mirror of https://github.com/msberends/AMR.git
477 lines
29 KiB
HTML
477 lines
29 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 susceptibility rules as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, http://eucast.org), see Source. This includes (1) expert rules and intrinsic resistance and (2) inferred resistance as defined in their breakpoint tables.
|
|
To improve the interpretation of the antibiogram before EUCAST rules are applied, some non-EUCAST rules are applied at default, see Details." />
|
|
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg" />
|
|
|
|
|
|
|
|
|
|
<!-- 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">1.3.0</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/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 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 fab fa-github"></span>
|
|
|
|
Source Code
|
|
</a>
|
|
</li>
|
|
<li>
|
|
<a href="../survey.html">
|
|
<span class="fa 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 susceptibility rules as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, <a href='http://eucast.org'>http://eucast.org</a>), see <em>Source</em>. This includes (1) expert rules and intrinsic resistance and (2) inferred resistance as defined in their breakpoint tables.</p>
|
|
<p>To improve the interpretation of the antibiogram before EUCAST rules are applied, some non-EUCAST rules are applied at default, see Details.</p>
|
|
</div>
|
|
|
|
<pre class="usage"><span class='fu'>eucast_rules</span>(
|
|
<span class='no'>x</span>,
|
|
<span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
|
|
<span class='kw'>info</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/interactive.html'>interactive</a></span>(),
|
|
<span class='kw'>rules</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/options.html'>getOption</a></span>(<span class='st'>"AMR.eucast_rules"</span>, <span class='kw'>default</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"breakpoints"</span>, <span class='st'>"expert"</span>)),
|
|
<span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
|
|
<span class='no'>...</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, like e.g. <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>print progress</p></td>
|
|
</tr>
|
|
<tr>
|
|
<th>rules</th>
|
|
<td><p>a character vector that specifies which rules should be applied. Must be one or more of <code>"breakpoints"</code>, <code>"expert"</code>, <code>"other"</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 using e.g. <code><a href='https://rdrr.io/r/base/options.html'>options(AMR.eucast_rules = "all")</a></code>.</p></td>
|
|
</tr>
|
|
<tr>
|
|
<th>verbose</th>
|
|
<td><p>a logical 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.</p></td>
|
|
</tr>
|
|
<tr>
|
|
<th>...</th>
|
|
<td><p>column name of an antibiotic, please see section <em>Antibiotics</em> below</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. <br />
|
|
<a href='https://doi.org/10.1111/j.1469-0691.2011.03703.x'>https://doi.org/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. <br />
|
|
<a href='http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf'>http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf</a></p></li>
|
|
<li><p>EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 9.0, 2019. <br />
|
|
<a href='http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx'>http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx</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 <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> 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.</p>
|
|
<p>Before further processing, some non-EUCAST rules can be applied to improve the efficacy of the EUCAST rules. These non-EUCAST rules, that are then applied to all isolates, are:</p><ul>
|
|
<li><p>Inherit amoxicillin (AMX) from ampicillin (AMP), where amoxicillin (AMX) is unavailable;</p></li>
|
|
<li><p>Inherit ampicillin (AMP) from amoxicillin (AMX), where ampicillin (AMP) is unavailable;</p></li>
|
|
<li><p>Set amoxicillin (AMX) = R where amoxicillin/clavulanic acid (AMC) = R;</p></li>
|
|
<li><p>Set piperacillin (PIP) = R where piperacillin/tazobactam (TZP) = R;</p></li>
|
|
<li><p>Set trimethoprim (TMP) = R where trimethoprim/sulfamethoxazole (SXT) = R;</p></li>
|
|
<li><p>Set amoxicillin/clavulanic acid (AMC) = S where amoxicillin (AMX) = S;</p></li>
|
|
<li><p>Set piperacillin/tazobactam (TZP) = S where piperacillin (PIP) = S;</p></li>
|
|
<li><p>Set trimethoprim/sulfamethoxazole (SXT) = S where trimethoprim (TMP) = S.</p></li>
|
|
</ul>
|
|
|
|
<p>These rules are not applied at default, since they are not approved by EUCAST. To use these rules, please use <code>eucast_rules(..., rules = "all")</code>, or set the default behaviour of the <code>[eucast_rules()]</code> function with <code><a href='https://rdrr.io/r/base/options.html'>options(AMR.eucast_rules = "all")</a></code> (or any other valid input value(s) to the <code>rules</code> parameter).</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>.</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 used for the functions <code>eucast_rules()</code> and <code><a href='mdro.html'>mdro()</a></code>. These are shown below in the format '<strong>antimicrobial ID</strong>: name (<a href='https://www.whocc.no/atc/structure_and_principles/'>ATC code</a>)', sorted by name:</p>
|
|
