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<img src="../logo.svg" class="logo" alt=""><h1>Add Manual Antimicrobials to This Package</h1>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/add_custom_antimicrobials.R" class="external-link"><code>R/add_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 class="ref-description section level2">
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<p>With <code>add_custom_antimicrobials()</code> you can add your own manual antimicrobial codes to the <code>AMR</code> package.</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 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>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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<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
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<p>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. It is possible to save the antimicrobial additions to your <code>.Rprofile</code> file to circumvent this, for example:</p>
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<p></p><div class="sourceCode r"><pre><code><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR/">AMR</a></span><span class="op">)</span></span>
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<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">"TEST"</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>
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<p>Use <code>clear_custom_antimicrobials()</code> to clear the previously added antimicrobials.</p>
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<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
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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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