mirror of https://github.com/msberends/AMR.git
357 lines
15 KiB
HTML
357 lines
15 KiB
HTML
<!-- Generated by pkgdown: do not edit by hand -->
|
|
<!DOCTYPE html>
|
|
<html lang="en">
|
|
<head>
|
|
<meta charset="utf-8">
|
|
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
|
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
|
|
|
<title>Data set with ~60,000 microorganisms — microorganisms • AMR (for R)</title>
|
|
|
|
<!-- favicons -->
|
|
<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
|
|
<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
|
|
<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png" />
|
|
<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png" />
|
|
<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png" />
|
|
<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png" />
|
|
<!-- jquery -->
|
|
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
|
|
<!-- Bootstrap -->
|
|
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
|
|
|
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
|
|
|
|
<!-- Font Awesome icons -->
|
|
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous" />
|
|
|
|
<!-- clipboard.js -->
|
|
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
|
|
|
|
<!-- sticky kit -->
|
|
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
|
|
|
|
<!-- pkgdown -->
|
|
<link href="../pkgdown.css" rel="stylesheet">
|
|
<script src="../pkgdown.js"></script>
|
|
|
|
|
|
<!-- docsearch -->
|
|
<script src="../docsearch.js"></script>
|
|
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.css" integrity="sha256-QOSRU/ra9ActyXkIBbiIB144aDBdtvXBcNc3OTNuX/Q=" crossorigin="anonymous" />
|
|
<link href="../docsearch.css" rel="stylesheet">
|
|
<script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/jquery.mark.min.js" integrity="sha256-4HLtjeVgH0eIB3aZ9mLYF6E8oU5chNdjU6p6rrXpl9U=" crossorigin="anonymous"></script>
|
|
|
|
|
|
<link href="../extra.css" rel="stylesheet">
|
|
<script src="../extra.js"></script>
|
|
<meta property="og:title" content="Data set with ~60,000 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.gitlab.io/AMR/logo.png" />
|
|
<meta name="twitter:card" content="summary" />
|
|
|
|
|
|
|
|
<!-- mathjax -->
|
|
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
|
|
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
|
|
|
|
<!--[if lt IE 9]>
|
|
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
|
|
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
|
|
<![endif]-->
|
|
|
|
|
|
</head>
|
|
|
|
<body>
|
|
<div class="container template-reference-topic">
|
|
<header>
|
|
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
|
|
<div class="container">
|
|
<div class="navbar-header">
|
|
<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
|
|
<span class="sr-only">Toggle navigation</span>
|
|
<span class="icon-bar"></span>
|
|
<span class="icon-bar"></span>
|
|
<span class="icon-bar"></span>
|
|
</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">0.5.0.9018</span>
|
|
</span>
|
|
</div>
|
|
|
|
<div id="navbar" class="navbar-collapse collapse">
|
|
<ul class="nav navbar-nav">
|
|
<li>
|
|
<a href="../index.html">
|
|
<span class="fa fa-home"></span>
|
|
|
|
Home
|
|
</a>
|
|
</li>
|
|
<li class="dropdown">
|
|
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
|
<span class="fa fa-question-circle"></span>
|
|
|
|
How to
|
|
|
|
<span class="caret"></span>
|
|
</a>
|
|
<ul class="dropdown-menu" role="menu">
|
|
<li>
|
|
<a href="../articles/AMR.html">
|
|
<span class="fa fa-directions"></span>
|
|
|
|
Conduct AMR analysis
|
|
</a>
|
|
</li>
|
|
<li>
|
|
<a href="../articles/resistance_predict.html">
|
|
<span class="fa fa-dice"></span>
|
|
|
|
Predict antimicrobial resistance
|
|
</a>
|
|
</li>
|
|
<li>
|
|
<a href="../articles/WHONET.html">
|
|
<span class="fa fa-globe-americas"></span>
|
|
|
|
Work with WHONET data
|
|
</a>
|
|
</li>
|
|
<li>
|
|
<a href="../articles/SPSS.html">
|
|
<span class="fa fa-file-upload"></span>
|
|
|
|
Import data from SPSS/SAS/Stata
|
|
</a>
|
|
</li>
|
|
<li>
|
|
<a href="../articles/EUCAST.html">
|
|
<span class="fa fa-exchange-alt"></span>
|
|
|
|
Apply EUCAST rules
|
|
</a>
|
|
</li>
|
|
<li>
|
|
<a href="../reference/mo_property.html">
|
|
<span class="fa fa-bug"></span>
|
|
|
|
Get properties of a microorganism
|
|
</a>
|
|
