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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9028</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9030</small>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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@ -185,95 +185,19 @@
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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: 4,957 × 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 4,947 more rows</span></span>
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<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</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-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</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> $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> $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-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</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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<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
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</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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