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(v1.8.0.9001) as.mo improvement, fixes #52

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dr. M.S. (Matthijs) Berends
2022-02-26 21:58:23 +01:00
parent be792cc9eb
commit 18e8525d10
108 changed files with 568 additions and 399 deletions
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docs/reference/microorganisms.html
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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="Released version">1.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
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<p>A data set containing the full microbial taxonomy (<strong>last updated: 5 October 2021</strong>) of six kingdoms from the Catalogue of Life (CoL) and the List of Prokaryotic names with Standing in Nomenclature (LPSN). MO codes can be looked up using <code><a href="as.mo.html">as.mo()</a></code>.</p>
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<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="va">microorganisms</span></code></pre></div></div>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span class="va">microorganisms</span></code></pre></div>
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<div id="format">
<h2>Format</h2>
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<h2>Catalogue of Life</h2>
<p><img src="figures/logo_col.png" height="40px" style="margin-bottom:5px"><br>
<p><img src="figures/logo_col.png" height="40" style='margin-bottom:"5"'><br>
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>
<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="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
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