mirror of https://github.com/msberends/AMR.git
368 lines
16 KiB
HTML
368 lines
16 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>Name of an antibiotic — abname • 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="Name of an antibiotic — abname" />
|
|
|
|
<meta property="og:description" content="Convert antibiotic codes to a (trivial) antibiotic name or ATC code, or vice versa. This uses the data from antibiotics." />
|
|
|
|
<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">0.5.0.9017</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/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>Name of an antibiotic</h1>
|
|
|
|
<div class="hidden name"><code>abname.Rd</code></div>
|
|
</div>
|
|
|
|
<div class="ref-description">
|
|
|
|
<p>Convert antibiotic codes to a (trivial) antibiotic name or ATC code, or vice versa. This uses the data from <code><a href='antibiotics.html'>antibiotics</a></code>.</p>
|
|
|
|
</div>
|
|
|
|
<pre class="usage"><span class='fu'>abname</span>(<span class='no'>abcode</span>, <span class='kw'>from</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"guess"</span>, <span class='st'>"atc"</span>, <span class='st'>"certe"</span>, <span class='st'>"umcg"</span>),
|
|
<span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"official"</span>, <span class='kw'>textbetween</span> <span class='kw'>=</span> <span class='st'>" + "</span>, <span class='kw'>tolower</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
|
|
|
|
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
|
|
<table class="ref-arguments">
|
|
<colgroup><col class="name" /><col class="desc" /></colgroup>
|
|
<tr>
|
|
<th>abcode</th>
|
|
<td><p>a code or name, like <code>"AMOX"</code>, <code>"AMCL"</code> or <code>"J01CA04"</code></p></td>
|
|
</tr>
|
|
<tr>
|
|
<th>from, to</th>
|
|
<td><p>type to transform from and to. See <code><a href='antibiotics.html'>antibiotics</a></code> for its column names. WIth <code>from = "guess"</code> the from will be guessed from <code>"atc"</code>, <code>"certe"</code> and <code>"umcg"</code>. When using <code>to = "atc"</code>, the ATC code will be searched using <code><a href='as.atc.html'>as.atc</a></code>.</p></td>
|
|
</tr>
|
|
<tr>
|
|
<th>textbetween</th>
|
|
<td><p>text to put between multiple returned texts</p></td>
|
|
</tr>
|
|
<tr>
|
|
<th>tolower</th>
|
|
<td><p>return output as lower case with function <code><a href='https://www.rdocumentation.org/packages/base/topics/chartr'>tolower</a></code>.</p></td>
|
|
</tr>
|
|
</table>
|
|
|
|
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
|
|
|
|
<p><code><a href='antibiotics.html'>antibiotics</a></code></p>
|
|
|
|
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
|
|
|
|
<p><strong>The <code><a href='AMR-deprecated.html'>ab_property</a></code> functions are faster and more concise</strong>, but do not support concatenated strings, like <code>abname("AMCL+GENT"</code>.</p>
|
|
|
|
<h2 class="hasAnchor" id="whocc"><a class="anchor" href="#whocc"></a>WHOCC</h2>
|
|
|
|
|
|
<p><img src='figures/logo_who.png' height=60px style=margin-bottom:5px /> <br />
|
|
This package contains <strong>all ~500 antimicrobial drugs</strong> and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, <a href='https://www.whocc.no'>https://www.whocc.no</a>) and the Pharmaceuticals Community Register of the European Commission (<a href='http://ec.europa.eu/health/documents/community-register/html/atc.htm'>http://ec.europa.eu/health/documents/community-register/html/atc.htm</a>).</p>
|
|
<p>These have become the gold standard for international drug utilisation monitoring and research.</p>
|
|
<p>The WHOCC is located in Oslo at the Norwegian Institute of Public Health and funded by the Norwegian government. The European Commission is the executive of the European Union and promotes its general interest.</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="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
|
<pre class="examples"><span class='co'># NOT RUN {</span>
|
|
<span class='fu'>abname</span>(<span class='st'>"AMCL"</span>)
|
|
<span class='co'># "Amoxicillin and beta-lactamase inhibitor"</span>
|
|
|
|
<span class='co'># It is quite flexible at default (having `from = "guess"`)</span>
|
|
<span class='fu'>abname</span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"amox"</span>, <span class='st'>"J01CA04"</span>, <span class='st'>"Trimox"</span>, <span class='st'>"dispermox"</span>, <span class='st'>"Amoxil"</span>))
|
|
<span class='co'># "Amoxicillin" "Amoxicillin" "Amoxicillin" "Amoxicillin" "Amoxicillin"</span>
|
|
|
|
<span class='co'># Multiple antibiotics can be combined with "+".</span>
|
|
<span class='co'># The second antibiotic will be set to lower case when `tolower` was not set:</span>
|
|
<span class='fu'>abname</span>(<span class='st'>"AMCL+GENT"</span>, <span class='kw'>textbetween</span> <span class='kw'>=</span> <span class='st'>"/"</span>)
|
|
<span class='co'># "amoxicillin and enzyme inhibitor/gentamicin"</span>
|
|
|
|
<span class='fu'>abname</span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"AMCL"</span>, <span class='st'>"GENT"</span>))
|
|
<span class='co'># "Amoxicillin and beta-lactamase inhibitor" "Gentamicin"</span>
|
|
|
|
<span class='fu'>abname</span>(<span class='st'>"AMCL"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"trivial_nl"</span>)
|
|
<span class='co'># "Amoxicilline/clavulaanzuur"</span>
|
|
|
|
<span class='fu'>abname</span>(<span class='st'>"AMCL"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"atc"</span>)
|
|
<span class='co'># "J01CR02"</span>
|
|
|
|
<span class='co'># specific codes for University Medical Center Groningen (UMCG):</span>
|
|
<span class='fu'>abname</span>(<span class='st'>"J01CR02"</span>, <span class='kw'>from</span> <span class='kw'>=</span> <span class='st'>"atc"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"umcg"</span>)
|
|
<span class='co'># "AMCL"</span>
|
|
|
|
<span class='co'># specific codes for Certe:</span>
|
|
<span class='fu'>abname</span>(<span class='st'>"J01CR02"</span>, <span class='kw'>from</span> <span class='kw'>=</span> <span class='st'>"atc"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"certe"</span>)
|
|
<span class='co'># "amcl"</span>
|
|
<span class='co'># }</span></pre>
|
|
</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="#arguments">Arguments</a></li>
|
|
|
|
<li><a href="#source">Source</a></li>
|
|
|
|
<li><a href="#details">Details</a></li>
|
|
|
|
<li><a href="#whocc">WHOCC</a></li>
|
|
|
|
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
|
|
|
|
<li><a href="#examples">Examples</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>
|
|
|