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<img src="../logo.svg" class="logo" alt=""><h1>Data Set with 534 Microorganisms In Species Groups</h1>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/R/data.R" class="external-link"><code>R/data.R</code></a></small>
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<div class="d-none name"><code>microorganisms.groups.Rd</code></div>
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<div class="ref-description section level2">
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<p>A data set containing species groups and microbiological complexes, which are used in <a href="clinical_breakpoints.html">the clinical breakpoints table</a>.</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="va">microorganisms.groups</span></span></code></pre></div>
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<div class="section level2">
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<h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
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<p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 534 observations and 4 variables:</p><ul><li><p><code>mo_group</code><br> ID of the species group / microbiological complex</p></li>
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<li><p><code>mo</code><br> ID of the microorganism belonging in the species group / microbiological complex</p></li>
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<li><p><code>mo_group_name</code><br> Name of the species group / microbiological complex, as retrieved with <code><a href="mo_property.html">mo_name()</a></code></p></li>
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<li><p><code>mo_name</code><br> Name of the microorganism belonging in the species group / microbiological complex, as retrieved with <code><a href="mo_property.html">mo_name()</a></code></p></li>
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<h2 id="download-our-reference-data">Download Our Reference Data<a class="anchor" aria-label="anchor" href="#download-our-reference-data"></a></h2>
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<p>All reference data sets in the AMR package - including information on microorganisms, antimicrobials, and clinical breakpoints - are freely available for download in multiple formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata.</p>
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<p>For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems.</p>
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<p>Visit <a href="https://amr-for-r.org/articles/datasets.html">our website for direct download links</a>, or explore the actual files in <a href="https://github.com/msberends/AMR/tree/main/data-raw" class="external-link">our GitHub repository</a>.</p>
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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="as.mo.html">as.mo()</a></code> <a href="microorganisms.html">microorganisms</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="va">microorganisms.groups</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 534 × 4</span></span>
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<span class="r-out co"><span class="r-pr">#></span> mo_group mo mo_group_name mo_name </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> <span style="color: #949494;">B_</span>ACNTB<span style="color: #949494;">_</span>BMNN-C <span style="color: #949494;">B_</span>ACNTB<span style="color: #949494;">_</span>BMNN Acinetobacter baumannii complex Acinetobacter ba…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> <span style="color: #949494;">B_</span>ACNTB<span style="color: #949494;">_</span>BMNN-C <span style="color: #949494;">B_</span>ACNTB<span style="color: #949494;">_</span>CLCC Acinetobacter baumannii complex Acinetobacter ca…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> <span style="color: #949494;">B_</span>ACNTB<span style="color: #949494;">_</span>BMNN-C <span style="color: #949494;">B_</span>ACNTB<span style="color: #949494;">_</span>LCTC Acinetobacter baumannii complex Acinetobacter di…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> <span style="color: #949494;">B_</span>ACNTB<span style="color: #949494;">_</span>BMNN-C <span style="color: #949494;">B_</span>ACNTB<span style="color: #949494;">_</span>NSCM Acinetobacter baumannii complex Acinetobacter no…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> <span style="color: #949494;">B_</span>ACNTB<span style="color: #949494;">_</span>BMNN-C <span style="color: #949494;">B_</span>ACNTB<span style="color: #949494;">_</span>PITT Acinetobacter baumannii complex Acinetobacter pi…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> <span style="color: #949494;">B_</span>ACNTB<span style="color: #949494;">_</span>BMNN-C <span style="color: #949494;">B_</span>ACNTB<span style="color: #949494;">_</span>SFRT Acinetobacter baumannii complex Acinetobacter se…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> <span style="color: #949494;">B_</span>BCTRD<span style="color: #949494;">_</span>FRGL-C <span style="color: #949494;">B_</span>BCTRD<span style="color: #949494;">_</span>FRGL Bacteroides fragilis complex Bacteroides frag…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> <span style="color: #949494;">B_</span>BCTRD<span style="color: #949494;">_</span>FRGL-C <span style="color: #949494;">B_</span>BCTRD<span style="color: #949494;">_</span>OVTS Bacteroides fragilis complex Bacteroides ovat…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> <span style="color: #949494;">B_</span>BCTRD<span style="color: #949494;">_</span>FRGL-C <span style="color: #949494;">B_</span>BCTRD<span style="color: #949494;">_</span>THTT Bacteroides fragilis complex Bacteroides thet…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> <span style="color: #949494;">B_</span>BCTRD<span style="color: #949494;">_</span>FRGL-C <span style="color: #949494;">B_</span>PHCCL<span style="color: #949494;">_</span>VLGT Bacteroides fragilis complex Bacteroides vulg…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 524 more rows</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"># these are all species in the Bacteroides fragilis group, as per WHONET:</span></span></span>
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<span class="r-in"><span><span class="va">microorganisms.groups</span><span class="op">[</span><span class="va">microorganisms.groups</span><span class="op">$</span><span class="va">mo_group</span> <span class="op">==</span> <span class="st">"B_BCTRD_FRGL-C"</span>, <span class="op">]</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 5 × 4</span></span>
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<span class="r-out co"><span class="r-pr">#></span> mo_group mo mo_group_name mo_name </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> <span style="color: #949494;">B_</span>BCTRD<span style="color: #949494;">_</span>FRGL-C <span style="color: #949494;">B_</span>BCTRD<span style="color: #949494;">_</span>FRGL Bacteroides fragilis complex Bacteroides fragilis </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> <span style="color: #949494;">B_</span>BCTRD<span style="color: #949494;">_</span>FRGL-C <span style="color: #949494;">B_</span>BCTRD<span style="color: #949494;">_</span>OVTS Bacteroides fragilis complex Bacteroides ovatus </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> <span style="color: #949494;">B_</span>BCTRD<span style="color: #949494;">_</span>FRGL-C <span style="color: #949494;">B_</span>BCTRD<span style="color: #949494;">_</span>THTT Bacteroides fragilis complex Bacteroides thetaiot…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">4</span> <span style="color: #949494;">B_</span>BCTRD<span style="color: #949494;">_</span>FRGL-C <span style="color: #949494;">B_</span>PHCCL<span style="color: #949494;">_</span>VLGT Bacteroides fragilis complex Bacteroides vulgatus </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">5</span> <span style="color: #949494;">B_</span>BCTRD<span style="color: #949494;">_</span>FRGL-C <span style="color: #949494;">B_</span>PRBCT<span style="color: #949494;">_</span>DSTS Bacteroides fragilis complex Parabacteroides dist…</span>
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</code></pre></div>
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