mirror of https://github.com/msberends/AMR.git
244 lines
12 KiB
HTML
244 lines
12 KiB
HTML
<!DOCTYPE html>
|
||
<!-- Generated by pkgdown: do not edit by hand --><html lang="en">
|
||
<head>
|
||
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
|
||
<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>Antimicrobial Resistance Analysis • 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="Antimicrobial Resistance Analysis">
|
||
<meta property="og:description" content="Functions to simplify the analysis and prediction of Antimicrobial
|
||
Resistance (AMR) and to work with microbial and antimicrobial properties by
|
||
using evidence-based methods.">
|
||
<meta property="og:image" content="https://msberends.gitlab.io/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-home">
|
||
<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">0.5.0.9008</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>
|
||
<a href="articles/AMR.html">
|
||
<span class="fa fa-directions"></span>
|
||
|
||
Get Started
|
||
</a>
|
||
</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>
|
||
<li>
|
||
<a href="https://gitlab.com/msberends/AMR">
|
||
<span class="fab fa fab fa-gitlab"></span>
|
||
|
||
Source Code
|
||
</a>
|
||
</li>
|
||
</ul>
|
||
<ul class="nav navbar-nav navbar-right">
|
||
<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="contents col-md-9">
|
||
<div id="amr-for-r" class="section level1">
|
||
<div class="page-header"><h1 class="hasAnchor">
|
||
<a href="#amr-for-r" class="anchor"></a><code>AMR</code> (for R) <img src="reference/figures/logo.png" align="right" height="120px">
|
||
</h1></div>
|
||
<p><em>(<help title="Too Long, Didn't Read">TLDR</help> - to find out how to conduct AMR analysis, please <a href="./articles/AMR.html">continue reading here to get started</a>.</em></p>
|
||
<hr>
|
||
<p><code>AMR</code> is a free and open-source <a href="https://www.r-project.org">R package</a> to simplify the analysis and prediction of <strong>Antimicrobial Resistance (AMR)</strong> and to work with antibiotic properties by using evidence-based methods.</p>
|
||
<p>We created this package for academic research at the Faculty of Medical Sciences of the University of Groningen and the Medical Microbiology & Infection Prevention (MMBI) department of the University Medical Center Groningen (UMCG). We released this under the GNU General Public Licence v2.0 (GPL-2) which makes it free for everybody to use and distribute, for personal and commercial use, but it may <strong>not</strong> be used for patent purposes. Read further about our GPL-2 licence <a href="./LICENSE-text.html">here</a>.</p>
|
||
<p>This package is ready-to-use for a professional environment by specialists in the following fields:</p>
|
||
<p>Medical Microbiology:</p>
|
||
<ul>
|
||
<li>Epidemiologists (both clinical microbiological and research)</li>
|
||
<li>Research Microbiologists</li>
|
||
<li>Biomedical Researchers</li>
|
||
<li>Research Pharmacologists</li>
|
||
</ul>
|
||
<p>Veterinary Microbiology:</p>
|
||
<ul>
|
||
<li>Research Veterinarians</li>
|
||
<li>Veterinary Epidemiologists</li>
|
||
<li>Biomedical Researchers</li>
|
||
</ul>
|
||
<p>Microbial Ecology:</p>
|
||
<ul>
|
||
<li>Soil Microbiologists</li>
|
||
<li>Extremophile Researchers</li>
|
||
<li>Astrobiologists</li>
|
||
</ul>
|
||
<p>Other specialists in any of the above fields:</p>
|
||
<ul>
|
||
<li>Data Scientists/Data Analysts</li>
|
||
<li>Biotechnologists</li>
|
||
<li>Biochemists</li>
|
||
<li>Geneticists</li>
|
||
<li>Molecular Biologists/Microbiologists</li>
|
||
</ul>
|
||
<p>Developers:</p>
|
||
<ul>
|
||
<li>Package developers for R</li>
|
||
<li>Software developers</li>
|
||
<li>Web application developers</li>
|
||
</ul>
|
||
<div id="get-this-package" class="section level3">
|
||
<h3 class="hasAnchor">
|
||
<a href="#get-this-package" class="anchor"></a>Get this package</h3>
|
||
<p>This package is available on the official R network. Install this package in R with:</p>
|
||
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/install.packages">install.packages</a></span>(<span class="st">"AMR"</span>)</a></code></pre></div>
|
||
<p>It will be downloaded and installed automatically.</p>
|
||
</div>
|
||
<div id="get-started" class="section level3">
|
||
<h3 class="hasAnchor">
|
||
<a href="#get-started" class="anchor"></a>Get started</h3>
|
||
<p>To find out how to conduct AMR analysis, please <a href="./articles/AMR.html">continue reading here to get started</a> or click the button ‘Get Started’ in the top menu.</p>
|
||
<hr>
|
||
<p><a href="https://www.rug.nl"><img src="./logo_rug.png" height="60px"></a> <a href="https://www.umcg.nl"><img src="./logo_umcg.png" height="60px"></a> <a href="https://www.certe.nl"><img src="./logo_certe.png" height="60px"></a> <a href="http://www.eurhealth-1health.eu"><img src="./logo_eh1h.png" height="60px"></a> <a href="http://www.eurhealth-1health.eu"><img src="./logo_interreg.png" height="60px"></a></p>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
|
||
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
|
||
<div class="links">
|
||
<h2>Links</h2>
|
||
<ul class="list-unstyled">
|
||
<li>Download from CRAN at <br><a href="https://cloud.r-project.org/package=AMR">https://cloud.r-project.org/package=AMR</a>
|
||
</li>
|
||
<li>Report a bug at <br><a href="https://gitlab.com/msberends/AMR/issues">https://gitlab.com/msberends/AMR/issues</a>
|
||
</li>
|
||
</ul>
|
||
</div>
|
||
<div class="license">
|
||
<h2>License</h2>
|
||
<ul class="list-unstyled">
|
||
<li>
|
||
<a href="https://www.r-project.org/Licenses/GPL-2">GPL-2</a> | file <a href="LICENSE-text.html">LICENSE</a>
|
||
</li>
|
||
</ul>
|
||
</div>
|
||
<div class="developers">
|
||
<h2>Developers</h2>
|
||
<ul class="list-unstyled">
|
||
<li>
|
||
<a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a> <br><small class="roles"> Author, maintainer </small> <a href="https://orcid.org/0000-0001-7620-1800" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" alt="ORCID" height="16"></a> </li>
|
||
<li>
|
||
<a href="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a> <br><small class="roles"> Author, reviewer </small> <a href="https://orcid.org/0000-0001-5809-5995" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" alt="ORCID" height="16"></a> </li>
|
||
<li>
|
||
<a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a> <br><small class="roles"> Author, thesis advisor </small> <a href="https://orcid.org/0000-0003-1241-1328" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" alt="ORCID" height="16"></a> </li>
|
||
<li>
|
||
<a href="https://www.rug.nl/staff/a.w.friedrich/">Alex W. Friedrich</a> <br><small class="roles"> Author, thesis advisor </small> <a href="https://orcid.org/0000-0003-4881-038X" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" alt="ORCID" height="16"></a> </li>
|
||
<li>
|
||
<a href="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a> <br><small class="roles"> Author, thesis advisor </small> <a href="https://orcid.org/0000-0003-1634-0010" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" alt="ORCID" height="16"></a> </li>
|
||
<li><a href="authors.html">All authors...</a></li>
|
||
</ul>
|
||
</div>
|
||
|
||
</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>
|