P281424
/
AMR
mirror of https://github.com/msberends/AMR.git
1
0
Fork 0
Code Releases Activity
AMR/docs/reference/microorganisms.html

334 lines
14 KiB
HTML
Raw Normal View History

gitlab pages
2018-12-23 21:26:21 +01:00
<!-- 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">
WHO update, antibiotics update
2019-01-25 13:18:41 +01:00
<title>Data set with ~20,000 microorganisms — microorganisms • AMR (for R)</title>
new website, freq updates
2018-12-29 22:24:19 +01:00
<!-- 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" />
gitlab pages
2018-12-23 21:26:21 +01:00
<!-- 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 -->
new website, freq updates
2018-12-29 22:24:19 +01:00
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
gitlab pages
2018-12-23 21:26:21 +01:00
<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>
new website, freq updates
2018-12-29 22:24:19 +01:00
<!-- 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>
gitlab pages
2018-12-23 21:26:21 +01:00
new website, freq updates
2018-12-29 22:24:19 +01:00
<link href="../extra.css" rel="stylesheet">
<script src="../extra.js"></script>
WHO update, antibiotics update
2019-01-25 13:18:41 +01:00
<meta property="og:title" content="Data set with ~20,000 microorganisms — microorganisms" />
gitlab pages
2018-12-23 21:26:21 +01:00
WHO update, antibiotics update
2019-01-25 13:18:41 +01:00
<meta property="og:description" content="A data set containing the complete microbial taxonomy of the kingdoms Bacteria, Fungi and Protozoa from ITIS. MO codes can be looked up using as.mo." />
new website, freq updates
2018-12-29 22:24:19 +01:00
big website update, licence txt update
2019-01-02 23:24:07 +01:00
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
gitlab pages
2018-12-23 21:26:21 +01:00
<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">
new website, freq updates
2018-12-29 22:24:19 +01:00
<a class="navbar-link" href="../index.html">AMR (for R)</a>
WHONET/EARS-Net support
2019-01-29 00:06:50 +01:00
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9015</span>
gitlab pages
2018-12-23 21:26:21 +01:00
</span>
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
new website, freq updates
2018-12-29 22:24:19 +01:00
<span class="fa fa-home"></span>
gitlab pages
2018-12-23 21:26:21 +01:00
new website, freq updates
2018-12-29 22:24:19 +01:00
Home
gitlab pages
2018-12-23 21:26:21 +01:00
</a>
</li>
big website update, licence txt update
2019-01-02 23:24:07 +01:00
<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
new website, freq updates
2018-12-29 22:24:19 +01:00
big website update, licence txt update
2019-01-02 23:24:07 +01:00
<span class="caret"></span>
new website, freq updates
2018-12-29 22:24:19 +01:00
</a>
big website update, licence txt update
2019-01-02 23:24:07 +01:00
<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/Predict.html">
<span class="fa fa-dice"></span>
Predict antimicrobial resistance
</a>
</li>
WHONET/EARS-Net support
2019-01-29 00:06:50 +01:00
<li>
<a href="../articles/WHONET.html">
<span class="fa fa-globe-americas"></span>
Work with WHONET data
</a>
</li>
big website update, licence txt update
2019-01-02 23:24:07 +01:00
<li>
<a href="../articles/EUCAST.html">
<span class="fa fa-exchange-alt"></span>
Apply EUCAST rules
</a>
</li>
<li>
<a href="../articles/mo_property.html">
<span class="fa fa-bug"></span>
Get properties of a microorganism
</a>
</li>
<li>
<a href="../articles/ab_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>
guess_ab_col, benchmarks
2019-01-11 20:37:23 +01:00
<li>
<a href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
Other: benchmarks
</a>
</li>
big website update, licence txt update
2019-01-02 23:24:07 +01:00
</ul>
gitlab pages
2018-12-23 21:26:21 +01:00
</li>
<li>
new website, freq updates
2018-12-29 22:24:19 +01:00
<a href="../reference/">
<span class="fa fa-book-open"></span>
Manual
</a>
gitlab pages
2018-12-23 21:26:21 +01:00
</li>
new website, freq updates
2018-12-29 22:24:19 +01:00
<li>
<a href="../authors.html">
<span class="fa fa-users"></span>
gitlab pages
2018-12-23 21:26:21 +01:00
new website, freq updates
2018-12-29 22:24:19 +01:00
Authors
gitlab pages
2018-12-23 21:26:21 +01:00
</a>
</li>
<li>
new website, freq updates
2018-12-29 22:24:19 +01:00
<a href="../news/">
<span class="far fa far fa-newspaper"></span>
Changelog
</a>
</li>
big website update, licence txt update
2019-01-02 23:24:07 +01:00
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
new website, freq updates
2018-12-29 22:24:19 +01:00
<a href="https://gitlab.com/msberends/AMR">
<span class="fab fa fab fa-gitlab"></span>
Source Code
</a>
gitlab pages
2018-12-23 21:26:21 +01:00
</li>
big website update, licence txt update
2019-01-02 23:24:07 +01:00
<li>
new website, freq updates
2018-12-29 22:24:19 +01:00
<a href="../LICENSE-text.html">
<span class="fa fa-book"></span>
Licence
</a>
</li>
gitlab pages
2018-12-23 21:26:21 +01:00
</ul>
new website, freq updates
2018-12-29 22:24:19 +01:00
<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>
gitlab pages
2018-12-23 21:26:21 +01:00
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
</header>
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
WHO update, antibiotics update
2019-01-25 13:18:41 +01:00
<h1>Data set with ~20,000 microorganisms</h1>
