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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 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 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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<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, SAS, 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 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="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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<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.old</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 14,338 × 4</span></span>
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<span class="r-out co"><span class="r-pr">#></span> fullname fullname_new ref preva…¹</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;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> Abaphospora petrucciana Nectria petrucciana Kirschst, 19… 2</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> Abathostoma stercoris Echinocyclidium stercoris Berger in Co… 3</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> Abbottina tannerbankensis Nonion tannerbankensis McCulloch, 1… 3</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> Abditodentrix rhomboidalis Tortoplectella rhomboidalis Millett, 1899 3</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> Abiotrophia adiacens Granulicatella adiacens Kawamura et … 2</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> Abiotrophia balaenopterae Granulicatella balaenopterae Lawson et al… 2</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> Abiotrophia elegans Granulicatella elegans Roggenkamp e… 2</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> Absidia blakesleeana Lichtheimia blakesleeana Lendn, 1924 3</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> Absidia butleri Gongronella butleri Lendn, 1926 3</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> Absidia corymbifera Lichtheimia corymbifera Sacc et al.,… 3</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 14,328 more rows, and abbreviated variable name ¹prevalence</span></span>
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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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