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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>Data Set with 4 971 Common Microorganism Codes — microorganisms.codes • 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-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/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="Data Set with 4 971 Common Microorganism Codes — microorganisms.codes"><meta name="description" content="A data set containing commonly used codes for microorganisms, from laboratory systems and WHONET. Define your own with set_mo_source(). They will all be searched when using as.mo() and consequently all the mo_* functions."><meta property="og:description" content="A data set containing commonly used codes for microorganisms, from laboratory systems and WHONET. Define your own with set_mo_source(). They will all be searched when using as.mo() and consequently all the mo_* functions."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"></head><body>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9120</small>
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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>Data Set with 4 971 Common Microorganism Codes</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.codes.Rd</code></div>
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</div>
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<div class="ref-description section level2">
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<p>A data set containing commonly used codes for microorganisms, from laboratory systems and <a href="https://whonet.org" class="external-link">WHONET</a>. Define your own with <code><a href="mo_source.html">set_mo_source()</a></code>. They will all be searched when using <code><a href="as.mo.html">as.mo()</a></code> and consequently all the <code><a href="mo_property.html">mo_*</a></code> functions.</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.codes</span></span></code></pre></div>
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</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 4 971 observations and 2 variables:</p><ul><li><p><code>code</code><br> Commonly used code of a microorganism. <em><strong>This is a unique identifier.</strong></em></p></li>
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<li><p><code>mo</code><br> ID of the microorganism in the <a href="microorganisms.html">microorganisms</a> data set</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>Like all data sets in this package, this data set is publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata. 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">
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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.codes</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 4,971 × 2</span></span>
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<span class="r-out co"><span class="r-pr">#></span> code mo </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 1011 B_GRAMP </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 1012 B_GRAMP </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 1013 B_GRAMN </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 1014 B_GRAMN </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 1015 F_YEAST </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 103 B_ESCHR_COLI </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 104 B_SLMNL_ENTR_ENTR</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 1100 B_STRPT </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 1101 B_STRPT_VIRI </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 1102 B_STRPT_HAEM </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 4,961 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"># 'ECO' or 'eco' is the WHONET code for E. coli:</span></span></span>
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<span class="r-in"><span><span class="va">microorganisms.codes</span><span class="op">[</span><span class="va">microorganisms.codes</span><span class="op">$</span><span class="va">code</span> <span class="op">==</span> <span class="st">"ECO"</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: 1 × 2</span></span>
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<span class="r-out co"><span class="r-pr">#></span> code mo </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> ECO B_ESCHR_COLI</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="co"># and therefore, 'eco' will be understood as E. coli in this package:</span></span></span>
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<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_info</a></span><span class="op">(</span><span class="st">"eco"</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> $mo</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "B_ESCHR_COLI"</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> $rank</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "species"</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> $kingdom</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "Bacteria"</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> $phylum</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "Pseudomonadota"</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> $class</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "Gammaproteobacteria"</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> $order</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "Enterobacterales"</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> $family</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "Enterobacteriaceae"</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> $genus</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "Escherichia"</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> $species</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "coli"</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> $subspecies</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] ""</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> $status</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "accepted"</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> $synonyms</span>
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<span class="r-out co"><span class="r-pr">#></span> NULL</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> $gramstain</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "Gram-negative"</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> $oxygen_tolerance</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "facultative anaerobe"</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> $url</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "https://lpsn.dsmz.de/species/escherichia-coli"</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> $ref</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "Castellani et al., 1919"</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> $snomed</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "1095001000112106" "715307006" "737528008" "416989002" </span>
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<span class="r-out co"><span class="r-pr">#></span> [5] "116397003" "414097009" "414098004" "414099007" </span>
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<span class="r-out co"><span class="r-pr">#></span> [9] "414100004" "116395006" "735270003" "116396007" </span>
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<span class="r-out co"><span class="r-pr">#></span> [13] "83285000" "116394005" "112283007" "710886005" </span>
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<span class="r-out co"><span class="r-pr">#></span> [17] "710887001" "710888006" "710889003" "414132004" </span>
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<span class="r-out co"><span class="r-pr">#></span> [21] "721892009" "416812001" "416740004" "417216001" </span>
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<span class="r-out co"><span class="r-pr">#></span> [25] "457541006" "710253004" "416530004" "417189006" </span>
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<span class="r-out co"><span class="r-pr">#></span> [29] "409800005" "713925008" "444771000124108" "838549008" </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> $lpsn</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "776057"</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> $mycobank</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> $gbif</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "11286021"</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_members</span>
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<span class="r-out co"><span class="r-pr">#></span> character(0)</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"># works for all AMR functions:</span></span></span>
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<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_is_intrinsic_resistant</a></span><span class="op">(</span><span class="st">"eco"</span>, ab <span class="op">=</span> <span class="st">"vancomycin"</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] TRUE</span>
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</code></pre></div>
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<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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