AMR/docs/reference/as.atc.html

269 lines
11 KiB
HTML
Raw Normal View History

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">
2018-12-29 22:24:19 +01:00
<title>Transform to ATC code — as.atc • 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" />
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 -->
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" />
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>
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>
2018-12-23 21:26:21 +01:00
2018-12-29 22:24:19 +01:00
<link href="../extra.css" rel="stylesheet">
<script src="../extra.js"></script>
2018-12-23 21:26:21 +01:00
<meta property="og:title" content="Transform to ATC code — as.atc" />
<meta property="og:description" content="Use this function to determine the ATC code of one or more antibiotics. The data set antibiotics will be searched for abbreviations, official names and trade names." />
2018-12-29 22:24:19 +01:00
<meta property="og:image" content="https://msberends.gitlab.io/logo.png" />
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">
2018-12-29 22:24:19 +01:00
<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>
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">
2018-12-29 22:24:19 +01:00
<span class="fa fa-home"></span>
2018-12-23 21:26:21 +01:00
2018-12-29 22:24:19 +01:00
Home
2018-12-23 21:26:21 +01:00
</a>
</li>
<li>
2018-12-29 22:24:19 +01:00
<a href="../articles/AMR.html">
<span class="fa fa-directions"></span>
Get Started
</a>
2018-12-23 21:26:21 +01:00
</li>
<li>
2018-12-29 22:24:19 +01:00
<a href="../reference/">
<span class="fa fa-book-open"></span>
Manual
</a>
2018-12-23 21:26:21 +01:00
</li>
2018-12-29 22:24:19 +01:00
<li>
<a href="../authors.html">
<span class="fa fa-users"></span>
2018-12-23 21:26:21 +01:00
2018-12-29 22:24:19 +01:00
Authors
2018-12-23 21:26:21 +01:00
</a>
</li>
<li>
2018-12-29 22:24:19 +01:00
<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>
2018-12-23 21:26:21 +01:00
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
2018-12-29 22:24:19 +01:00
<li>
<a href="../LICENSE-text.html">
<span class="fa fa-book"></span>
Licence
</a>
</li>
2018-12-23 21:26:21 +01:00
</ul>
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>
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">
<h1>Transform to ATC code</h1>
<div class="hidden name"><code>as.atc.Rd</code></div>
</div>
<div class="ref-description">
<p>Use this function to determine the ATC code of one or more antibiotics. The data set <code><a href='antibiotics.html'>antibiotics</a></code> will be searched for abbreviations, official names and trade names.</p>
2018-12-23 21:26:21 +01:00
</div>
<pre class="usage"><span class='fu'>as.atc</span>(<span class='no'>x</span>)
<span class='fu'>guess_atc</span>(<span class='no'>x</span>)
<span class='fu'>is.atc</span>(<span class='no'>x</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>x</th>
<td><p>character vector to determine <code>ATC</code> code</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>Character (vector) with class <code>"act"</code>. Unknown values will return <code>NA</code>.</p>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>Use the <code><a href='ab_property.html'>ab_property</a></code> functions to get properties based on the returned ATC code, see Examples.</p>
2018-12-23 21:26:21 +01:00
<p>In the ATC classification system, the active substances are classified in a hierarchy with five different levels. The system has fourteen main anatomical/pharmacological groups or 1st levels. Each ATC main group is divided into 2nd levels which could be either pharmacological or therapeutic groups. The 3rd and 4th levels are chemical, pharmacological or therapeutic subgroups and the 5th level is the chemical substance. The 2nd, 3rd and 4th levels are often used to identify pharmacological subgroups when that is considered more appropriate than therapeutic or chemical subgroups.
Source: <a href='https://www.whocc.no/atc/structure_and_principles/'>https://www.whocc.no/atc/structure_and_principles/</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='antibiotics.html'>antibiotics</a></code> for the dataframe that is being used to determine ATCs.</p></div>
2018-12-23 21:26:21 +01:00
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
2018-12-29 22:24:19 +01:00
<pre class="examples"><span class='co'># NOT RUN {</span>
<span class='co'># These examples all return "J01FA01", the ATC code of Erythromycin:</span>
<span class='fu'>as.atc</span>(<span class='st'>"J01FA01"</span>)
<span class='fu'>as.atc</span>(<span class='st'>"Erythromycin"</span>)
<span class='fu'>as.atc</span>(<span class='st'>"eryt"</span>)
<span class='fu'>as.atc</span>(<span class='st'>" eryt 123"</span>)
<span class='fu'>as.atc</span>(<span class='st'>"ERYT"</span>)
<span class='fu'>as.atc</span>(<span class='st'>"ERY"</span>)
<span class='fu'>as.atc</span>(<span class='st'>"Erythrocin"</span>) <span class='co'># Trade name</span>
<span class='fu'>as.atc</span>(<span class='st'>"Eryzole"</span>) <span class='co'># Trade name</span>
<span class='fu'>as.atc</span>(<span class='st'>"Pediamycin"</span>) <span class='co'># Trade name</span>
2018-12-23 21:26:21 +01:00
<span class='co'># Use ab_* functions to get a specific property based on an ATC code</span>
<span class='no'>Cipro</span> <span class='kw'>&lt;-</span> <span class='fu'>as.atc</span>(<span class='st'>"cipro"</span>) <span class='co'># returns `J01MA02`</span>
<span class='fu'><a href='ab_property.html'>ab_official</a></span>(<span class='no'>Cipro</span>) <span class='co'># returns "Ciprofloxacin"</span>
<span class='fu'><a href='ab_property.html'>ab_umcg</a></span>(<span class='no'>Cipro</span>) <span class='co'># returns "CIPR", the code used in the UMCG</span>
2018-12-29 22:24:19 +01:00
<span class='co'># }</span></pre>
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="#arguments">Arguments</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#see-also">See also</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
</div>
</div>
<footer>
<div class="copyright">
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>
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>
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>
2018-12-23 21:26:21 +01:00
</body>
</html>