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<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Add Custom Antimicrobials — add_custom_antimicrobials • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.9/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.9/font.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Add Custom Antimicrobials — add_custom_antimicrobials"><meta name="description" content="With add_custom_antimicrobials() you can add your own custom antimicrobial drug names and codes."><meta property="og:description" content="With add_custom_antimicrobials() you can add your own custom antimicrobial drug names and codes."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"></head><body>
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<main id="main" class="col-md-9"><div class="page-header">
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<img src="../logo.svg" class="logo" alt=""><h1>Add Custom Antimicrobials</h1>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/R/custom_antimicrobials.R" class="external-link"><code>R/custom_antimicrobials.R</code></a></small>
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<div class="d-none name"><code>add_custom_antimicrobials.Rd</code></div>
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</div>
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<div class="ref-description section level2">
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<p>With <code>add_custom_antimicrobials()</code> you can add your own custom antimicrobial drug names and codes.</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">add_custom_antimicrobials</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span>
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<span></span>
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<span><span class="fu">clear_custom_antimicrobials</span><span class="op">(</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 id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
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<dd><p>a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> resembling the <a href="antibiotics.html">antibiotics</a> data set, at least containing columns "ab" and "name"</p></dd>
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</dl></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><strong>Important:</strong> Due to how <span style="R">R</span> works, the <code>add_custom_antimicrobials()</code> function has to be run in every <span style="R">R</span> session - added antimicrobials are not stored between sessions and are thus lost when <span style="R">R</span> is exited.</p>
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<p>There are two ways to circumvent this and automate the process of adding antimicrobials:</p>
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<p><strong>Method 1:</strong> Using the package option <code><a href="AMR-options.html">AMR_custom_ab</a></code>, which is the preferred method. To use this method:</p><ol><li><p>Create a data set in the structure of the <a href="antibiotics.html">antibiotics</a> data set (containing at the very least columns "ab" and "name") and save it with <code><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">saveRDS()</a></code> to a location of choice, e.g. <code>"~/my_custom_ab.rds"</code>, or any remote location.</p></li>
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<li><p>Set the file location to the package option <code><a href="AMR-options.html">AMR_custom_ab</a></code>: <code>options(AMR_custom_ab = "~/my_custom_ab.rds")</code>. This can even be a remote file location, such as an https URL. Since options are not saved between <span style="R">R</span> sessions, it is best to save this option to the <code>.Rprofile</code> file so that it will be loaded on start-up of <span style="R">R</span>. To do this, open the <code>.Rprofile</code> file using e.g. <code>utils::file.edit("~/.Rprofile")</code>, add this text and save the file:</p>
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<p></p><div class="sourceCode r"><pre><code><span><span class="co"># Add custom antimicrobial codes:</span></span>
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<span><span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">options</a></span><span class="op">(</span>AMR_custom_ab <span class="op">=</span> <span class="st">"~/my_custom_ab.rds"</span><span class="op">)</span></span></code></pre><p></p></div>
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<p>Upon package load, this file will be loaded and run through the <code>add_custom_antimicrobials()</code> function.</p></li>
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</ol><p><strong>Method 2:</strong> Loading the antimicrobial additions directly from your <code>.Rprofile</code> file. Note that the definitions will be stored in a user-specific <span style="R">R</span> file, which is a suboptimal workflow. To use this method:</p><ol><li><p>Edit the <code>.Rprofile</code> file using e.g. <code>utils::file.edit("~/.Rprofile")</code>.</p></li>
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<li><p>Add a text like below and save the file:</p>
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<p></p><div class="sourceCode r"><pre><code><span> <span class="co"># Add custom antibiotic drug codes:</span></span>
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<span> <span class="fu">AMR</span><span class="fu">::</span><span class="fu"><a href="../reference/add_custom_antimicrobials.html">add_custom_antimicrobials</a></span><span class="op">(</span></span>
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<span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>ab <span class="op">=</span> <span class="st">"TESTAB"</span>,</span>
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<span> name <span class="op">=</span> <span class="st">"Test Antibiotic"</span>,</span>
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<span> group <span class="op">=</span> <span class="st">"Test Group"</span><span class="op">)</span></span>
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<span> <span class="op">)</span></span></code></pre><p></p></div></li>
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</ol><p>Use <code>clear_custom_antimicrobials()</code> to clear the previously added antimicrobials.</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><code><a href="add_custom_microorganisms.html">add_custom_microorganisms()</a></code> to add custom microorganisms.</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"># \donttest{</span></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"># returns NA and throws a warning (which is suppressed here):</span></span></span>
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<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/warning.html" class="external-link">suppressWarnings</a></span><span class="op">(</span></span></span>
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<span class="r-in"><span> <span class="fu"><a href="as.ab.html">as.ab</a></span><span class="op">(</span><span class="st">"testab"</span><span class="op">)</span></span></span>
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<span class="r-in"><span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> Class 'ab'</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] <NA></span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="co"># now add a custom entry - it will be considered by as.ab() and</span></span></span>
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<span class="r-in"><span><span class="co"># all ab_*() functions</span></span></span>
