P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2024-12-27 09:26:11 +01:00
Code Releases Activity
24ac18a99d
AMR/docs/reference/custom_eucast_rules.html

313 lines
13 KiB
HTML
Raw Blame History

<!-- 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>Create Custom EUCAST Rules — custom_eucast_rules • 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="Create Custom EUCAST Rules — custom_eucast_rules" />
<meta property="og:description" content="Create Custom EUCAST Rules" />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.png" />
<!-- 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="Latest development version">1.6.0.9001</span>
</span>
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
<span class="fas fa-home"></span>
Home
</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas 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="fas fa-directions"></span>
Conduct AMR analysis
</a>
</li>
<li>
<a href="../articles/resistance_predict.html">
<span class="fas fa-dice"></span>
Predict antimicrobial resistance
</a>
</li>
<li>
<a href="../articles/datasets.html">
<span class="fas fa-database"></span>
Data sets for download / own use
</a>
</li>
<li>
<a href="../articles/PCA.html">
<span class="fas fa-compress"></span>
Conduct principal component analysis for AMR
</a>
</li>
<li>
<a href="../articles/MDR.html">
<span class="fas fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
</a>
</li>
<li>
<a href="../articles/WHONET.html">
<span class="fas fa-globe-americas"></span>
Work with WHONET data
</a>
</li>
<li>
<a href="../articles/SPSS.html">
<span class="fas fa-file-upload"></span>
Import data from SPSS/SAS/Stata
</a>
</li>
<li>
<a href="../articles/EUCAST.html">
<span class="fas fa-exchange-alt"></span>
Apply EUCAST rules
</a>
</li>
<li>
<a href="../reference/mo_property.html">
<span class="fas fa-bug"></span>
Get properties of a microorganism
</a>
</li>
<li>
<a href="../reference/ab_property.html">
<span class="fas fa-capsules"></span>
Get properties of an antibiotic
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fas fa-shipping-fast"></span>
Other: benchmarks
</a>
</li>
</ul>
</li>
<li>
<a href="../reference/index.html">
<span class="fas fa-book-open"></span>
Manual
</a>
</li>
<li>
<a href="../authors.html">
<span class="fas 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">
<span class="fab fa-github"></span>
Source Code
</a>
</li>
<li>
<a href="../survey.html">
<span class="fas fa-clipboard-list"></span>
Survey
</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>Create Custom EUCAST Rules</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/custom_eucast_rules.R'><code>R/custom_eucast_rules.R</code></a></small>
<div class="hidden name"><code>custom_eucast_rules.Rd</code></div>
</div>
<div class="ref-description">
<p>Create Custom EUCAST Rules</p>
</div>
<pre class="usage"><span class='fu'>custom_eucast_rules</span><span class='op'>(</span><span class='va'>...</span><span class='op'>)</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>...</th>
<td><p>rules in formula notation, see <em>Examples</em></p></td>
</tr>
</table>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>This documentation page will be updated shortly. <strong>This function is experimental.</strong></p>
<h2 class="hasAnchor" id="how-it-works"><a class="anchor" href="#how-it-works"></a>How it works</h2>
<p>..</p>
<p>It is also possible to define antibiotic groups instead of single antibiotics. The following groups are allowed (case-insensitive): <code>aminoglycosides</code>, <code>aminopenicillins</code>, <code>betalactams</code>, <code>carbapenems</code>, <code>cephalosporins</code>, <code>cephalosporins_1st</code>, <code>cephalosporins_2nd</code>, <code>cephalosporins_3rd</code>, <code>cephalosporins_except_caz</code>, <code>fluoroquinolones</code>, <code>glycopeptides</code>, <code>glycopeptides_except_lipo</code>, <code>lincosamides</code>, <code>lipoglycopeptides</code>, <code>macrolides</code>, <code>oxazolidinones</code>, <code>penicillins</code>, <code>polymyxins</code>, <code>streptogramins</code>, <code>tetracyclines</code>, <code>tetracyclines_except_tgc</code> and <code>ureidopenicillins</code>.</p>
<h2 class="hasAnchor" id="experimental-lifecycle"><a class="anchor" href="#experimental-lifecycle"></a>Experimental Lifecycle</h2>
<p><img src='figures/lifecycle_experimental.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>experimental</strong>. An experimental function is in early stages of development. The unlying code might be changing frequently. Experimental functions might be removed without deprecation, so you are generally best off waiting until a function is more mature before you use it in production code. Experimental functions are only available in development versions of this <code>AMR</code> package and will thus not be included in releases that are submitted to CRAN, since such functions have not yet matured enough.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='va'>x</span> <span class='op'>&lt;-</span> <span class='fu'>custom_eucast_rules</span><span class='op'>(</span><span class='va'>AMC</span> <span class='op'>==</span> <span class='st'>"R"</span> <span class='op'>&amp;</span> <span class='va'>genus</span> <span class='op'>==</span> <span class='st'>"Klebsiella"</span> <span class='op'>~</span> <span class='va'>aminopenicillins</span> <span class='op'>==</span> <span class='st'>"R"</span>,
<span class='va'>AMC</span> <span class='op'>==</span> <span class='st'>"I"</span> <span class='op'>&amp;</span> <span class='va'>genus</span> <span class='op'>==</span> <span class='st'>"Klebsiella"</span> <span class='op'>~</span> <span class='va'>aminopenicillins</span> <span class='op'>==</span> <span class='st'>"I"</span><span class='op'>)</span>
<span class='fu'><a href='eucast_rules.html'>eucast_rules</a></span><span class='op'>(</span><span class='va'>example_isolates</span>,
rules <span class='op'>=</span> <span class='st'>"custom"</span>,
custom_rules <span class='op'>=</span> <span class='va'>x</span>,
info <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<span class='co'># combine rule sets</span>
<span class='va'>x2</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='va'>x</span>,
<span class='fu'>custom_eucast_rules</span><span class='op'>(</span><span class='va'>TZP</span> <span class='op'>==</span> <span class='st'>"R"</span> <span class='op'>~</span> <span class='va'>carbapenems</span> <span class='op'>==</span> <span class='st'>"R"</span><span class='op'>)</span><span class='op'>)</span>
<span class='va'>x2</span>
</pre>
</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>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>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
</div>
</footer>
</div>
</body>
</html>
View Git Blame Copy Permalink