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(v1.5.0.9006) major documentation update

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dr. M.S. (Matthijs) Berends
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<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Data set with 67,151 microorganisms — microorganisms • AMR (for R)</title>
<title>Data Set with 67,151 Microorganisms — microorganisms • AMR (for R)</title>
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<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
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<link href="../extra.css" rel="stylesheet">
<script src="../extra.js"></script>
<meta property="og:title" content="Data set with 67,151 microorganisms — microorganisms" />
<meta property="og:title" content="Data Set with 67,151 Microorganisms — microorganisms" />
<meta property="og:description" content="A data set containing the microbial taxonomy of six kingdoms from the Catalogue of Life. MO codes can be looked up using as.mo()." />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.png" />
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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9006</span>
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</div>
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<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Data set with 67,151 microorganisms</h1>
<h1>Data Set with 67,151 Microorganisms</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
<div class="hidden name"><code>microorganisms.Rd</code></div>
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<li><p><code>rank</code><br /> Text of the taxonomic rank of the microorganism, like <code>"species"</code> or <code>"genus"</code></p></li>
<li><p><code>ref</code><br /> Author(s) and year of concerning scientific publication</p></li>
<li><p><code>species_id</code><br /> ID of the species as used by the Catalogue of Life</p></li>
<li><p><code>source</code><br /> Either "CoL", "DSMZ" (see Source) or "manually added"</p></li>
<li><p><code>source</code><br /> Either "CoL", "DSMZ" (see <em>Source</em>) or "manually added"</p></li>
<li><p><code>prevalence</code><br /> Prevalence of the microorganism, see <code><a href='as.mo.html'>as.mo()</a></code></p></li>
<li><p><code>snomed</code><br /> SNOMED code of the microorganism. Use <code><a href='mo_property.html'>mo_snomed()</a></code> to retrieve it quickly, see <code><a href='mo_property.html'>mo_property()</a></code>.</p></li>
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</ul>
<h2 class="hasAnchor" id="about-the-records-from-dsmz-see-source-"><a class="anchor" href="#about-the-records-from-dsmz-see-source-"></a>About the records from DSMZ (see source)</h2>
<h2 class="hasAnchor" id="about-the-records-from-dsmz-see-source-"><a class="anchor" href="#about-the-records-from-dsmz-see-source-"></a>About the Records from DSMZ (see <em>Source</em>)</h2>
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<p><img src='figures/logo_col.png' height=40px style=margin-bottom:5px /> <br />
This package contains the complete taxonomic tree of almost all microorganisms (~70,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, <a href='http://www.catalogueoflife.org'>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'>lpsn.dsmz.de</a>). This supplementation is needed until the <a href='https://github.com/CatalogueOfLife/general'>CoL+ project</a> is finished, which we await.</p>
<p><a href='catalogue_of_life.html'>Click here</a> for more information about the included taxa. Check which versions of the CoL and LSPN were included in this package with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version()</a></code>.</p>
<h2 class="hasAnchor" id="reference-data-publicly-available"><a class="anchor" href="#reference-data-publicly-available"></a>Reference data publicly available</h2>
<h2 class="hasAnchor" id="reference-data-publicly-available"><a class="anchor" href="#reference-data-publicly-available"></a>Reference Data Publicly Available</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 <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>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on Our Website!</h2>