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Conduct AMR Analysis
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<a class="dropdown-item" href="../reference/antibiogram.html">
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Generate Antibiogram (Trad./Syndromic/WISCA)
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Get Taxonomy of a Microorganism
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Get Properties of an Antibiotic Drug
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Get Properties of an Antiviral Drug
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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 drug 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 - the default is the current system language (see <code><a href="translate.html">get_AMR_locale()</a></code>) and can also be set with the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_locale</a></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>: columns 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>
|
|
<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>
|
|
<div class="section level2">
|
|
<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 data sets in this <code>AMR</code> package (about microorganisms, antibiotics, SIR 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 <a href="https://msberends.github.io/AMR/articles/datasets.html">our website for the download links</a>. The actual files are of course available on <a href="https://github.com/msberends/AMR/tree/main/data-raw" class="external-link">our GitHub repository</a>.</p>
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</div>
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|
<div class="section level2">
|
|
<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">
|
|
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
|
|
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># all properties:</span></span></span>
|
|
<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></span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [1] "Amoxicillin"</span>
|
|
<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></span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [1] "J01CA04"</span>
|
|
<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></span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [1] 33613</span>
|
|
<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></span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [1] "actimoxi" "amoclen" "amolin" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [4] "amopen" "amopenixin" "amoxibiotic" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [7] "amoxicaps" "amoxicilina" "amoxicillin" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [10] "amoxicillin hydrate" "amoxicilline" "amoxicillinum" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [13] "amoxiden" "amoxil" "amoxivet" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [16] "amoxy" "amoxycillin" "amoxyke" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [19] "anemolin" "aspenil" "atoksilin" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [22] "biomox" "bristamox" "cemoxin" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [25] "clamoxyl" "damoxy" "delacillin" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [28] "demoksil" "dispermox" "efpenix" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [31] "flemoxin" "hiconcil" "histocillin" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [34] "hydroxyampicillin" "ibiamox" "imacillin" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [37] "lamoxy" "largopen" "metafarma capsules" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [40] "metifarma capsules" "moksilin" "moxacin" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [43] "moxatag" "ospamox" "pamoxicillin" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [46] "piramox" "promoxil" "remoxil" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [49] "robamox" "sawamox pm" "tolodina" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [52] "topramoxin" "unicillin" "utimox" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [55] "vetramox" </span>
|
|
<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></span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [1] "actimoxi" "amoclen" "amolin" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [4] "amopen" "amopenixin" "amoxibiotic" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [7] "amoxicaps" "amoxicilina" "amoxicillin" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [10] "amoxicillin hydrate" "amoxicilline" "amoxicillinum" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [13] "amoxiden" "amoxil" "amoxivet" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [16] "amoxy" "amoxycillin" "amoxyke" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [19] "anemolin" "aspenil" "atoksilin" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [22] "biomox" "bristamox" "cemoxin" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [25] "clamoxyl" "damoxy" "delacillin" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [28] "demoksil" "dispermox" "efpenix" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [31] "flemoxin" "hiconcil" "histocillin" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [34] "hydroxyampicillin" "ibiamox" "imacillin" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [37] "lamoxy" "largopen" "metafarma capsules" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [40] "metifarma capsules" "moksilin" "moxacin" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [43] "moxatag" "ospamox" "pamoxicillin" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [46] "piramox" "promoxil" "remoxil" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [49] "robamox" "sawamox pm" "tolodina" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [52] "topramoxin" "unicillin" "utimox" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [55] "vetramox" </span>
|
|
<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></span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [1] "Beta-lactams/penicillins"</span>
|
|
<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></span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [1] "Beta-lactam antibacterials, penicillins"</span>
|
|
<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></span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [1] "Penicillins with extended spectrum"</span>
|
|
<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></span>
|
|
<span class="r-out co"><span class="r-pr">#></span> Amoxicillin </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> "https://www.whocc.no/atc_ddd_index/?code=J01CA04&showdescription=no" </span>
|
|
<span class="r-in"><span></span></span>
|
|
<span class="r-in"><span><span class="co"># smart lowercase tranformation</span></span></span>
|
|
<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></span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [1] "Amoxicillin/clavulanic acid" "Polymyxin B" </span>
|
|
<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>, tolower <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [1] "amoxicillin/clavulanic acid" "polymyxin B" </span>
|
|
<span class="r-in"><span></span></span>
|
|
<span class="r-in"><span><span class="co"># defined daily doses (DDD)</span></span></span>
|
|
<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></span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [1] 1.5</span>
|
|
<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></span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [1] "g"</span>
|
|
<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></span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [1] 3</span>
|
|
<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></span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [1] "g"</span>
|
|
<span class="r-in"><span></span></span>
|
|
<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>
|
|
<span class="r-out co"><span class="r-pr">#></span> $ab</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [1] "AMX"</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> $cid</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [1] 33613</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> $name</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [1] "Amoxicillin"</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> $group</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [1] "Beta-lactams/penicillins"</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> $atc</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [1] "J01CA04"</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> $atc_group1</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [1] "Beta-lactam antibacterials, penicillins"</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> $atc_group2</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [1] "Penicillins with extended spectrum"</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> $tradenames</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [1] "actimoxi" "amoclen" "amolin" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [4] "amopen" "amopenixin" "amoxibiotic" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [7] "amoxicaps" "amoxicilina" "amoxicillin" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [10] "amoxicillin