</li>
|
|
<li>
|
|
<a href="../reference/atc_property.html">
|
|
<span class="fa fa-capsules"></span>
|
|
|
|
Get properties of an antibiotic
|
|
</a>
|
|
</li>
|
|
<li>
|
|
<a href="../articles/freq.html">
|
|
<span class="fa fa-sort-amount-down"></span>
|
|
|
|
Create frequency tables
|
|
</a>
|
|
</li>
|
|
<li>
|
|
<a href="../articles/G_test.html">
|
|
<span class="fa fa-clipboard-check"></span>
|
|
|
|
Use the G-test
|
|
</a>
|
|
</li>
|
|
<li>
|
|
<a href="../articles/benchmarks.html">
|
|
<span class="fa fa-shipping-fast"></span>
|
|
|
|
Other: benchmarks
|
|
</a>
|
|
</li>
|
|
</ul>
|
|
</li>
|
|
<li>
|
|
<a href="../reference/">
|
|
<span class="fa fa-book-open"></span>
|
|
|
|
Manual
|
|
</a>
|
|
</li>
|
|
<li>
|
|
<a href="../authors.html">
|
|
<span class="fa fa-users"></span>
|
|
|
|
Authors
|
|
</a>
|
|
</li>
|
|
<li>
|
|
<a href="../news/">
|
|
<span class="far fa far fa-newspaper"></span>
|
|
|
|
Changelog
|
|
</a>
|
|
</li>
|
|
</ul>
|
|
|
|
<ul class="nav navbar-nav navbar-right">
|
|
<li>
|
|
<a href="https://gitlab.com/msberends/AMR">
|
|
<span class="fab fa fab fa-gitlab"></span>
|
|
|
|
Source Code
|
|
</a>
|
|
</li>
|
|
<li>
|
|
<a href="../LICENSE-text.html">
|
|
<span class="fa fa-book"></span>
|
|
|
|
Licence
|
|
</a>
|
|
</li>
|
|
</ul>
|
|
|
|
<form class="navbar-form navbar-right" role="search">
|
|
<div class="form-group">
|
|
<input type="search" class="form-control" name="search-input" id="search-input" placeholder="Search..." aria-label="Search for..." autocomplete="off">
|
|
</div>
|
|
</form>
|
|
|
|
</div><!--/.nav-collapse -->
|
|
</div><!--/.container -->
|
|
</div><!--/.navbar -->
|
|
|
|
|
|
</header>
|
|
|
|
<div class="row">
|
|
<div class="col-md-9 contents">
|
|
<div class="page-header">
|
|
<h1>Data set with ~60,000 microorganisms</h1>
|
|
|
|
<div class="hidden name"><code>microorganisms.Rd</code></div>
|
|
</div>
|
|
|
|
<div class="ref-description">
|
|
|
|
<p>A data set containing the microbial taxonomy of six kingdoms from the Catalogue of Life. MO codes can be looked up using <code><a href='as.mo.html'>as.mo</a></code>.</p>
|
|
|
|
</div>
|
|
|
|
<pre class="usage"><span class='no'>microorganisms</span></pre>
|
|
|
|
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
|
|
|
|
<p>A <code><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></code> with 56,672 observations and 14 variables:</p><dl class='dl-horizontal'>
|
|
<dt><code>mo</code></dt><dd><p>ID of microorganism as used by this package</p></dd>
|
|
<dt><code>col_id</code></dt><dd><p>Catalogue of Life ID</p></dd>
|
|
<dt><code>fullname</code></dt><dd><p>Full name, like <code>"Echerichia coli"</code></p></dd>
|
|
<dt><code>kingdom</code></dt><dd><p>Taxonomic kingdom of the microorganism</p></dd>
|
|
<dt><code>phylum</code></dt><dd><p>Taxonomic phylum of the microorganism</p></dd>
|
|
<dt><code>class</code></dt><dd><p>Taxonomic class of the microorganism</p></dd>
|
|
<dt><code>order</code></dt><dd><p>Taxonomic order of the microorganism</p></dd>
|
|
<dt><code>family</code></dt><dd><p>Taxonomic family of the microorganism</p></dd>
|
|
<dt><code>genus</code></dt><dd><p>Taxonomic genus of the microorganism</p></dd>
|
|
<dt><code>species</code></dt><dd><p>Taxonomic species of the microorganism</p></dd>
|
|
<dt><code>subspecies</code></dt><dd><p>Taxonomic subspecies of the microorganism</p></dd>
|
|
<dt><code>rank</code></dt><dd><p>Taxonomic rank of the microorganism, like <code>"species"</code> or <code>"genus"</code></p></dd>
|
|
<dt><code>ref</code></dt><dd><p>Author(s) and year of concerning scientific publication</p></dd>
|
|
<dt><code>species_id</code></dt><dd><p>ID of the species as used by the Catalogue of Life</p></dd>
|
|
</dl>
|
|
|
|
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
|
|
|
|
<p>Catalogue of Life: Annual Checklist (public online database), <a href='www.catalogueoflife.org'>www.catalogueoflife.org</a>.</p>
|
|
|
|
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
|
|
|
|
<p>Manually added were:</p><ul>
|
|
<li><p>9 species of <em>Streptococcus</em> (beta haemolytic groups A, B, C, D, F, G, H, K and unspecified)</p></li>
|
|
<li><p>2 species of <em>Staphylococcus</em> (coagulase-negative [CoNS] and coagulase-positive [CoPS])</p></li>
|
|
<li><p>2 other undefined (unknown Gram negatives and unknown Gram positives)</p></li>
