin" "piramox" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [40] "robamox" "sawamox pm" "tolodina" </span>
|
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<span class="r-out co"><span class="r-pr">#></span> [43] "unicillin" "utimox" "vetramox" </span>
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<span class="r-out co"><span class="r-pr">#></span> </span>
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<span class="r-out co"><span class="r-pr">#></span> $loinc</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "16365-9" "25274-2" "3344-9" "80133-2"</span>
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<span class="r-out co"><span class="r-pr">#></span> </span>
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<span class="r-out co"><span class="r-pr">#></span> $ddd</span>
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<span class="r-out co"><span class="r-pr">#></span> $ddd$oral</span>
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<span class="r-out co"><span class="r-pr">#></span> $ddd$oral$amount</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 1.5</span>
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<span class="r-out co"><span class="r-pr">#></span> </span>
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<span class="r-out co"><span class="r-pr">#></span> $ddd$oral$units</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "g"</span>
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<span class="r-out co"><span class="r-pr">#></span> </span>
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<span class="r-out co"><span class="r-pr">#></span> </span>
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<span class="r-out co"><span class="r-pr">#></span> $ddd$iv</span>
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<span class="r-out co"><span class="r-pr">#></span> $ddd$iv$amount</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 3</span>
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<span class="r-out co"><span class="r-pr">#></span> </span>
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<span class="r-out co"><span class="r-pr">#></span> $ddd$iv$units</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "g"</span>
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<span class="r-out co"><span class="r-pr">#></span> </span>
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<span class="r-out co"><span class="r-pr">#></span> </span>
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<span class="r-out co"><span class="r-pr">#></span> </span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="co"># all ab_* functions use as.ab() internally, so you can go from 'any' to 'any':</span></span></span>
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<span class="r-in"><span><span class="fu">ab_atc</span><span class="op">(</span><span class="st">"AMP"</span><span class="op">)</span> <span class="co"># ATC code of AMP (ampicillin)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "J01CA01" "S01AA19"</span>
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<span class="r-in"><span><span class="fu">ab_group</span><span class="op">(</span><span class="st">"J01CA01"</span><span class="op">)</span> <span class="co"># Drug group of ampicillins ATC code</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "Beta-lactams/penicillins"</span>
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<span class="r-in"><span><span class="fu">ab_loinc</span><span class="op">(</span><span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># LOINC codes of ampicillin</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "21066-6" "3355-5" "33562-0" "33919-2" "43883-8" "43884-6" "87604-5"</span>
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<span class="r-in"><span><span class="fu">ab_name</span><span class="op">(</span><span class="st">"21066-6"</span><span class="op">)</span> <span class="co"># "Ampicillin" (using LOINC)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "Ampicillin"</span>
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|
<span class="r-in"><span><span class="fu">ab_name</span><span class="op">(</span><span class="fl">6249</span><span class="op">)</span> <span class="co"># "Ampicillin" (using CID)</span></span></span>
|
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<span class="r-out co"><span class="r-pr">#></span> [1] "Ampicillin"</span>
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|
<span class="r-in"><span><span class="fu">ab_name</span><span class="op">(</span><span class="st">"J01CA01"</span><span class="op">)</span> <span class="co"># "Ampicillin" (using ATC)</span></span></span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [1] "Ampicillin"</span>
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|
<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="co"># spelling from different languages and dyslexia are no problem</span></span></span>
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<span class="r-in"><span><span class="fu">ab_atc</span><span class="op">(</span><span class="st">"ceftriaxon"</span><span class="op">)</span></span></span>
|
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<span class="r-out co"><span class="r-pr">#></span> [1] "J01DD04"</span>
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<span class="r-in"><span><span class="fu">ab_atc</span><span class="op">(</span><span class="st">"cephtriaxone"</span><span class="op">)</span></span></span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [1] "J01DD04"</span>
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<span class="r-in"><span><span class="fu">ab_atc</span><span class="op">(</span><span class="st">"cephthriaxone"</span><span class="op">)</span></span></span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [1] "J01DD04"</span>
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<span class="r-in"><span><span class="fu">ab_atc</span><span class="op">(</span><span class="st">"seephthriaaksone"</span><span class="op">)</span></span></span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [1] "J01DD04"</span>
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|
<span class="r-in"><span></span></span>
|
|
<span class="r-in"><span><span class="co"># use set_ab_names() for renaming columns</span></span></span>
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|
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">colnames</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "date" "hospital_id" "ward_icu" "ward_clinical" </span>
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<span class="r-out co"><span class="r-pr">#></span> [5] "ward_outpatient" "age" "gender" "patient_id" </span>
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<span class="r-out co"><span class="r-pr">#></span> [9] "mo" "PEN" "OXA" "FLC" </span>
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<span class="r-out co"><span class="r-pr">#></span> [13] "AMX" "AMC" "AMP" "TZP" </span>
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<span class="r-out co"><span class="r-pr">#></span> [17] "CZO" "FEP" "CXM" "FOX" </span>
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<span class="r-out co"><span class="r-pr">#></span> [21] "CTX" "CAZ" "CRO" "GEN" </span>
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<span class="r-out co"><span class="r-pr">#></span> [25] "TOB" "AMK" "KAN" "TMP" </span>
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<span class="r-out co"><span class="r-pr">#></span> [29] "SXT" "NIT" "FOS" "LNZ" </span>
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<span class="r-out co"><span class="r-pr">#></span> [33] "CIP" "MFX" "VAN" "TEC" </span>
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<span class="r-out co"><span class="r-pr">#></span> [37] "TCY" "TGC" "DOX" "ERY" </span>
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<span class="r-out co"><span class="r-pr">#></span> [41] "CLI" "AZM" "IPM" "MEM" </span>
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<span class="r-out co"><span class="r-pr">#></span> [45] "MTR" "CHL" "COL" "MUP" </span>
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<span class="r-out co"><span class="r-pr">#></span> [49] "RIF" </span>
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|
