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<img src="../logo.svg" class="logo" alt=""><h1>Data Set with Previously Accepted Taxonomic Names</h1>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/data.R" class="external-link"><code>R/data.R</code></a></small>
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<div class="d-none name"><code>microorganisms.old.Rd</code></div>
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<div class="ref-description section level2">
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<p>A data set containing old (previously valid or accepted) taxonomic names according to the Catalogue of Life. This data set is used internally by <code><a href="as.mo.html">as.mo()</a></code>.</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.old</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://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> with 14,338 observations and 4 variables:</p><ul><li><p><code>fullname</code><br> Old full taxonomic name of the microorganism</p></li>
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<li><p><code>fullname_new</code><br> New full taxonomic name of the microorganism</p></li>
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<li><p><code>ref</code><br> Author(s) and year of concerning scientific publication</p></li>
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<li><p><code>prevalence</code><br> Prevalence of the microorganism, see <code><a href="as.mo.html">as.mo()</a></code></p></li>
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</ul></div>
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<div class="section level2">
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<h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
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<p>Catalogue of Life: Annual Checklist (public online taxonomic database), <a href="http://www.catalogueoflife.org" class="external-link">http://www.catalogueoflife.org</a> (check included annual version with <code><a href="catalogue_of_life_version.html">catalogue_of_life_version()</a></code>).</p>
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<p>Parte, A.C. (2018). LPSN - List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. International Journal of Systematic and Evolutionary Microbiology, 68, 1825-1829; <a href="https://doi.org/10.1099/ijsem.0.002786" class="external-link">doi:10.1099/ijsem.0.002786</a></p>
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<div class="section level2">
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<h2 id="catalogue-of-life">Catalogue of Life<a class="anchor" aria-label="anchor" href="#catalogue-of-life"></a></h2>
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<p><img src="figures/logo_col.png" height="40" style='margin-bottom:"5"'><br>
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This package contains the complete taxonomic tree of almost all microorganisms (~71,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, <a href="http://www.catalogueoflife.org" class="external-link">http://www.catalogueoflife.org</a>). The CoL is the most comprehensive and authoritative global index of species currently available. Nonetheless, we supplemented the CoL data with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, <a href="https://lpsn.dsmz.de" class="external-link">lpsn.dsmz.de</a>). This supplementation is needed until the <a href="https://github.com/CatalogueOfLife/general" class="external-link">CoL+ project</a> is finished, which we await.</p>
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<p><a href="catalogue_of_life.html">Click here</a> for more information about the included taxa. Check which versions of the CoL and LPSN were included in this package with <code><a href="catalogue_of_life_version.html">catalogue_of_life_version()</a></code>.</p>
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<div class="section level2">
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<h2 id="reference-data-publicly-available">Reference Data Publicly Available<a class="anchor" aria-label="anchor" href="#reference-data-publicly-available"></a></h2>
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<p>All reference data sets (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find <a href="https://msberends.github.io/AMR/articles/datasets.html">all download links on our website</a>, which is automatically updated with every code change.</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> <code><a href="mo_property.html">mo_property()</a></code> <a href="microorganisms.html">microorganisms</a></p></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="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">microorganisms.old</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> fullname fullname_new</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 Abaphospora petrucciana Nectria petrucciana</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 Abathostoma stercoris Echinocyclidium stercoris</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 Abbottina tannerbankensis Nonion tannerbankensis</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 Abditodentrix rhomboidalis Tortoplectella rhomboidalis</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 Abiotrophia adiacens Granulicatella adiacens</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 Abiotrophia balaenopterae Granulicatella balaenopterae</span>
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<span class="r-out co"><span class="r-pr">#></span> ref prevalence</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 Kirschst, 1939 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 Berger in Corliss, 1979 3</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 McCulloch, 1977 3</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 Millett, 1899 3</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 Kawamura et al., 1995 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 Lawson et al., 1999 2</span>
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</code></pre></div>
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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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