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<span class="r-in"><span><span class="fu">add_custom_antimicrobials</span><span class="op">(</span></span></span>
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<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
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<span class="r-in"><span> ab <span class="op">=</span> <span class="st">"TESTAB"</span>,</span></span>
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<span class="r-in"><span> name <span class="op">=</span> <span class="st">"Test Antibiotic"</span>,</span></span>
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<span class="r-in"><span> <span class="co"># you can add any property present in the</span></span></span>
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<span class="r-in"><span> <span class="co"># 'antibiotics' data set, such as 'group':</span></span></span>
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<span class="r-in"><span> group <span class="op">=</span> <span class="st">"Test Group"</span></span></span>
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<span class="r-in"><span> <span class="op">)</span></span></span>
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<span class="r-in"><span><span class="op">)</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> ℹ Added one record to the internal antibiotics data set.</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="co"># "testab" is now a new antibiotic:</span></span></span>
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<span class="r-in"><span><span class="fu"><a href="as.ab.html">as.ab</a></span><span class="op">(</span><span class="st">"testab"</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> Class 'ab'</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] TESTAB</span>
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<span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_name</a></span><span class="op">(</span><span class="st">"testab"</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "Test Antibiotic"</span>
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<span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_group</a></span><span class="op">(</span><span class="st">"testab"</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "Test Group"</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_info</a></span><span class="op">(</span><span class="st">"testab"</span><span class="op">)</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] "TESTAB"</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] NA</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] "Test Antibiotic"</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] "Test Group"</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] NA</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] NA</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] NA</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] NA</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] NA</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] NA</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] NA</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] NA</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] NA</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></span>
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<span class="r-in"><span><span class="co"># Add Co-fluampicil, which is one of the many J01CR50 codes, see</span></span></span>
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<span class="r-in"><span><span class="co"># https://atcddd.fhi.no/ddd/list_of_ddds_combined_products/</span></span></span>
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<span class="r-in"><span><span class="fu">add_custom_antimicrobials</span><span class="op">(</span></span></span>
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||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
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||
<span class="r-in"><span> ab <span class="op">=</span> <span class="st">"COFLU"</span>,</span></span>
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||
<span class="r-in"><span> name <span class="op">=</span> <span class="st">"Co-fluampicil"</span>,</span></span>
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||
<span class="r-in"><span> atc <span class="op">=</span> <span class="st">"J01CR50"</span>,</span></span>
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||
<span class="r-in"><span> group <span class="op">=</span> <span class="st">"Beta-lactams/penicillins"</span></span></span>
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||
<span class="r-in"><span> <span class="op">)</span></span></span>
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<span class="r-in"><span><span class="op">)</span></span></span>
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||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Added one record to the internal antibiotics data set.</span>
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||
<span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_atc</a></span><span class="op">(</span><span class="st">"Co-fluampicil"</span><span class="op">)</span></span></span>
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||
<span class="r-out co"><span class="r-pr">#></span> [1] "J01CR50"</span>
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||
<span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_name</a></span><span class="op">(</span><span class="st">"J01CR50"</span><span class="op">)</span></span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] "Co-fluampicil"</span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span><span class="co"># even antibiotic selectors work</span></span></span>
|
||
<span class="r-in"><span><span class="va">x</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
|
||
<span class="r-in"><span> random_column <span class="op">=</span> <span class="st">"some value"</span>,</span></span>
|
||
<span class="r-in"><span> coflu <span class="op">=</span> <span class="fu"><a href="as.sir.html">as.sir</a></span><span class="op">(</span><span class="st">"S"</span><span class="op">)</span>,</span></span>
|
||
<span class="r-in"><span> ampicillin <span class="op">=</span> <span class="fu"><a href="as.sir.html">as.sir</a></span><span class="op">(</span><span class="st">"R"</span><span class="op">)</span></span></span>
|
||
<span class="r-in"><span><span class="op">)</span></span></span>
|
||
<span class="r-in"><span><span class="va">x</span></span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> random_column coflu ampicillin</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> 1 some value S R</span>
|
||
<span class="r-in"><span><span class="va">x</span><span class="op">[</span>, <span class="fu"><a href="antibiotic_class_selectors.html">betalactams</a></span><span class="op">(</span><span class="op">)</span><span class="op">]</span></span></span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> ℹ For betalactams() using columns 'coflu' (co-fluampicil) and</span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> 'ampicillin'</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> coflu ampicillin</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> 1 S R</span>
|
||
<span class="r-in"><span><span class="co"># }</span></span></span>
|
||
</code></pre></div>
|
||
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|
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