mirror of https://github.com/msberends/AMR.git
458 lines
52 KiB
HTML
458 lines
52 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>Apply EUCAST Rules — 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="Apply EUCAST Rules — eucast_rules" />
|
|
<meta property="og:description" content="Apply rules for clinical breakpoints and intrinsic resistance as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, https://eucast.org), see Source. Use eucast_dosage() to get a data.frame with advised dosages of a certain bug-drug combination, which is based on the dosage data set.
|
|
To improve the interpretation of the antibiogram before EUCAST rules are applied, some non-EUCAST rules can applied at default, see Details." />
|
|
<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">1.7.0.9001</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>Apply EUCAST Rules</h1>
|
|
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/eucast_rules.R'><code>R/eucast_rules.R</code></a></small>
|
|
<div class="hidden name"><code>eucast_rules.Rd</code></div>
|
|
</div>
|
|
|
|
<div class="ref-description">
|
|
<p>Apply rules for clinical breakpoints and intrinsic resistance as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, <a href='https://eucast.org'>https://eucast.org</a>), see <em>Source</em>. Use <code>eucast_dosage()</code> to get a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with advised dosages of a certain bug-drug combination, which is based on the <a href='dosage.html'>dosage</a> data set.</p>
|
|
<p>To improve the interpretation of the antibiogram before EUCAST rules are applied, some non-EUCAST rules can applied at default, see <em>Details</em>.</p>
|
|
</div>
|
|
|
|
<pre class="usage"><span class='fu'>eucast_rules</span><span class='op'>(</span>
|
|
<span class='va'>x</span>,
|
|
col_mo <span class='op'>=</span> <span class='cn'>NULL</span>,
|
|
info <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/interactive.html'>interactive</a></span><span class='op'>(</span><span class='op'>)</span>,
|
|
rules <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/options.html'>getOption</a></span><span class='op'>(</span><span class='st'>"AMR_eucastrules"</span>, default <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"breakpoints"</span>, <span class='st'>"expert"</span><span class='op'>)</span><span class='op'>)</span>,
|
|
verbose <span class='op'>=</span> <span class='cn'>FALSE</span>,
|
|
version_breakpoints <span class='op'>=</span> <span class='fl'>11</span>,
|
|
version_expertrules <span class='op'>=</span> <span class='fl'>3.2</span>,
|
|
ampc_cephalosporin_resistance <span class='op'>=</span> <span class='cn'>NA</span>,
|
|
only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>,
|
|
custom_rules <span class='op'>=</span> <span class='cn'>NULL</span>,
|
|
<span class='va'>...</span>
|
|
<span class='op'>)</span>
|
|
|
|
<span class='fu'>eucast_dosage</span><span class='op'>(</span><span class='va'>ab</span>, administration <span class='op'>=</span> <span class='st'>"iv"</span>, version_breakpoints <span class='op'>=</span> <span class='fl'>11</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>x</th>
|
|
<td><p>data with antibiotic columns, such as <code>amox</code>, <code>AMX</code> and <code>AMC</code></p></td>
|
|
</tr>
|
|
<tr>
|
|
<th>col_mo</th>
|
|
<td><p>column name of the IDs of the microorganisms (see <code><a href='as.mo.html'>as.mo()</a></code>), defaults to the first column of class <code><a href='as.mo.html'>mo</a></code>. Values will be coerced using <code><a href='as.mo.html'>as.mo()</a></code>.</p></td>
|
|
</tr>
|
|
<tr>
|
|
<th>info</th>
|
|
<td><p>a <a href='https://rdrr.io/r/base/logical.html'>logical</a> to indicate whether progress should be printed to the console, defaults to only print while in interactive sessions</p></td>
|
|
</tr>
|
|
<tr>
|
|
<th>rules</th>
|
|
<td><p>a <a href='https://rdrr.io/r/base/character.html'>character</a> vector that specifies which rules should be applied. Must be one or more of <code>"breakpoints"</code>, <code>"expert"</code>, <code>"other"</code>, <code>"custom"</code>, <code>"all"</code>, and defaults to <code><a href='https://rdrr.io/r/base/c.html'>c("breakpoints", "expert")</a></code>. The default value can be set to another value, e.g. using <code><a href='https://rdrr.io/r/base/options.html'>options(AMR_eucastrules = "all")</a></code>. If using <code>"custom"</code>, be sure to fill in argument <code>custom_rules</code> too. Custom rules can be created with <code><a href='custom_eucast_rules.html'>custom_eucast_rules()</a></code>.</p></td>
|
|
</tr>
|
|
<tr>
|
|
<th>verbose</th>
|
|
<td><p>a <a href='https://rdrr.io/r/base/logical.html'>logical</a> to turn Verbose mode on and off (default is off). In Verbose mode, the function does not apply rules to the data, but instead returns a data set in logbook form with extensive info about which rows and columns would be effected and in which way. Using Verbose mode takes a lot more time.</p></td>
