AMR/docs/reference/guess_ab_col.html

338 lines
14 KiB
HTML
Raw Normal View History

2019-01-11 20:37:23 +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">
<title>Guess antibiotic column — guess_ab_col • 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" />
2019-10-13 09:31:58 +02:00
2019-01-11 20:37:23 +01:00
<!-- jquery -->
2020-04-13 21:09:56 +02:00
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
2019-01-11 20:37:23 +01:00
<!-- Bootstrap -->
2020-04-13 21:09:56 +02:00
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
2019-01-11 20:37:23 +01:00
2019-10-13 09:31:58 +02:00
2020-04-13 21:09:56 +02:00
<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>
2019-01-11 20:37:23 +01:00
2020-04-17 19:16:30 +02:00
<!-- bootstrap-toc -->
<link rel="stylesheet" href="../bootstrap-toc.css">
<script src="../bootstrap-toc.js"></script>
2019-01-11 20:37:23 +01:00
<!-- Font Awesome icons -->
2020-04-17 19:16:30 +02:00
<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" />
2019-01-11 20:37:23 +01:00
<!-- clipboard.js -->
2020-04-17 19:16:30 +02:00
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
2019-01-11 20:37:23 +01:00
2019-10-13 09:31:58 +02:00
<!-- headroom.js -->
2020-04-17 19:16:30 +02:00
<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>
2019-01-11 20:37:23 +01:00
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../pkgdown.js"></script>
<link href="../extra.css" rel="stylesheet">
<script src="../extra.js"></script>
2019-10-13 09:31:58 +02:00
<meta property="og:title" content="Guess antibiotic column — guess_ab_col" />
2019-05-31 14:40:15 +02:00
<meta property="og:description" content="This tries to find a column name in a data set based on information from the antibiotics data set. Also supports WHONET abbreviations." />
2020-07-08 14:48:06 +02:00
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
2019-01-11 20:37:23 +01:00
2019-10-13 09:31:58 +02:00
2019-01-11 20:37:23 +01:00
<!-- 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]-->
2019-10-13 09:31:58 +02:00
2019-01-11 20:37:23 +01:00
</head>
2020-04-17 19:16:30 +02:00
<body data-spy="scroll" data-target="#toc">
2019-01-11 20:37:23 +01:00
<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>
2020-08-21 11:40:13 +02:00
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9006</span>
2019-01-11 20:37:23 +01:00
</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>
2019-02-14 10:23:51 +01:00
<a href="../articles/resistance_predict.html">
2019-01-11 20:37:23 +01:00
<span class="fa fa-dice"></span>
Predict antimicrobial resistance
</a>
</li>
2020-08-21 11:40:13 +02:00
<li>
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
Download our reference data sets for own use
</a>
</li>
2020-04-13 21:09:56 +02:00
<li>
<a href="../articles/PCA.html">
<span class="fa fa-compress"></span>
Conduct principal component analysis for AMR
</a>
</li>
2019-05-28 16:50:40 +02:00
<li>
<a href="../articles/MDR.html">
<span class="fa fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
</a>
</li>
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>
2019-02-14 15:18:17 +01:00
<li>
<a href="../articles/SPSS.html">
<span class="fa fa-file-upload"></span>
Import data from SPSS/SAS/Stata
</a>
</li>
2019-01-11 20:37:23 +01:00
<li>
<a href="../articles/EUCAST.html">
<span class="fa fa-exchange-alt"></span>
Apply EUCAST rules
</a>
</li>
<li>
2019-02-14 10:23:51 +01:00
<a href="../reference/mo_property.html">
2019-01-11 20:37:23 +01:00
<span class="fa fa-bug"></span>
Get properties of a microorganism
</a>
</li>
<li>
2019-05-10 16:44:59 +02:00
<a href="../reference/ab_property.html">
2019-01-11 20:37:23 +01:00
<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>
2020-07-28 18:39:57 +02:00
<a href="../reference/index.html">
2019-01-11 20:37:23 +01:00
<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>
2020-07-28 18:39:57 +02:00
<a href="../news/index.html">
2019-01-11 20:37:23 +01:00
<span class="far fa far fa-newspaper"></span>
Changelog
</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
2020-07-08 14:48:06 +02:00
<a href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
2019-01-11 20:37:23 +01:00
Source Code
</a>
</li>
<li>
2020-07-28 18:39:57 +02:00
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
2019-01-11 20:37:23 +01:00
2020-07-28 18:39:57 +02:00
Survey
2019-01-11 20:37:23 +01:00
</a>
</li>
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
2019-10-13 09:31:58 +02:00
2019-01-11 20:37:23 +01:00
</header>
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Guess antibiotic column</h1>
2020-07-08 14:48:06 +02:00
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/guess_ab_col.R'><code>R/guess_ab_col.R</code></a></small>
2019-01-11 20:37:23 +01:00
<div class="hidden name"><code>guess_ab_col.Rd</code></div>
</div>
<div class="ref-description">
<p>This tries to find a column name in a data set based on information from the <a href='antibiotics.html'>antibiotics</a> data set. Also supports WHONET abbreviations.</p>
2019-01-11 20:37:23 +01:00
</div>
2020-08-10 12:46:03 +02:00
<pre class="usage"><span class='fu'>guess_ab_col</span>(x = <span class='kw'>NULL</span>, search_string = <span class='kw'>NULL</span>, verbose = <span class='fl'>FALSE</span>)</pre>