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">colnames</a></span><span class="op">(</span><span class="fu">set_ab_names</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span><span class="op">)</span></span></span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [1] "date" "hospital_id" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [3] "ward_icu" "ward_clinical" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [5] "ward_outpatient" "age" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [7] "gender" "patient_id" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [9] "mo" "benzylpenicillin" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [11] "oxacillin" "flucloxacillin" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [13] "amoxicillin" "amoxicillin_clavulanic_acid" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [15] "ampicillin" "piperacillin_tazobactam" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [17] "cefazolin" "cefepime" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [19] "cefuroxime" "cefoxitin" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [21] "cefotaxime" "ceftazidime" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [23] "ceftriaxone" "gentamicin" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [25] "tobramycin" "amikacin" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [27] "kanamycin" "trimethoprim" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [29] "trimethoprim_sulfamethoxazole" "nitrofurantoin" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [31] "fosfomycin" "linezolid" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [33] "ciprofloxacin" "moxifloxacin" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [35] "vancomycin" "teicoplanin" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [37] "tetracycline" "tigecycline" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [39] "doxycycline" "erythromycin" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [41] "clindamycin" "azithromycin" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [43] "imipenem" "meropenem" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [45] "metronidazole" "chloramphenicol" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [47] "colistin" "mupirocin" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [49] "rifampicin" </span>
|
|
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">colnames</a></span><span class="op">(</span><span class="fu">set_ab_names</span><span class="op">(</span><span class="va">example_isolates</span>, <span class="va">NIT</span><span class="op">:</span><span class="va">VAN</span><span class="op">)</span><span class="op">)</span></span></span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [1] "date" "hospital_id" "ward_icu" "ward_clinical" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [5] "ward_outpatient" "age" "gender" "patient_id" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [9] "mo" "PEN" "OXA" "FLC" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [13] "AMX" "AMC" "AMP" "TZP" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [17] "CZO" "FEP" "CXM" "FOX" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [21] "CTX" "CAZ" "CRO" "GEN" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [25] "TOB" "AMK" "KAN" "TMP" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [29] "SXT" "nitrofurantoin" "fosfomycin" "linezolid" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [33] "ciprofloxacin" "moxifloxacin" "vancomycin" "TEC" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [37] "TCY" "TGC" "DOX" "ERY" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [41] "CLI" "AZM" "IPM" "MEM" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [45] "MTR" "CHL" "COL" "MUP" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [49] "RIF" </span>
|
|
<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
|
|
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
|
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
|
<span class="r-in"><span> <span class="fu">set_ab_names</span><span class="op">(</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
|
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="op">)</span></span></span>
|
|
<span class="r-in"><span> </span></span>
|
|
<span class="r-in"><span> <span class="co"># this does the same:</span></span></span>
|
|
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
|
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/rename.html" class="external-link">rename_with</a></span><span class="op">(</span><span class="va">set_ab_names</span><span class="op">)</span><span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
|
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="op">)</span></span></span>
|
|
<span class="r-in"><span> </span></span>
|
|
<span class="r-in"><span> <span class="co"># set_ab_names() works with any AB property:</span></span></span>
|
|
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
|
<span class="r-in"><span> <span class="fu">set_ab_names</span><span class="op">(</span>property <span class="op">=</span> <span class="st">"atc"</span><span class="op">)</span><span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
|
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="op">)</span></span></span>
|
|
<span class="r-in"><span> </span></span>
|
|
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
|
<span class="r-in"><span> <span class="fu">set_ab_names</span><span class="op">(</span><span class="fu">where</span><span class="op">(</span><span class="va">is.rsi</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
|
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">colnames</a></span><span class="op">(</span><span class="op">)</span></span></span>
|
|
<span class="r-in"><span> </span></span>
|
|
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
|
<span class="r-in"><span> <span class="fu">set_ab_names</span><span class="op">(</span><span class="va">NIT</span><span class="op">:</span><span class="va">VAN</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
|
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">colnames</a></span><span class="op">(</span><span class="op">)</span></span></span>
|
|
<span class="r-in"><span><span class="op">}</span></span></span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [1] "date" "hospital_id" "ward_icu" "ward_clinical" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [5] "ward_outpatient" "age" "gender" "patient_id" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [9] "mo" "PEN" "OXA" "FLC" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [13] "AMX" "AMC" "AMP" "TZP" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [17] "CZO" "FEP" "CXM" "FOX" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [21] "CTX" "CAZ" "CRO" "GEN" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [25] "TOB" "AMK" "KAN" "TMP" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [29] "SXT" "nitrofurantoin" "fosfomycin" "linezolid" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [33] "ciprofloxacin" "moxifloxacin" "vancomycin" "TEC" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [37] "TCY" "TGC" "DOX" "ERY" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [41] "CLI" "AZM" "IPM" "MEM" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [45] "MTR" "CHL" "COL" "MUP" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [49] "RIF" </span>
|
|
<span class="r-in"><span><span class="co"># }</span></span></span>
|
|
</code></pre></div>
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</div>
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</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
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</nav></aside></div>
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<footer><div class="pkgdown-footer-left">
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<p></p><p><code>AMR</code> (for R). Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> in collaboration with non-profit organisations<br><a target="_blank" href="https://www.certe.nl" class="external-link">Certe Medical Diagnostics and Advice Foundation</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>.</p>
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<div class="pkgdown-footer-right">
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<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>
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