|
|
</tr>
|
|
<tr>
|
|
<th>version_breakpoints</th>
|
|
<td><p>the version number to use for the EUCAST Clinical Breakpoints guideline. Can be either "11.0" or "10.0".</p></td>
|
|
</tr>
|
|
<tr>
|
|
<th>version_expertrules</th>
|
|
<td><p>the version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be either "3.2" or "3.1".</p></td>
|
|
</tr>
|
|
<tr>
|
|
<th>ampc_cephalosporin_resistance</th>
|
|
<td><p>a <a href='https://rdrr.io/r/base/character.html'>character</a> value that should be applied to cefotaxime, ceftriaxone and ceftazidime for AmpC de-repressed cephalosporin-resistant mutants, defaults to <code>NA</code>. Currently only works when <code>version_expertrules</code> is <code>3.2</code>; '<em>EUCAST Expert Rules v3.2 on Enterobacterales</em>' states that results of cefotaxime, ceftriaxone and ceftazidime should be reported with a note, or results should be suppressed (emptied) for these three agents. A value of <code>NA</code> (the default) for this argument will remove results for these three agents, while e.g. a value of <code>"R"</code> will make the results for these agents resistant. Use <code>NULL</code> or <code>FALSE</code> to not alter results for these three agents of AmpC de-repressed cephalosporin-resistant mutants. Using <code>TRUE</code> is equal to using <code>"R"</code>. <br /> For <em>EUCAST Expert Rules</em> v3.2, this rule applies to: <em>Citrobacter braakii</em>, <em>Citrobacter freundii</em>, <em>Citrobacter gillenii</em>, <em>Citrobacter murliniae</em>, <em>Citrobacter rodenticum</em>, <em>Citrobacter sedlakii</em>, <em>Citrobacter werkmanii</em>, <em>Citrobacter youngae</em>, <em>Enterobacter</em>, <em>Hafnia alvei</em>, <em>Klebsiella aerogenes</em>, <em>Morganella morganii</em>, <em>Providencia</em> and <em>Serratia</em>.</p></td>
|
|
</tr>
|
|
<tr>
|
|
<th>only_rsi_columns</th>
|
|
<td><p>a <a href='https://rdrr.io/r/base/logical.html'>logical</a> to indicate whether only antibiotic columns must be detected that were transformed to class <code><rsi></code> (see <code><a href='as.rsi.html'>as.rsi()</a></code>) on beforehand (defaults to <code>FALSE</code>)</p></td>
|
|
</tr>
|
|
<tr>
|
|
<th>custom_rules</th>
|
|
<td><p>custom rules to apply, created with <code><a href='custom_eucast_rules.html'>custom_eucast_rules()</a></code></p></td>
|
|
</tr>
|
|
<tr>
|
|
<th>...</th>
|
|
<td><p>column name of an antibiotic, see section <em>Antibiotics</em> below</p></td>
|
|
</tr>
|
|
<tr>
|
|
<th>ab</th>
|
|
<td><p>any (vector of) text that can be coerced to a valid antibiotic code with <code><a href='as.ab.html'>as.ab()</a></code></p></td>
|
|
</tr>
|
|
<tr>
|
|
<th>administration</th>
|
|
<td><p>route of administration, either "im", "iv" or "oral"</p></td>
|
|
</tr>
|
|
</table>
|
|
|
|
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
|
|
|
|
|
|
<ul>
|
|
<li><p>EUCAST Expert Rules. Version 2.0, 2012.<br />
|
|
Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility testing.</strong> <em>Clin Microbiol Infect.</em> 2013;19(2):141-60; doi: <a href='https://doi.org/10.1111/j.1469-0691.2011.03703.x'>10.1111/j.1469-0691.2011.03703.x</a></p></li>
|
|
<li><p>EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes Tables. Version 3.1, 2016. <a href='https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf'>(link)</a></p></li>
|
|
<li><p>EUCAST Intrinsic Resistance and Unusual Phenotypes. Version 3.2, 2020. <a href='https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2020/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.2_20200225.pdf'>(link)</a></p></li>
|
|
<li><p>EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 9.0, 2019. <a href='https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx'>(link)</a></p></li>
|
|
<li><p>EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 10.0, 2020. <a href='https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_10.0_Breakpoint_Tables.xlsx'>(link)</a></p></li>
|
|
<li><p>EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 11.0, 2021. <a href='https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_11.0_Breakpoint_Tables.xlsx'>(link)</a></p></li>
|
|
</ul>
|
|
|
|
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
|
|
|
|
<p>The input of <code>x</code>, possibly with edited values of antibiotics. Or, if <code>verbose = TRUE</code>, a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with all original and new values of the affected bug-drug combinations.</p>
|
|
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
|
|
|
|
<p><strong>Note:</strong> This function does not translate MIC values to RSI values. Use <code><a href='as.rsi.html'>as.rsi()</a></code> for that. <br />
|
|
<strong>Note:</strong> When ampicillin (AMP, J01CA01) is not available but amoxicillin (AMX, J01CA04) is, the latter will be used for all rules where there is a dependency on ampicillin. These drugs are interchangeable when it comes to expression of antimicrobial resistance. <br /></p>
