mirror of
https://github.com/msberends/AMR.git
synced 2024-12-26 07:26:13 +01:00
274 lines
16 KiB
HTML
274 lines
16 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>Get ATC Properties from WHOCC Website — atc_online_property • 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/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Get ATC Properties from WHOCC Website — atc_online_property"><meta property="og:description" content="Gets data from the WHOCC website to determine properties of an Anatomical Therapeutic Chemical (ATC) (e.g. an antibiotic), such as the name, defined daily dose (DDD) or standard unit."><meta property="og:image" content="https://msberends.github.io/AMR/logo.png"><meta name="twitter:card" content="summary_large_image"><meta name="twitter:creator" content="@msberends"><meta name="twitter:site" content="@univgroningen"><!-- 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 data-spy="scroll" data-target="#toc">
|
|
|
|
|
|
<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">1.7.1.9062</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/datasets.html">
|
|
<span class="fa fa-database"></span>
|
|
|
|
Data sets for download / own use
|
|
</a>
|
|
</li>
|
|
<li>
|
|
<a href="../articles/PCA.html">
|
|
<span class="fa fa-compress"></span>
|
|
|
|
Conduct principal component analysis for AMR
|
|
</a>
|
|
</li>
|
|
<li>
|
|
<a href="../articles/MDR.html">
|
|
<span class="fa fa-skull-crossbones"></span>
|
|
|
|
Determine multi-drug resistance (MDR)
|
|
</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/ab_property.html">
|
|
<span class="fa fa-capsules"></span>
|
|
|
|
Get properties of an antibiotic
|
|
</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/index.html">
|
|
<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/index.html">
|
|
<span class="far fa-newspaper"></span>
|
|
|
|
Changelog
|
|
</a>
|
|
</li>
|
|
</ul><ul class="nav navbar-nav navbar-right"><li>
|
|
<a href="https://github.com/msberends/AMR" class="external-link">
|
|
<span class="fab fa-github"></span>
|
|
|
|
Source Code
|
|
</a>
|
|
</li>
|
|
</ul></div><!--/.nav-collapse -->
|
|
</div><!--/.container -->
|
|
</div><!--/.navbar -->
|
|
|
|
|
|
|
|
</header><div class="row">
|
|
<div class="col-md-9 contents">
|
|
<div class="page-header">
|
|
<h1>Get ATC Properties from WHOCC Website</h1>
|
|
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/atc_online.R" class="external-link"><code>R/atc_online.R</code></a></small>
|
|
<div class="hidden name"><code>atc_online.Rd</code></div>
|
|
</div>
|
|
|
|
<div class="ref-description">
|
|
<p>Gets data from the WHOCC website to determine properties of an Anatomical Therapeutic Chemical (ATC) (e.g. an antibiotic), such as the name, defined daily dose (DDD) or standard unit.</p>
|
|
</div>
|
|
|
|
<div id="ref-usage">Usage,<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">atc_online_property</span><span class="op">(</span>
|
|
<span class="va">atc_code</span>,
|
|
<span class="va">property</span>,
|
|
administration <span class="op">=</span> <span class="st">"O"</span>,
|
|
url <span class="op">=</span> <span class="st">"https://www.whocc.no/atc_ddd_index/?code=%s&showdescription=no"</span>,
|
|
url_vet <span class="op">=</span> <span class="st">"https://www.whocc.no/atcvet/atcvet_index/?code=%s&showdescription=no"</span>
|
|
<span class="op">)</span>
|
|
|
|
<span class="fu">atc_online_groups</span><span class="op">(</span><span class="va">atc_code</span>, <span class="va">...</span><span class="op">)</span>
|
|
|
|
<span class="fu">atc_online_ddd</span><span class="op">(</span><span class="va">atc_code</span>, <span class="va">...</span><span class="op">)</span>
|
|
|
|
<span class="fu">atc_online_ddd_units</span><span class="op">(</span><span class="va">atc_code</span>, <span class="va">...</span><span class="op">)</span></code></pre></div></div>
|
|
|
|
<div id="source">
|
|
<h2>Source</h2>
|
|
<p><a href="https://www.whocc.no/atc_ddd_alterations__cumulative/ddd_alterations/abbrevations/" class="external-link">https://www.whocc.no/atc_ddd_alterations__cumulative/ddd_alterations/abbrevations/</a></p>
|
|
</div>
|
|
<div id="arguments">
|
|
<h2>Arguments</h2>
|
|
<dl><dt>atc_code</dt>
|
|
<dd><p>a <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> (vector) with ATC code(s) of antibiotics, will be coerced with <code><a href="as.ab.html">as.ab()</a></code> and <code><a href="ab_property.html">ab_atc()</a></code> internally if not a valid ATC code</p></dd>
|
|
<dt>property</dt>
|
|
<dd><p>property of an ATC code. Valid values are <code>"ATC"</code>, <code>"Name"</code>, <code>"DDD"</code>, <code>"U"</code> (<code>"unit"</code>), <code>"Adm.R"</code>, <code>"Note"</code> and <code>groups</code>. For this last option, all hierarchical groups of an ATC code will be returned, see <em>Examples</em>.</p></dd>
|
|
<dt>administration</dt>
|
|
<dd><p>type of administration when using <code>property = "Adm.R"</code>, see <em>Details</em></p></dd>
|
