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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><ahref="as.mo.html">as.mo()</a></code>.</p>
<p>A <ahref="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>
<li><p><code>fullname_new</code><br> New full taxonomic name of the microorganism</p></li>
<li><p><code>ref</code><br> Author(s) and year of concerning scientific publication</p></li>
<li><p><code>prevalence</code><br> Prevalence of the microorganism, see <code><ahref="as.mo.html">as.mo()</a></code></p></li>
<p>Catalogue of Life: Annual Checklist (public online taxonomic database), <ahref="http://www.catalogueoflife.org"class="external-link">http://www.catalogueoflife.org</a> (check included annual version with <code><ahref="catalogue_of_life_version.html">catalogue_of_life_version()</a></code>).</p>
<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; <ahref="https://doi.org/10.1099/ijsem.0.002786"class="external-link">doi:10.1099/ijsem.0.002786</a></p>
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<h2id="catalogue-of-life">Catalogue of Life<aclass="anchor"aria-label="anchor"href="#catalogue-of-life"></a></h2>
This package contains the complete taxonomic tree of almost all microorganisms (~71,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, <ahref="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, <ahref="https://lpsn.dsmz.de"class="external-link">lpsn.dsmz.de</a>). This supplementation is needed until the <ahref="https://github.com/CatalogueOfLife/general"class="external-link">CoL+ project</a> is finished, which we await.</p>
<p><ahref="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><ahref="catalogue_of_life_version.html">catalogue_of_life_version()</a></code>.</p>
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<h2id="reference-data-publicly-available">Reference Data Publicly Available<aclass="anchor"aria-label="anchor"href="#reference-data-publicly-available"></a></h2>
<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 <ahref="https://msberends.github.io/AMR/articles/datasets.html">all download links on our website</a>, which is automatically updated with every code change.</p>
<spanclass="r-out co"><spanclass="r-pr">#></span> 5 Kawamura et al., 1995 2</span>
<spanclass="r-out co"><spanclass="r-pr">#></span> 6 Lawson et al., 1999 2</span>
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<p></p><p><code>AMR</code> (for R). Developed at the <atarget="_blank"href="https://www.rug.nl"class="external-link">University of Groningen</a> in collaboration with non-profit organisations<br><atarget="_blank"href="https://www.certe.nl"class="external-link">Certe Medical Diagnostics and Advice Foundation</a> and <atarget="_blank"href="https://www.umcg.nl"class="external-link">University Medical Center Groningen</a>.</p>