|
|
<p>The file containing all EUCAST rules is located here: <a href='https://github.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv'>https://github.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv</a>. <strong>Note:</strong> Old taxonomic names are replaced with the current taxonomy where applicable. For example, <em>Ochrobactrum anthropi</em> was renamed to <em>Brucella anthropi</em> in 2020; the original EUCAST rules v3.1 and v3.2 did not yet contain this new taxonomic name. The file used as input for this <code>AMR</code> package contains the taxonomy updated until <a href='catalogue_of_life.html'>March 2021</a>.</p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Custom Rules</h3>
|
|
|
|
|
|
<p>Custom rules can be created using <code><a href='custom_eucast_rules.html'>custom_eucast_rules()</a></code>, e.g.:</p><pre><span class='va'>x</span> <span class='op'><-</span> <span class='fu'><a href='custom_eucast_rules.html'>custom_eucast_rules</a></span><span class='op'>(</span><span class='va'>AMC</span> <span class='op'>==</span> <span class='st'>"R"</span> <span class='op'>&</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'>&</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'>eucast_rules</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><span class='op'>)</span>
|
|
</pre>
|
|
|
|
|
|
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>'Other' Rules</h3>
|
|
|
|
|
|
<p>Before further processing, two non-EUCAST rules about drug combinations can be applied to improve the efficacy of the EUCAST rules, and the reliability of your data (analysis). These rules are:</p><ol>
|
|
<li><p>A drug <strong>with</strong> enzyme inhibitor will be set to S if the same drug <strong>without</strong> enzyme inhibitor is S</p></li>
|
|
<li><p>A drug <strong>without</strong> enzyme inhibitor will be set to R if the same drug <strong>with</strong> enzyme inhibitor is R</p></li>
|
|
</ol>
|
|
|
|
<p>Important examples include amoxicillin and amoxicillin/clavulanic acid, and trimethoprim and trimethoprim/sulfamethoxazole. Needless to say, for these rules to work, both drugs must be available in the data set.</p>
|
|
<p>Since these rules are not officially approved by EUCAST, they are not applied at default. To use these rules, include <code>"other"</code> to the <code>rules</code> argument, or use <code>eucast_rules(..., rules = "all")</code>. You can also set the option <code>AMR_eucastrules</code>, i.e. run <code><a href='https://rdrr.io/r/base/options.html'>options(AMR_eucastrules = "all")</a></code>.</p>
|
|
|
|
<h2 class="hasAnchor" id="antibiotics"><a class="anchor" href="#antibiotics"></a>Antibiotics</h2>
|
|
|
|
|
|
|
|
<p>To define antibiotics column names, leave as it is to determine it automatically with <code><a href='guess_ab_col.html'>guess_ab_col()</a></code> or input a text (case-insensitive), or use <code>NULL</code> to skip a column (e.g. <code>TIC = NULL</code> to skip ticarcillin). Manually defined but non-existing columns will be skipped with a warning.</p>
|
|
<p>The following antibiotics are eligible for the functions <code>eucast_rules()</code> and <code><a href='mdro.html'>mdro()</a></code>. These are shown below in the format 'name (<code>antimicrobial ID</code>, <a href='https://www.whocc.no/atc/structure_and_principles/'>ATC code</a>)', sorted alphabetically:</p>
|
|
<p>Amikacin (<code>AMK</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01GB06&showdescription=no'>J01MA02</a>), amoxicillin (<code>AMX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA04&showdescription=no'>J01MA04</a>), amoxicillin/clavulanic acid (<code>AMC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CR02&showdescription=no'>J01MA08</a>), ampicillin (<code>AMP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA01&showdescription=no'>J01MA16</a>), ampicillin/sulbactam (<code>SAM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CR01&showdescription=no'>J01MA15</a>), azidocillin (<code>AZD</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CE04&showdescription=no'>J01MA11</a>), azithromycin (<code>AZM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01FA10&showdescription=no'>J01MA12</a>), azlocillin (<code>AZL</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA09&showdescription=no'>J01MA07</a>), aztreonam (<code>ATM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DF01&showdescription=no'>J01MA14</a>), bacampicillin (<code>BAM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA06&showdescription=no'>J01MA06</a>), benzathine benzylpenicillin (<code>BNB</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CE08&showdescription=no'>J01MA01</a>), benzathine phenoxymethylpenicillin (<code>BNP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CE10&showdescription=no'>J01MA18</a>), benzylpenicillin (<code>PEN</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CE01&showdescription=no'>J01MA03</a>), cadazolid (<code>CDZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD09&showdescription=no'>J01MA17</a>), carbenicillin (<code>CRB</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA03&showdescription=no'>J01MA10</a>), carindacillin (<code>CRN</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA05&showdescription=no'>J01MA09</a>), cefacetrile (<code>CAC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB10&showdescription=no'>J01MA05</a>), cefaclor (<code>CEC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC04&showdescription=no'>J01MA13</a>), cefadroxil (<code>CFR</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB05&showdescription=no'>J01CA01</a>), cefaloridine (<code>RID</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB02&showdescription=no'>J01CA04</a>), cefamandole (<code>MAN</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC03&showdescription=no'>J01CA12</a>), cefatrizine (<code>CTZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB07&showdescription=no'>J01CR05</a>), cefazedone (<code>CZD</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB06&showdescription=no'>J01CA13</a>), cefazolin (<code>CZO</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB04&showdescription=no'>J01AA02</a>), cefdinir (<code>CDR</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD15&showdescription=no'>J01FA10</a>), cefditoren (<code>DIT</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD16&showdescription=no'>J01FA09</a>), cefepime (<code>FEP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DE01&showdescription=no'>J01CR02</a>), cefetamet (<code>CAT</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD10&showdescription=no'>J01AA08</a>), cefixime (<code>CFM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD08&showdescription=no'>J01FA06</a>), cefmenoxime (<code>CMX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD05&showdescription=no'>J01CF04</a>), cefmetazole (<code>CMZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC09&showdescription=no'>J01CF05</a>), cefodizime (<code>DIZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD09&showdescription=no'>J01CR01</a>), cefonicid (<code>CID</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC06&showdescription=no'>J01CE04</a>), cefoperazone (<code>CFP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD12&showdescription=no'>J01CA09</a>), cefoperazone/sulbactam (<code>CSL</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD62&showdescription=no'>J01DF01</a>), ceforanide (<code>CND</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC11&showdescription=no'>J01CA06</a>), cefotaxime (<code>CTX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD01&showdescription=no'>J01CE08</a>), cefotetan (<code>CTT</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC05&showdescription=no'>J01CE10</a>), cefotiam (<code>CTF</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC07&showdescription=no'>J01CE01</a>), cefoxitin (<code>FOX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC01&showdescription=no'>J01CA03</a>), cefpiramide (<code>CPM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD11&showdescription=no'>J01CA05</a>), cefpirome (<code>CPO</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DE02&showdescription=no'>J01CE07</a>), cefpodoxime (<code>CPD</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD13&showdescription=no'>J01CF02</a>), cefprozil (<code>CPR</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC10&showdescription=no'>J01CF01</a>), cefroxadine (<code>CRD</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB11&showdescription=no'>J01CA07</a>), cefsulodin (<code>CFS</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD03&showdescription=no'>J01CA18</a>), ceftaroline (<code>CPT</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DI02&showdescription=no'>J01CA11</a>), ceftazidime (<code>CAZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD02&showdescription=no'>J01CA14</a>), ceftazidime/avibactam (<code>CZA</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD52&showdescription=no'>J01CF03</a>), ceftazidime/clavulanic acid (<code>CCV</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD52&showdescription=no'>J01CA10</a>), ceftezole (<code>CTL</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB12&showdescription=no'>J01CE06</a>), ceftibuten (<code>CTB</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD14&showdescription=no'>J01CE05</a>), ceftizoxime (<code>CZX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD07&showdescription=no'>J01CE02</a>), ceftobiprole (<code>BPR</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DI01&showdescription=no'>J01CA02</a>), ceftobiprole medocaril (<code>CFM1</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DI01&showdescription=no'>J01CA08</a>), ceftolozane/enzyme inhibitor (<code>CEI</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DI54&showdescription=no'>J01CE09</a>), ceftriaxone (<code>CRO</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD04&showdescription=no'>J01CE03</a>), cefuroxime (<code>CXM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC02&showdescription=no'>J01CG01</a>), cephalexin (<code>LEX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB01&showdescription=no'>J01CA16</a>), cephalothin (<code>CEP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB03&showdescription=no'>J01CR04</a>), cephapirin (<code>HAP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB08&showdescription=no'>J01CA15</a>), cephradine (<code>CED</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB09&showdescription=no'>J01CG02</a>), chloramphenicol (<code>CHL</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01BA01&showdescription=no'>J01CA17</a>), ciprofloxacin (<code>CIP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01MA02&showdescription=no'>J01CR03</a>), clarithromycin (<code>CLR</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01FA09&showdescription=no'>J01DD09</a>), clindamycin (<code>CLI</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01FF01&showdescription=no'>J01DB10</a>), clometocillin (<code>CLM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CE07&showdescription=no'>J01DC04</a>), cloxacillin (<code>CLO</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CF02&showdescription=no'>J01DB05</a>), colistin (<code>COL</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01XB01&showdescription=no'>J01DB02</a>), cycloserine (<code>CYC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J04AB01&showdescription=no'>J01DC03</a>), dalbavancin (<code>DAL</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01XA04&showdescription=no'>J01DB07</a>), daptomycin (<code>DAP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01XX09&showdescription=no'>J01DB06</a>), dibekacin (<code>DKB</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01GB09&showdescription=no'>J01DB04</a>), dicloxacillin (<code>DIC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CF01&showdescription=no'>J01DD15</a>), dirithromycin (<code>DIR</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01FA13&showdescription=no'>J01DD16</a>), doripenem (<code>DOR</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DH04&showdescription=no'>J01DE01</a>), doxycycline (<code>DOX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01AA02&showdescription=no'>J01DD10</a>), enoxacin (<code>ENX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01MA04&showdescription=no'>J01DD08</a>), epicillin (<code>EPC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA07&showdescription=no'>J01DD05</a>), ertapenem (<code>ETP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DH03&showdescription=no'>J01DC09</a>), erythromycin (<code>ERY</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01FA01&showdescription=no'>J01DD09</a>), fleroxacin (<code>FLE</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01MA08&showdescription=no'>J01DC06</a>), flucloxacillin (<code>FLC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CF05&showdescription=no'>J01DD12</a>), flurithromycin (<code>FLR1</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01FA14&showdescription=no'>J01DD62</a>), fosfomycin (<code>FOS</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01XX01&showdescription=no'>J01DC11</a>), fusidic acid (<code>FUS</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01XC01&showdescription=no'>J01DD01</a>), gatifloxacin (<code>GAT</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01MA16&showdescription=no'>J01DC05</a>), gemifloxacin (<code>GEM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01MA15&showdescription=no'>J01DC07</a>), gentamicin (<code>GEN</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01GB03&showdescription=no'>J01DC01</a>), grepafloxacin (<code>GRX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01MA11&showdescription=no'>J01DD11</a>), hetacillin (<code>HET</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA18&showdescription=no'>J01DE02</a>), imipenem (<code>IPM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DH51&showdescription=no'>J01DD13</a>), isepamicin (<code>ISE</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01GB11&showdescription=no'>J01DC10</a>), josamycin (<code>JOS</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01FA07&showdescription=no'>J01DB11</a>), kanamycin (<code>KAN</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01GB04&showdescription=no'>J01DD03</a>), latamoxef (<code>LTM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD06&showdescription=no'>J01DI02</a>), levofloxacin (<code>LVX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01MA12&showdescription=no'>J01DD02</a>), lincomycin (<code>LIN</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01FF02&showdescription=no'>J01DD52</a>), linezolid (<code>LNZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01XX08&showdescription=no'>J01DD52</a>), lomefloxacin (<code>LOM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01MA07&showdescription=no'>J01DB12</a>), loracarbef (<code>LOR</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC08&showdescription=no'>J01DD14</a>), mecillinam (Amdinocillin) (<code>MEC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA11&showdescription=no'>J01DD07</a>), meropenem (<code>MEM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DH02&showdescription=no'>J01DI01</a>), meropenem/vaborbactam (<code>MEV</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DH52&showdescription=no'>J01DI01</a>), metampicillin (<code>MTM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA14&showdescription=no'>J01DI54</a>), methicillin (<code>MET</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CF03&showdescription=no'>J01DD04</a>), mezlocillin (<code>MEZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA10&showdescription=no'>J01DC02</a>), midecamycin (<code>MID</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01FA03&showdescription=no'>J01DB01</a>), minocycline (<code>MNO</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01AA08&showdescription=no'>J01DB03</a>), miocamycin (<code>MCM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01FA11&showdescription=no'>J01DB08</a>), moxifloxacin (<code>MFX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01MA14&showdescription=no'>J01DB09</a>), nalidixic acid (<code>NAL</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01MB02&showdescription=no'>J01DD06</a>), neomycin (<code>NEO</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01GB05&showdescription=no'>J01DC08</a>), netilmicin (<code>NET</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01GB07&showdescription=no'>J01DH04</a>), nitrofurantoin (<code>NIT</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01XE01&showdescription=no'>J01DH03</a>), norfloxacin (<code>NOR</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01MA06&showdescription=no'>J01DH51</a>), novobiocin (<code>NOV</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=QJ01XX95&showdescription=no'>J01DH02</a>), ofloxacin (<code>OFX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01MA01&showdescription=no'>J01DH52</a>), oleandomycin (<code>OLE</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01FA05&showdescription=no'>J01XA02</a>), oritavancin (<code>ORI</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01XA05&showdescription=no'>J01XA01</a>), oxacillin (<code>OXA</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CF04&showdescription=no'>J01XC01</a>), pazufloxacin (<code>PAZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01MA18&showdescription=no'>J01FA13</a>), pefloxacin (<code>PEF</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01MA03&showdescription=no'>J01FA01</a>), penamecillin (<code>PNM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CE06&showdescription=no'>J01FA14</a>), phenethicillin (<code>PHE</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CE05&showdescription=no'>J01FA07</a>), phenoxymethylpenicillin (<code>PHN</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CE02&showdescription=no'>J01FA03</a>), piperacillin (<code>PIP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA12&showdescription=no'>J01FA11</a>), piperacillin/tazobactam (<code>TZP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CR05&showdescription=no'>J01FA05</a>), pivampicillin (<code>PVM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA02&showdescription=no'>J01FA12</a>), pivmecillinam (<code>PME</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA08&showdescription=no'>J01FA02</a>), polymyxin B (<code>PLB</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01XB02&showdescription=no'>J01FA15</a>), pristinamycin (<code>PRI</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01FG01&showdescription=no'>J01FA08</a>), procaine benzylpenicillin (<code>PRB</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CE09&showdescription=no'>J01FF02</a>), propicillin (<code>PRP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CE03&showdescription=no'>J01FG01</a>), prulifloxacin (<code>PRU</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01MA17&showdescription=no'>J01FG02</a>), quinupristin/dalfopristin (<code>QDA</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01FG02&showdescription=no'>J04AB02</a>), ribostamycin (<code>RST</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01GB10&showdescription=no'>J01XX09</a>), rifampicin (<code>RIF</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J04AB02&showdescription=no'>J01XX08</a>), rokitamycin (<code>ROK</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01FA12&showdescription=no'>J01AA07</a>), roxithromycin (<code>RXT</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01FA06&showdescription=no'>J01XB01</a>), rufloxacin (<code>RFL</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01MA10&showdescription=no'>J01XB02</a>), sisomicin (<code>SIS</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01GB08&showdescription=no'>J01XE01</a>), sparfloxacin (<code>SPX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01MA09&showdescription=no'>J01AA12</a>), spiramycin (<code>SPI</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01FA02&showdescription=no'>J01EA01</a>), streptoduocin (<code>STR</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01GA02&showdescription=no'>J01XX01</a>), streptomycin (<code>STR1</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01GA01&showdescription=no'>J01BA01</a>), sulbactam (<code>SUL</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CG01&showdescription=no'>J01GB06</a>), sulbenicillin (<code>SBC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA16&showdescription=no'>J01GB09</a>), sulfadiazine (<code>SDI</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01EC02&showdescription=no'>J01GB03</a>), sulfadiazine/trimethoprim (<code>SLT1</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01EE02&showdescription=no'>J01GB11</a>), sulfadimethoxine (<code>SUD</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01ED01&showdescription=no'>J01GB04</a>), sulfadimidine (<code>SDM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01EB03&showdescription=no'>J01GB05</a>), sulfadimidine/trimethoprim (<code>SLT2</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01EE05&showdescription=no'>J01GB07</a>), sulfafurazole (<code>SLF</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01EB05&showdescription=no'>J01GB10</a>), sulfaisodimidine (<code>SLF1</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01EB01&showdescription=no'>J01GB08</a>), sulfalene (<code>SLF2</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01ED02&showdescription=no'>J01GA02</a>), sulfamazone (<code>SZO</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01ED09&showdescription=no'>J01GA01</a>), sulfamerazine (<code>SLF3</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01ED07&showdescription=no'>J01GB01</a>), sulfamerazine/trimethoprim (<code>SLT3</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01EE07&showdescription=no'>J01EE01</a>), sulfamethizole (<code>SLF4</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01EB02&showdescription=no'>J01MB02</a>), sulfamethoxazole (<code>SMX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01EC01&showdescription=no'>QJ01XX95</a>), sulfamethoxypyridazine (<code>SLF5</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01ED05&showdescription=no'>J01FF01</a>), sulfametomidine (<code>SLF6</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01ED03&showdescription=no'>J01XA04</a>), sulfametoxydiazine (<code>SLF7</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01ED04&showdescription=no'>J01XA05</a>), sulfametrole/trimethoprim (<code>SLT4</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01EE03&showdescription=no'>J01XA03</a>), sulfamoxole (<code>SLF8</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01EC03&showdescription=no'>J04AB01</a>), sulfamoxole/trimethoprim (<code>SLT5</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01EE04&showdescription=no'>J01XX11</a>), sulfanilamide (<code>SLF9</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01EB06&showdescription=no'>J01EC02</a>), sulfaperin (<code>SLF10</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01ED06&showdescription=no'>J01ED01</a>), sulfaphenazole (<code>SLF11</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01ED08&showdescription=no'>J01EB03</a>), sulfapyridine (<code>SLF12</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01EB04&showdescription=no'>J01EB05</a>), sulfathiazole (<code>SUT</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01EB07&showdescription=no'>J01EB01</a>), sulfathiourea (<code>SLF13</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01EB08&showdescription=no'>J01ED02</a>), sultamicillin (<code>SLT6</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CR04&showdescription=no'>J01ED09</a>), talampicillin (<code>TAL</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA15&showdescription=no'>J01ED07</a>), tazobactam (<code>TAZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CG02&showdescription=no'>J01EB02</a>), tedizolid (<code>TZD</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01XX11&showdescription=no'>J01EC01</a>), teicoplanin (<code>TEC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01XA02&showdescription=no'>J01ED05</a>), telavancin (<code>TLV</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01XA03&showdescription=no'>J01ED03</a>), telithromycin (<code>TLT</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01FA15&showdescription=no'>J01ED04</a>), temafloxacin (<code>TMX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01MA05&showdescription=no'>J01EC03</a>), temocillin (<code>TEM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA17&showdescription=no'>J01EB06</a>), tetracycline (<code>TCY</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01AA07&showdescription=no'>J01ED06</a>), ticarcillin (<code>TIC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA13&showdescription=no'>J01ED08</a>), ticarcillin/clavulanic acid (<code>TCC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CR03&showdescription=no'>J01EB04</a>), tigecycline (<code>TGC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01AA12&showdescription=no'>J01EB07</a>), tobramycin (<code>TOB</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01GB01&showdescription=no'>J01EB08</a>), trimethoprim (<code>TMP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01EA01&showdescription=no'>J01EE02</a>), trimethoprim/sulfamethoxazole (<code>SXT</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01EE01&showdescription=no'>J01EE05</a>), troleandomycin (<code>TRL</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01FA08&showdescription=no'>J01EE07</a>), trovafloxacin (<code>TVA</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01MA13&showdescription=no'>J01EE03</a>), vancomycin (<code>VAN</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01XA01&showdescription=no'>J01EE04</a>)</p>
|
|
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>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, a 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>
|
|
<h2 class="hasAnchor" id="reference-data-publicly-available"><a class="anchor" href="#reference-data-publicly-available"></a>Reference Data Publicly Available</h2>
|
|
|
|
|
|
|
|
<p>All reference data sets (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find <a href='https://msberends.github.io/AMR/articles/datasets.html'>all download links on our website</a>, which is automatically updated with every code change.</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>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>
|
|
|
|
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
|
<pre class="examples"><span class='co'># \donttest{</span>
|
|
<span class='va'>a</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span><span class='op'>(</span>mo <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"Staphylococcus aureus"</span>,
|
|
<span class='st'>"Enterococcus faecalis"</span>,
|
|
<span class='st'>"Escherichia coli"</span>,
|
|
<span class='st'>"Klebsiella pneumoniae"</span>,
|
|
<span class='st'>"Pseudomonas aeruginosa"</span><span class='op'>)</span>,
|
|
VAN <span class='op'>=</span> <span class='st'>"-"</span>, <span class='co'># Vancomycin</span>
|
|
AMX <span class='op'>=</span> <span class='st'>"-"</span>, <span class='co'># Amoxicillin</span>
|
|
COL <span class='op'>=</span> <span class='st'>"-"</span>, <span class='co'># Colistin</span>
|
|
CAZ <span class='op'>=</span> <span class='st'>"-"</span>, <span class='co'># Ceftazidime</span>
|
|
CXM <span class='op'>=</span> <span class='st'>"-"</span>, <span class='co'># Cefuroxime</span>
|
|
PEN <span class='op'>=</span> <span class='st'>"S"</span>, <span class='co'># Benzylpenicillin</span>
|
|
FOX <span class='op'>=</span> <span class='st'>"S"</span>, <span class='co'># Cefoxitin</span>
|
|
stringsAsFactors <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
|
|
|
|
<span class='va'>a</span>
|
|
<span class='co'># mo VAN AMX COL CAZ CXM PEN FOX</span>
|
|
<span class='co'># 1 Staphylococcus aureus - - - - - S S</span>
|
|
<span class='co'># 2 Enterococcus faecalis - - - - - S S</span>
|
|
<span class='co'># 3 Escherichia coli - - - - - S S</span>
|
|
<span class='co'># 4 Klebsiella pneumoniae - - - - - S S</span>
|
|
<span class='co'># 5 Pseudomonas aeruginosa - - - - - S S</span>
|
|
|
|
|
|
<span class='co'># apply EUCAST rules: some results wil be changed</span>
|
|
<span class='va'>b</span> <span class='op'><-</span> <span class='fu'>eucast_rules</span><span class='op'>(</span><span class='va'>a</span><span class='op'>)</span>
|
|
|
|
<span class='va'>b</span>
|
|
<span class='co'># mo VAN AMX COL CAZ CXM PEN FOX</span>
|
|
<span class='co'># 1 Staphylococcus aureus - S R R S S S</span>
|
|
<span class='co'># 2 Enterococcus faecalis - - R R R S R</span>
|
|
<span class='co'># 3 Escherichia coli R - - - - R S</span>
|
|
<span class='co'># 4 Klebsiella pneumoniae R R - - - R S</span>
|
|
<span class='co'># 5 Pseudomonas aeruginosa R R - - R R R</span>
|
|
|
|
|
|
<span class='co'># do not apply EUCAST rules, but rather get a data.frame</span>
|
|
<span class='co'># containing all details about the transformations:</span>
|
|
<span class='va'>c</span> <span class='op'><-</span> <span class='fu'>eucast_rules</span><span class='op'>(</span><span class='va'>a</span>, verbose <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
|
|
<span class='co'># }</span>
|
|
|
|
<span class='fu'>eucast_dosage</span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"tobra"</span>, <span class='st'>"genta"</span>, <span class='st'>"cipro"</span><span class='op'>)</span>, <span class='st'>"iv"</span><span class='op'>)</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>
|
|
|
|
|