|
<dt>url</dt>
|
|
<dd><p>url of website of the WHOCC. The sign <code>%s</code> can be used as a placeholder for ATC codes.</p></dd>
|
|
<dt>url_vet</dt>
|
|
<dd><p>url of website of the WHOCC for veterinary medicine. The sign <code>%s</code> can be used as a placeholder for ATC_vet codes (that all start with "Q").</p></dd>
|
|
<dt>...</dt>
|
|
<dd><p>arguments to pass on to <code>atc_property</code></p></dd>
|
|
</dl></div>
|
|
<div id="details">
|
|
<h2>Details</h2>
|
|
<p>Options for argument <code>administration</code>:</p><ul><li><p><code>"Implant"</code> = Implant</p></li>
|
|
<li><p><code>"Inhal"</code> = Inhalation</p></li>
|
|
<li><p><code>"Instill"</code> = Instillation</p></li>
|
|
<li><p><code>"N"</code> = nasal</p></li>
|
|
<li><p><code>"O"</code> = oral</p></li>
|
|
<li><p><code>"P"</code> = parenteral</p></li>
|
|
<li><p><code>"R"</code> = rectal</p></li>
|
|
<li><p><code>"SL"</code> = sublingual/buccal</p></li>
|
|
<li><p><code>"TD"</code> = transdermal</p></li>
|
|
<li><p><code>"V"</code> = vaginal</p></li>
|
|
</ul><p>Abbreviations of return values when using <code>property = "U"</code> (unit):</p><ul><li><p><code>"g"</code> = gram</p></li>
|
|
<li><p><code>"mg"</code> = milligram</p></li>
|
|
<li><p>`"mcg"`` = microgram</p></li>
|
|
<li><p><code>"U"</code> = unit</p></li>
|
|
<li><p><code>"TU"</code> = thousand units</p></li>
|
|
<li><p><code>"MU"</code> = million units</p></li>
|
|
<li><p><code>"mmol"</code> = millimole</p></li>
|
|
<li><p><code>"ml"</code> = millilitre (e.g. eyedrops)</p></li>
|
|
</ul><p><strong>N.B. This function requires an internet connection and only works if the following packages are installed: <code>curl</code>, <code>rvest</code>, <code>xml2</code>.</strong></p>
|
|
</div>
|
|
<div id="stable-lifecycle">
|
|
<h2>Stable Lifecycle</h2>
|
|
|
|
|
|
<p><img src="figures/lifecycle_stable.svg" style="margin-bottom:5px"><br>
|
|
The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
|
|
<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
|
|
</div>
|
|
<div id="read-more-on-our-website-">
|
|
<h2>Read more on Our Website!</h2>
|
|
|
|
|
|
<p>On our website <a href="https://msberends.github.io/AMR/">https://msberends.github.io/AMR/</a> you can find <a href="https://msberends.github.io/AMR/articles/AMR.html">a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href="https://msberends.github.io/AMR/reference/">complete documentation of all functions</a> and <a href="https://msberends.github.io/AMR/articles/WHONET.html">an example analysis using WHONET data</a>.</p>
|
|
</div>
|
|
|
|
<div id="ref-examples">
|
|
<h2>Examples</h2>
|
|
<div class="sourceCode"><pre class="sourceCode r"><code><span class="co"># \donttest{</span>
|
|
<span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/ns-load.html" class="external-link">requireNamespace</a></span><span class="op">(</span><span class="st">"curl"</span><span class="op">)</span> <span class="op">&&</span> <span class="fu"><a href="https://rdrr.io/r/base/ns-load.html" class="external-link">requireNamespace</a></span><span class="op">(</span><span class="st">"rvest"</span><span class="op">)</span> <span class="op">&&</span> <span class="fu"><a href="https://rdrr.io/r/base/ns-load.html" class="external-link">requireNamespace</a></span><span class="op">(</span><span class="st">"xml2"</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span>
|
|
<span class="co"># oral DDD (Defined Daily Dose) of amoxicillin</span>
|
|
<span class="fu">atc_online_property</span><span class="op">(</span><span class="st">"J01CA04"</span>, <span class="st">"DDD"</span>, <span class="st">"O"</span><span class="op">)</span>
|
|
<span class="fu">atc_online_ddd</span><span class="op">(</span><span class="fu"><a href="ab_property.html">ab_atc</a></span><span class="op">(</span><span class="st">"amox"</span><span class="op">)</span><span class="op">)</span>
|
|
|
|
<span class="co"># parenteral DDD (Defined Daily Dose) of amoxicillin</span>
|
|
<span class="fu">atc_online_property</span><span class="op">(</span><span class="st">"J01CA04"</span>, <span class="st">"DDD"</span>, <span class="st">"P"</span><span class="op">)</span>
|
|
|
|
<span class="fu">atc_online_property</span><span class="op">(</span><span class="st">"J01CA04"</span>, property <span class="op">=</span> <span class="st">"groups"</span><span class="op">)</span> <span class="co"># search hierarchical groups of amoxicillin</span>
|
|
<span class="op">}</span>
|
|
<span class="co"># }</span>
|
|
</code></pre></div>
|
|
</div>
|
|
</div>
|
|
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
|
<nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
|
|
</nav></div>
|
|
</div>
|
|
|
|
|
|
<footer><div class="copyright">
|
|
<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
|
|
</div>
|
|
|
|
<div class="pkgdown">
|
|
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
|
|
</div>
|
|
|
|
</footer></div>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
</body></html>
|
|
|