<p><strong>AMK</strong>: amikacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB06'>J01GB06</a>),
|
|
<strong>AMX</strong>: amoxicillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA04'>J01CA04</a>),
|
|
<strong>AMC</strong>: amoxicillin/clavulanic acid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CR02'>J01CR02</a>),
|
|
<strong>AMP</strong>: ampicillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA01'>J01CA01</a>),
|
|
<strong>SAM</strong>: ampicillin/sulbactam (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CR01'>J01CR01</a>),
|
|
<strong>AZM</strong>: azithromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA10'>J01FA10</a>),
|
|
<strong>AZL</strong>: azlocillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA09'>J01CA09</a>),
|
|
<strong>ATM</strong>: aztreonam (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DF01'>J01DF01</a>),
|
|
<strong>CAP</strong>: capreomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J04AB30'>J04AB30</a>),
|
|
<strong>RID</strong>: cefaloridine (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DB02'>J01DB02</a>),
|
|
<strong>CZO</strong>: cefazolin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DB04'>J01DB04</a>),
|
|
<strong>FEP</strong>: cefepime (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DE01'>J01DE01</a>),
|
|
<strong>CTX</strong>: cefotaxime (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DD01'>J01DD01</a>),
|
|
<strong>CTT</strong>: cefotetan (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DC05'>J01DC05</a>),
|
|
<strong>FOX</strong>: cefoxitin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DC01'>J01DC01</a>),
|
|
<strong>CPT</strong>: ceftaroline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DI02'>J01DI02</a>),
|
|
<strong>CAZ</strong>: ceftazidime (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DD02'>J01DD02</a>),
|
|
<strong>CRO</strong>: ceftriaxone (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DD04'>J01DD04</a>),
|
|
<strong>CXM</strong>: cefuroxime (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DC02'>J01DC02</a>),
|
|
<strong>CED</strong>: cephradine (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DB09'>J01DB09</a>),
|
|
<strong>CHL</strong>: chloramphenicol (<a href='https://www.whocc.no/atc_ddd_index/?code=J01BA01'>J01BA01</a>),
|
|
<strong>CIP</strong>: ciprofloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA02'>J01MA02</a>),
|
|
<strong>CLR</strong>: clarithromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA09'>J01FA09</a>),
|
|
<strong>CLI</strong>: clindamycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FF01'>J01FF01</a>),
|
|
<strong>COL</strong>: colistin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XB01'>J01XB01</a>),
|
|
<strong>DAP</strong>: daptomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XX09'>J01XX09</a>),
|
|
<strong>DOR</strong>: doripenem (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DH04'>J01DH04</a>),
|
|
<strong>DOX</strong>: doxycycline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01AA02'>J01AA02</a>),
|
|
<strong>ETP</strong>: ertapenem (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DH03'>J01DH03</a>),
|
|
<strong>ERY</strong>: erythromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA01'>J01FA01</a>),
|
|
<strong>ETH</strong>: ethambutol (<a href='https://www.whocc.no/atc_ddd_index/?code=J04AK02'>J04AK02</a>),
|
|
<strong>FLC</strong>: flucloxacillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CF05'>J01CF05</a>),
|
|
<strong>FOS</strong>: fosfomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XX01'>J01XX01</a>),
|
|
<strong>FUS</strong>: fusidic acid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XC01'>J01XC01</a>),
|
|
<strong>GAT</strong>: gatifloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA16'>J01MA16</a>),
|
|
<strong>GEN</strong>: gentamicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB03'>J01GB03</a>),
|
|
<strong>GEH</strong>: gentamicin-high (no ATC code),
|
|
<strong>IPM</strong>: imipenem (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DH51'>J01DH51</a>),
|
|
<strong>INH</strong>: isoniazid (<a href='https://www.whocc.no/atc_ddd_index/?code=J04AC01'>J04AC01</a>),
|
|
<strong>KAN</strong>: kanamycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB04'>J01GB04</a>),
|
|
<strong>LVX</strong>: levofloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA12'>J01MA12</a>),
|
|
<strong>LIN</strong>: lincomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FF02'>J01FF02</a>),
|
|
<strong>LNZ</strong>: linezolid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XX08'>J01XX08</a>),
|
|
<strong>MEM</strong>: meropenem (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DH02'>J01DH02</a>),
|
|
<strong>MTR</strong>: metronidazole (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XD01'>J01XD01</a>),
|
|
<strong>MEZ</strong>: mezlocillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA10'>J01CA10</a>),
|
|
<strong>MNO</strong>: minocycline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01AA08'>J01AA08</a>),
|
|
<strong>MFX</strong>: moxifloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA14'>J01MA14</a>),
|
|
<strong>NAL</strong>: nalidixic acid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MB02'>J01MB02</a>),
|
|
<strong>NEO</strong>: neomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB05'>J01GB05</a>),
|
|