hydrate" "amoxicilline" "amoxicillinum" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [13] "amoxiden" "amoxil" "amoxivet" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [16] "amoxy" "amoxycillin" "amoxyke" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [19] "anemolin" "aspenil" "atoksilin" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [22] "biomox" "bristamox" "cemoxin" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [25] "clamoxyl" "damoxy" "delacillin" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [28] "demoksil" "dispermox" "efpenix" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [31] "flemoxin" "hiconcil" "histocillin" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [34] "hydroxyampicillin" "ibiamox" "imacillin" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [37] "lamoxy" "largopen" "metafarma capsules" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [40] "metifarma capsules" "moksilin" "moxacin" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [43] "moxatag" "ospamox" "pamoxicillin" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [46] "piramox" "promoxil" "remoxil" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [49] "robamox" "sawamox pm" "tolodina" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [52] "topramoxin" "unicillin" "utimox" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [55] "vetramox" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> $loinc</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [1] "16365-9" "25274-2" "3344-9" "80133-2"</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> $ddd</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> $ddd$oral</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> $ddd$oral$amount</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [1] 1.5</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> $ddd$oral$units</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [1] "g"</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> $ddd$iv</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> $ddd$iv$amount</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [1] 3</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> $ddd$iv$units</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [1] "g"</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> </span>
|
|
<span class="r-in"><span></span></span>
|
|
<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>
|
|
<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></span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [1] "J01CA01" "S01AA19"</span>
|
|
<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></span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [1] "Beta-lactams/penicillins"</span>
|
|
<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></span>
|
|
<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>
|
|
<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></span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [1] "Ampicillin"</span>
|
|
<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></span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [1] "Ampicillin"</span>
|
|
<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></span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [1] "Ampicillin"</span>
|
|
<span class="r-in"><span></span></span>
|
|
<span class="r-in"><span><span class="co"># spelling from different languages and dyslexia are no problem</span></span></span>
|
|
<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>
|
|
<span class="r-out co"><span class="r-pr">#></span> [1] "J01DD04"</span>
|
|
<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>
|
|
<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>
|
|
<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>
|
|
<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" "patient" "age" "gender" "ward" "mo" "PEN" </span>
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<span class="r-out co"><span class="r-pr">#></span> [8] "OXA" "FLC" "AMX" "AMC" "AMP" "TZP" "CZO" </span>
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<span class="r-out co"><span class="r-pr">#></span> [15] "FEP" "CXM" "FOX" "CTX" "CAZ" "CRO" "GEN" </span>
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|
<span class="r-out co"><span class="r-pr">#></span> [22] "TOB" "AMK" "KAN" "TMP" "SXT" "NIT" "FOS" </span>
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|
<span class="r-out co"><span class="r-pr">#></span> [29] "LNZ" "CIP" "MFX" "VAN" "TEC" "TCY" "TGC" </span>
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|
<span class="r-out co"><span class="r-pr">#></span> [36] "DOX" "ERY" "CLI" "AZM" "IPM" "MEM" "MTR" </span>
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|
<span class="r-out co"><span class="r-pr">#></span> [43] "CHL" "COL" "MUP" "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" "patient" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [3] "age" "gender" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [5] "ward" "mo" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [7] "benzylpenicillin" "oxacillin" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [9] "flucloxacillin" "amoxicillin" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [11] "amoxicillin_clavulanic_acid" "ampicillin" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [13] "piperacillin_tazobactam" "cefazolin" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [15] "cefepime" "cefuroxime" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [17] "cefoxitin" "cefotaxime" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [19] "ceftazidime" "ceftriaxone" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [21] "gentamicin" "tobramycin" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [23] "amikacin" "kanamycin" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [25] "trimethoprim" "trimethoprim_sulfamethoxazole"</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [27] "nitrofurantoin" "fosfomycin" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [29] "linezolid" "ciprofloxacin" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [31] "moxifloxacin" "vancomycin" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [33] "teicoplanin" "tetracycline" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [35] "tigecycline" "doxycycline" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [37] "erythromycin" "clindamycin" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [39] "azithromycin" "imipenem" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [41] "meropenem" "metronidazole" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [43] "chloramphenicol" "colistin" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [45] "mupirocin" "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" "patient" "age" "gender" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [5] "ward" "mo" "PEN" "OXA" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [9] "FLC" "AMX" "AMC" "AMP" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [13] "TZP" "CZO" "FEP" "CXM" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [17] "FOX" "CTX" "CAZ" "CRO" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [21] "GEN" "TOB" "AMK" "KAN" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [25] "TMP" "SXT" "nitrofurantoin" "fosfomycin" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [29] "linezolid" "ciprofloxacin" "moxifloxacin" "vancomycin" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [33] "TEC" "TCY" "TGC" "DOX" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [37] "ERY" "CLI" "AZM" "IPM" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [41] "MEM" "MTR" "CHL" "COL" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [45] "MUP" "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></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></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></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"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.sir</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" "patient" "age" "gender" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [5] "ward" "mo" "PEN" "OXA" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [9] "FLC" "AMX" "AMC" "AMP" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [13] "TZP" "CZO" "FEP" "CXM" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [17] "FOX" "CTX" "CAZ" "CRO" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [21] "GEN" "TOB" "AMK" "KAN" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [25] "TMP" "SXT" "nitrofurantoin" "fosfomycin" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [29] "linezolid" "ciprofloxacin" "moxifloxacin" "vancomycin" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [33] "TEC" "TCY" "TGC" "DOX" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [37] "ERY" "CLI" "AZM" "IPM" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [41] "MEM" "MTR" "CHL" "COL" </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [45] "MUP" "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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<footer><div class="pkgdown-footer-left">
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<p></p><p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p>
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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.svg" style="max-width: 150px;"></a><a target="_blank" href="https://www.umcg.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_umcg.svg" style="max-width: 150px;"></a></p>
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