2019-10-13 09:31:58 +02:00
2019-01-11 20:37:23 +01:00
<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>
2019-05-13 10:10:16 +02:00
<th>x</th>
<td><p>a <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code></p></td>
2019-01-11 20:37:23 +01:00
</tr>
<tr>
2019-05-13 10:10:16 +02:00
<th>search_string</th>
<td><p>a text to search <code>x</code> for, will be checked with <code><a href='as.ab.html'>as.ab()</a></code> if this value is not a column in <code>x</code></p></td>
2019-01-11 20:37:23 +01:00
</tr>
<tr>
<th>verbose</th>
<td><p>a logical to indicate whether additional info should be printed</p></td>
</tr>
</table>
2019-10-13 09:31:58 +02:00
2019-05-13 10:10:16 +02:00
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>A column name of <code>x</code>, or <code>NULL</code> when no result is found.</p>
2019-05-31 14:40:15 +02:00
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>You can look for an antibiotic (trade) name or abbreviation and it will search <code>x</code> and the <a href='antibiotics.html'>antibiotics</a> data set for any column containing a name or code of that antibiotic. <strong>Longer columns names take precendence over shorter column names.</strong></p>
<h2 class="hasAnchor" id="maturing-lifecycle"><a class="anchor" href="#maturing-lifecycle"></a>Maturing lifecycle</h2>
<p><img src='figures/lifecycle_maturing.svg' style=margin-bottom:5px /> <br />
2020-07-08 14:48:06 +02:00
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing</strong>. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome <a href='https://github.com/msberends/AMR/issues'>to suggest changes at our repository</a> or <a href='AMR.html'>write us an email (see section 'Contact Us')</a>.</p>
2019-01-11 20:37:23 +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>
2019-10-13 09:31:58 +02:00
2020-07-28 18:39:57 +02:00
<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 analysis, the <a href='https://msberends.github.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
2019-01-11 20:37:23 +01:00
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
2020-08-10 12:46:03 +02:00
<pre class="examples"><span class='kw'>df</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(amox = <span class='st'>"S"</span>,
tetr = <span class='st'>"R"</span>)
2019-01-11 20:37:23 +01:00
2020-08-10 12:46:03 +02:00
<span class='fu'>guess_ab_col</span>(<span class='kw'>df</span>, <span class='st'>"amoxicillin"</span>)
2019-01-11 20:37:23 +01:00
<span class='co'># [1] "amox"</span>
2020-08-10 12:46:03 +02:00
<span class='fu'>guess_ab_col</span>(<span class='kw'>df</span>, <span class='st'>"J01AA07"</span>) <span class='co'># ATC code of tetracycline</span>
2019-01-11 20:37:23 +01:00
<span class='co'># [1] "tetr"</span>
2020-08-10 12:46:03 +02:00
<span class='fu'>guess_ab_col</span>(<span class='kw'>df</span>, <span class='st'>"J01AA07"</span>, verbose = <span class='fl'>TRUE</span>)
<span class='co'># NOTE: Using column `tetr` as input for `J01AA07` (tetracycline).</span>
2019-01-11 20:37:23 +01:00
<span class='co'># [1] "tetr"</span>
2019-01-29 00:06:50 +01:00
<span class='co'># WHONET codes</span>
2020-08-10 12:46:03 +02:00
<span class='kw'>df</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(AMP_ND10 = <span class='st'>"R"</span>,
AMC_ED20 = <span class='st'>"S"</span>)
<span class='fu'>guess_ab_col</span>(<span class='kw'>df</span>, <span class='st'>"ampicillin"</span>)
2019-01-29 00:06:50 +01:00
<span class='co'># [1] "AMP_ND10"</span>
2020-08-10 12:46:03 +02:00
<span class='fu'>guess_ab_col</span>(<span class='kw'>df</span>, <span class='st'>"J01CR02"</span>)
2019-01-29 00:06:50 +01:00
<span class='co'># [1] "AMC_ED20"</span>
2020-08-10 12:46:03 +02:00
<span class='fu'>guess_ab_col</span>(<span class='kw'>df</span>, <span class='fu'><a href='as.ab.html'>as.ab</a></span>(<span class='st'>"augmentin"</span>))
2019-01-29 00:06:50 +01:00
<span class='co'># [1] "AMC_ED20"</span>
2019-05-31 14:40:15 +02:00
<span class='co'># Longer names take precendence:</span>
2020-08-10 12:46:03 +02:00
<span class='kw'>df</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(AMP_ED2 = <span class='st'>"S"</span>,
AMP_ED20 = <span class='st'>"S"</span>)
<span class='fu'>guess_ab_col</span>(<span class='kw'>df</span>, <span class='st'>"ampicillin"</span>)
2019-10-13 09:31:58 +02:00
<span class='co'># [1] "AMP_ED20"</span></pre>
2019-01-11 20:37:23 +01:00
</div>
2020-04-13 21:09:56 +02:00
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
2020-04-17 19:16:30 +02:00
<nav id="toc" data-toggle="toc" class="sticky-top">
<h2 data-toc-skip>Contents</h2>
</nav>
2019-01-11 20:37:23 +01:00
</div>
</div>
2019-10-13 09:31:58 +02:00
2019-01-11 20:37:23 +01:00
<footer>
<div class="copyright">
2020-01-26 20:38:54 +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/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
2019-01-11 20:37:23 +01:00
</div>
<div class="pkgdown">
2020-08-10 12:46:03 +02:00
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.9000.</p>
2019-01-11 20:37:23 +01:00
</div>
2019-10-13 09:31:58 +02:00
2019-01-11 20:37:23 +01:00
</footer>
</div>
2019-10-13 09:31:58 +02:00
2019-01-11 20:37:23 +01:00
</body>
</html>
2019-10-13 09:31:58 +02:00