<strong>NET</strong>: netilmicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB07'>J01GB07</a>),
|
|
<strong>NIT</strong>: nitrofurantoin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XE01'>J01XE01</a>),
|
|
<strong>NOR</strong>: norfloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA06'>J01MA06</a>),
|
|
<strong>NOV</strong>: novobiocin (<a href='https://www.whocc.no/atc_ddd_index/?code=QJ01XX95'>QJ01XX95</a>),
|
|
<strong>OFX</strong>: ofloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA01'>J01MA01</a>),
|
|
<strong>OXA</strong>: oxacillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CF04'>J01CF04</a>),
|
|
<strong>PEN</strong>: penicillin G (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CE01'>J01CE01</a>),
|
|
<strong>PIP</strong>: piperacillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA12'>J01CA12</a>),
|
|
<strong>TZP</strong>: piperacillin/tazobactam (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CR05'>J01CR05</a>),
|
|
<strong>PLB</strong>: polymyxin B (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XB02'>J01XB02</a>),
|
|
<strong>PRI</strong>: pristinamycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FG01'>J01FG01</a>),
|
|
<strong>PZA</strong>: pyrazinamide (<a href='https://www.whocc.no/atc_ddd_index/?code=J04AK01'>J04AK01</a>),
|
|
<strong>QDA</strong>: quinupristin/dalfopristin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FG02'>J01FG02</a>),
|
|
<strong>RIB</strong>: rifabutin (<a href='https://www.whocc.no/atc_ddd_index/?code=J04AB04'>J04AB04</a>),
|
|
<strong>RIF</strong>: rifampicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J04AB02'>J04AB02</a>),
|
|
<strong>RFP</strong>: rifapentine (<a href='https://www.whocc.no/atc_ddd_index/?code=J04AB05'>J04AB05</a>),
|
|
<strong>RXT</strong>: roxithromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA06'>J01FA06</a>),
|
|
<strong>SIS</strong>: sisomicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB08'>J01GB08</a>),
|
|
<strong>STH</strong>: streptomycin-high (no ATC code),
|
|
<strong>TEC</strong>: teicoplanin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XA02'>J01XA02</a>),
|
|
<strong>TLV</strong>: telavancin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XA03'>J01XA03</a>),
|
|
<strong>TCY</strong>: tetracycline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01AA07'>J01AA07</a>),
|
|
<strong>TIC</strong>: ticarcillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA13'>J01CA13</a>),
|
|
<strong>TCC</strong>: ticarcillin/clavulanic acid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CR03'>J01CR03</a>),
|
|
<strong>TGC</strong>: tigecycline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01AA12'>J01AA12</a>),
|
|
<strong>TOB</strong>: tobramycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB01'>J01GB01</a>),
|
|
<strong>TMP</strong>: trimethoprim (<a href='https://www.whocc.no/atc_ddd_index/?code=J01EA01'>J01EA01</a>),
|
|
<strong>SXT</strong>: trimethoprim/sulfamethoxazole (<a href='https://www.whocc.no/atc_ddd_index/?code=J01EE01'>J01EE01</a>),
|
|
<strong>VAN</strong>: vancomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XA01'>J01XA01</a>).</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 />
|
|
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>
|
|
<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 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>
|
|
|
|
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
|
<pre class="examples"><span class='co'># \donttest{</span>
|
|
<span class='no'>a</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(<span class='kw'>mo</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></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='kw'>VAN</span> <span class='kw'>=</span> <span class='st'>"-"</span>, <span class='co'># Vancomycin</span>
|
|
<span class='kw'>AMX</span> <span class='kw'>=</span> <span class='st'>"-"</span>, <span class='co'># Amoxicillin</span>
|
|
<span class='kw'>COL</span> <span class='kw'>=</span> <span class='st'>"-"</span>, <span class='co'># Colistin</span>
|
|
<span class='kw'>CAZ</span> <span class='kw'>=</span> <span class='st'>"-"</span>, <span class='co'># Ceftazidime</span>
|
|
<span class='kw'>CXM</span> <span class='kw'>=</span> <span class='st'>"-"</span>, <span class='co'># Cefuroxime</span>
|
|
<span class='kw'>PEN</span> <span class='kw'>=</span> <span class='st'>"S"</span>, <span class='co'># Penicillin G</span>
|
|
<span class='kw'>FOX</span> <span class='kw'>=</span> <span class='st'>"S"</span>, <span class='co'># Cefoxitin</span>
|
|
<span class='kw'>stringsAsFactors</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
|
|
|
|
<span class='no'>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: 18 results are forced as R or S</span>
|
|
<span class='no'>b</span> <span class='kw'><-</span> <span class='fu'>eucast_rules</span>(<span class='no'>a</span>)
|
|
|
|
<span class='no'>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'># with 18 rows, containing all details about the transformations:</span>
|
|
<span class='no'>c</span> <span class='kw'><-</span> <span class='fu'>eucast_rules</span>(<span class='no'>a</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
|
|
<span class='co'># }</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> 1.5.1.</p>
|
|
</div>
|
|
|
|
</footer>
|
|
</div>
|
|
|
|
|
|
|
|
|
|
</body>
|
|
</html>
|
|
|
|
|