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<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="hidden name"><code>microorganisms.old.Rd</code></div>
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<div class="ref-description">
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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 id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="va">microorganisms.old</span></code></pre></div></div>
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<div id="format">
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<h2>Format</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 id="source">
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<h2>Source</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; doi: <a href="https://doi.org/10.1099/ijsem.0.002786" class="external-link">10.1099/ijsem.0.002786</a></p>
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<div id="catalogue-of-life">
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<h2>Catalogue of Life</h2>
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<p><img src="figures/logo_col.png" height="40px" style="margin-bottom:5px"><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>
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<div id="reference-data-publicly-available">
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<h2>Reference Data Publicly Available</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 id="read-more-on-our-website-">
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<h2>Read more on Our Website!</h2>
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<p>On our website <a href="https://msberends.github.io/AMR/">https://msberends.github.io/AMR/</a> you can find <a href="https://msberends.github.io/AMR/articles/AMR.html">a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href="https://msberends.github.io/AMR/reference/">complete documentation of all functions</a> and <a href="https://msberends.github.io/AMR/articles/WHONET.html">an example analysis using WHONET data</a>.</p>
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<div id="see-also">
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<h2>See also</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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<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
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