gitlab pages
2018-12-23 21:26:21 +01:00
<div class="hidden name"><code>microorganisms.Rd</code></div>
</div>
<div class="ref-description">
WHO update, antibiotics update
2019-01-25 13:18:41 +01:00
<p>A data set containing the complete microbial taxonomy of the kingdoms Bacteria, Fungi and Protozoa from ITIS. MO codes can be looked up using <code><a href='as.mo.html'>as.mo</a></code>.</p>
gitlab pages
2018-12-23 21:26:21 +01:00
</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 18,833 observations and 15 variables:</p><dl class='dl-horizontal'>
<dt><code>mo</code></dt><dd><p>ID of microorganism</p></dd>
<dt><code>tsn</code></dt><dd><p>Taxonomic Serial Number (TSN), as defined by ITIS</p></dd>
<dt><code>genus</code></dt><dd><p>Taxonomic genus of the microorganism as found in ITIS, see Source</p></dd>
<dt><code>species</code></dt><dd><p>Taxonomic species of the microorganism as found in ITIS, see Source</p></dd>
<dt><code>subspecies</code></dt><dd><p>Taxonomic subspecies of the microorganism as found in ITIS, see Source</p></dd>
<dt><code>fullname</code></dt><dd><p>Full name, like <code>"Echerichia coli"</code></p></dd>
<dt><code>family</code></dt><dd><p>Taxonomic family of the microorganism as found in ITIS, see Source</p></dd>
<dt><code>order</code></dt><dd><p>Taxonomic order of the microorganism as found in ITIS, see Source</p></dd>
<dt><code>class</code></dt><dd><p>Taxonomic class of the microorganism as found in ITIS, see Source</p></dd>
<dt><code>phylum</code></dt><dd><p>Taxonomic phylum of the microorganism as found in ITIS, see Source</p></dd>
<dt><code>subkingdom</code></dt><dd><p>Taxonomic subkingdom of the microorganism as found in ITIS, see Source</p></dd>
<dt><code>kingdom</code></dt><dd><p>Taxonomic kingdom of the microorganism as found in ITIS, see Source</p></dd>
<dt><code>gramstain</code></dt><dd><p>Gram of microorganism, like <code>"Gram negative"</code></p></dd>
eucast rules fix, 1st isolate fix, website update
2018-12-31 01:48:53 +01:00
<dt><code>prevalence</code></dt><dd><p>An integer based on estimated prevalence of the microorganism in humans. Used internally by <code><a href='as.mo.html'>as.mo</a></code>, otherwise quite meaningless. It has a value of 25 for manually added items and a value of 1000 for all unprevalent microorganisms whose genus was somewhere in the top 250 (with another species).</p></dd>
gitlab pages
2018-12-23 21:26:21 +01:00
<dt><code>ref</code></dt><dd><p>Author(s) and year of concerning publication as found in ITIS, see Source</p></dd>
</dl>
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
WHO update, antibiotics update
2019-01-25 13:18:41 +01:00
<p>Integrated Taxonomic Information System (ITIS) public online database, <a href='https://www.itis.gov'>https://www.itis.gov</a>.</p>
gitlab pages
2018-12-23 21:26:21 +01:00
<h2 class="hasAnchor" id="itis"><a class="anchor" href="#itis"></a>ITIS</h2>
WHO update, antibiotics update
2019-01-25 13:18:41 +01:00
<p><img src='figures/logo_itis.jpg' height=60px style=margin-bottom:5px /> <br />
gitlab pages
2018-12-23 21:26:21 +01:00
This package contains the <strong>complete microbial taxonomic data</strong> (with all nine taxonomic ranks - from kingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, <a href='https://www.itis.gov'>https://www.itis.gov</a>).</p>
text updates
2019-01-27 13:55:23 +01:00
<p>All ~20,000 (sub)species from <strong>the taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package</strong>, as well as all their ~2,500 previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This allows users to use authoritative taxonomic information for their data analysis on any microorganism, not only human pathogens. It also helps to quickly determine the Gram stain of bacteria, since ITIS honours the taxonomic branching order of bacterial phyla according to Cavalier-Smith (2002), which defines that all bacteria are classified into either subkingdom Negibacteria or subkingdom Posibacteria.</p>
gitlab pages
2018-12-23 21:26:21 +01:00
<p>ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3].</p>
big website update, licence txt update
2019-01-02 23:24:07 +01:00
<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 />
freq update
2019-01-29 20:20:09 +01:00
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>
big website update, licence txt update
2019-01-02 23:24:07 +01:00
gitlab pages
2018-12-23 21:26:21 +01:00
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
set_mo_source
2019-01-21 15:53:01 +01:00
<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>
gitlab pages
2018-12-23 21:26:21 +01:00
</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="#itis">ITIS</a></li>
big website update, licence txt update
2019-01-02 23:24:07 +01:00
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
gitlab pages
2018-12-23 21:26:21 +01:00
<li><a href="#see-also">See also</a></li>
</ul>
</div>
</div>
<footer>
<div class="copyright">
new website, freq updates
2018-12-29 22:24:19 +01:00
<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>
gitlab pages
2018-12-23 21:26:21 +01:00
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
</footer>
</div>
new website, freq updates
2018-12-29 22:24:19 +01:00
<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>
gitlab pages
2018-12-23 21:26:21 +01:00
</body>
</html>