|
|
</ul>
|
|
|
|
<h2 class="hasAnchor" id="catalogue-of-life"><a class="anchor" href="#catalogue-of-life"></a>Catalogue of Life</h2>
|
|
|
|
|
|
<p><img src='figures/logo_col.png' height=60px style=margin-bottom:5px /> <br />
|
|
This package contains the complete taxonomic tree of almost all microorganisms from the authoritative and comprehensive Catalogue of Life (<a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>). This data is updated annually - check the included version with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version</a></code>.</p>
|
|
<p>Included are:</p><ul>
|
|
<li><p>All ~55,000 (sub)species from the kingdoms of Archaea, Bacteria, Protozoa and Viruses</p></li>
|
|
<li><p>All ~3,000 (sub)species from these orders of the kingdom of Fungi: Eurotiales, Onygenales, Pneumocystales, Saccharomycetales and Schizosaccharomycetales. The kingdom of Fungi is a very large taxon with almost 300,000 different species, of which most are not microbial. Including everything tremendously slows down our algortihms, and not all fungi fit the scope of this package. By only including the aforementioned taxonomic orders, the most relevant species are covered (like genera <em>Aspergillus</em>, <em>Candida</em>, <em>Pneumocystis</em>, <em>Saccharomyces</em> and <em>Trichophyton</em>).</p></li>
|
|
<li><p>All ~15,000 previously accepted names of inckuded (sub)species that have been taxonomically renamed</p></li>
|
|
<li><p>The complete taxonomic tree of all included (sub)species: from kingdom to subspecies</p></li>
|
|
<li><p>The responsible author(s) and year of scientific publication</p></li>
|
|
</ul>
|
|
<p>The Catalogue of Life (<a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>) is the most comprehensive and authoritative global index of species currently available. It holds essential information on the names, relationships and distributions of over 1.6 million species. The Catalogue of Life is used to support the major biodiversity and conservation information services such as the Global Biodiversity Information Facility (GBIF), Encyclopedia of Life (EoL) and the International Union for Conservation of Nature Red List. It is recognised by the Convention on Biological Diversity as a significant component of the Global Taxonomy Initiative and a contribution to Target 1 of the Global Strategy for Plant Conservation.</p>
|
|
<p>The syntax used to transform the original data to a cleansed R format, can be found here: <a href='https://gitlab.com/msberends/AMR/blob/master/reproduction_of_microorganisms.R'>https://gitlab.com/msberends/AMR/blob/master/reproduction_of_microorganisms.R</a>.</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>
|
|
|
|
|
|
<p><img src='figures/logo.png' height=40px style=margin-bottom:5px /> <br />
|
|
On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
|
|
|
|
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
|
|
|
|
<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>, <code><a href='microorganisms.codes.html'>microorganisms.codes</a></code></p></div>
|
|
|
|
|
|
</div>
|
|
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
|
|
<h2>Contents</h2>
|
|
<ul class="nav nav-pills nav-stacked">
|
|
|
|
<li><a href="#format">Format</a></li>
|
|
|
|
<li><a href="#source">Source</a></li>
|
|
|
|
<li><a href="#details">Details</a></li>
|
|
|
|
<li><a href="#catalogue-of-life">Catalogue of Life</a></li>
|
|
|
|
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
|
|
|
|
<li><a href="#see-also">See also</a></li>
|
|
</ul>
|
|
|
|
</div>
|
|
</div>
|
|
|
|
<footer>
|
|
<div class="copyright">
|
|
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>.</p>
|
|
</div>
|
|
|
|
<div class="pkgdown">
|
|
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
|
|
</div>
|
|
</footer>
|
|
</div>
|
|
|
|
|
|
<script src="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.js" integrity="sha256-GKvGqXDznoRYHCwKXGnuchvKSwmx9SRMrZOTh2g4Sb0=" crossorigin="anonymous"></script>
|
|
<script>
|
|
docsearch({
|
|
|
|
|
|
apiKey: 'f737050abfd4d726c63938e18f8c496e',
|
|
indexName: 'amr',
|
|
inputSelector: 'input#search-input.form-control',
|
|
transformData: function(hits) {
|
|
return hits.map(function (hit) {
|
|
hit.url = updateHitURL(hit);
|
|
return hit;
|
|
});
|
|
}
|
|
});
|
|
</script>
|
|
|
|
|
|
</body>
|
|
</html>
|
|
|