<!-- 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>Determine multidrug-resistant organisms (MDRO) — mdro • 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/3.3.1/jquery.min.js" 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guidelines." /> <meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" /> <meta name="twitter:card" content="summary" /> <!-- 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> <div class="container template-reference-topic"> <header> <div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> <span class="sr-only">Toggle navigation</span> <span class="icon-bar"></span> <span class="icon-bar"></span> <span class="icon-bar"></span> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">AMR (for R)</a> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9023</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/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/atc_property.html"> <span class="fa fa-capsules"></span> Get properties of an antibiotic </a> </li> <li> <a href="../articles/freq.html"> <span class="fa fa-sort-amount-down"></span> Create frequency tables </a> </li> <li> <a href="../articles/G_test.html"> <span class="fa fa-clipboard-check"></span> Use the G-test </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/"> <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/"> <span class="far fa far fa-newspaper"></span> Changelog </a> </li> </ul> <ul class="nav navbar-nav navbar-right"> <li> <a href="https://gitlab.com/msberends/AMR"> <span class="fab fa fab fa-gitlab"></span> Source Code </a> </li> <li> <a href="../LICENSE-text.html"> <span class="fa fa-book"></span> Licence </a> </li> </ul> <form class="navbar-form navbar-right" role="search"> <div class="form-group"> <input type="search" class="form-control" name="search-input" id="search-input" placeholder="Search..." aria-label="Search for..." autocomplete="off"> </div> </form> </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> </header> <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Determine multidrug-resistant organisms (MDRO)</h1> <div class="hidden name"><code>mdro.Rd</code></div> </div> <div class="ref-description"> <p>Determine which isolates are multidrug-resistant organisms (MDRO) according to country-specific guidelines.</p> </div> <pre class="usage"><span class='fu'>mdro</span>(<span class='no'>tbl</span>, <span class='kw'>country</span> <span class='kw'>=</span> <span class='kw'>NULL</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='fl'>TRUE</span>, <span class='kw'>amcl</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>amik</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>amox</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>ampi</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>azit</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>aztr</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>cefa</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>cfra</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>cfep</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>cfot</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>cfox</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>cfta</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>cftr</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>cfur</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>chlo</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>cipr</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>clar</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>clin</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>clox</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>coli</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>czol</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>dapt</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>doxy</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>erta</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>eryt</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>fosf</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>fusi</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>gent</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>imip</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>kana</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>levo</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>linc</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>line</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>mero</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>metr</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>mino</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>moxi</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>nali</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>neom</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>neti</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>nitr</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>novo</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>norf</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>oflo</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>peni</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>pipe</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>pita</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>poly</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>qida</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>rifa</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>roxi</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>siso</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>teic</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>tetr</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>tica</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>tige</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>tobr</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>trim</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>trsu</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(), <span class='kw'>vanc</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>()) <span class='fu'>brmo</span>(<span class='no'>...</span>, <span class='kw'>country</span> <span class='kw'>=</span> <span class='st'>"nl"</span>) <span class='fu'>mrgn</span>(<span class='no'>tbl</span>, <span class='kw'>country</span> <span class='kw'>=</span> <span class='st'>"de"</span>, <span class='no'>...</span>) <span class='fu'>eucast_exceptional_phenotypes</span>(<span class='no'>tbl</span>, <span class='kw'>country</span> <span class='kw'>=</span> <span class='st'>"EUCAST"</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>tbl</th> <td><p>table with antibiotic columns, like e.g. <code>amox</code> and <code>amcl</code></p></td> </tr> <tr> <th>country</th> <td><p>country code to determine guidelines. EUCAST rules will be used when left empty, see Details. Should be or a code from the <a href='https://en.wikipedia.org/wiki/ISO_3166-1_alpha-2#Officially_assigned_code_elements'>list of ISO 3166-1 alpha-2 country codes</a>. Case-insensitive. Currently supported are <code>de</code> (Germany) and <code>nl</code> (the Netherlands).</p></td> </tr> <tr> <th>col_mo</th> <td><p>column name of the unique IDs of the microorganisms (see <code><a href='as.mo.html'>mo</a></code>), defaults to the first column of class <code>mo</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>amcl</th> <td><p>column name of an antibiotic, see Antibiotics</p></td> </tr> <tr> <th>amik</th> <td><p>column name of an antibiotic, see Antibiotics</p></td> </tr> <tr> <th>amox</th> <td><p>column name of an antibiotic, see Antibiotics</p></td> </tr> <tr> <th>ampi</th> <td><p>column name of an antibiotic, see Antibiotics</p></td> </tr> <tr> <th>azit</th> <td><p>column name of an antibiotic, see Antibiotics</p></td> </tr> <tr> <th>aztr</th> <td><p>column name of an antibiotic, see Antibiotics</p></td> </tr> <tr> <th>cefa</th> <td><p>column name of an antibiotic, see Antibiotics</p></td> </tr> <tr> <th>cfra</th> <td><p>column name of an antibiotic, see Antibiotics</p></td> </tr> <tr> <th>cfep</th> <td><p>column name of an antibiotic, see Antibiotics</p></td> </tr> <tr> <th>cfot</th> <td><p>column name of an antibiotic, see Antibiotics</p></td> </tr> <tr> <th>cfox</th> <td><p>column name of an antibiotic, see Antibiotics</p></td> </tr> <tr> <th>cfta</th> <td><p>column name of an antibiotic, see Antibiotics</p></td> </tr> <tr> <th>cftr</th> <td><p>column name of an antibiotic, see Antibiotics</p></td> </tr> <tr> <th>cfur</th> <td><p>column name of an antibiotic, see Antibiotics</p></td> </tr> <tr> <th>chlo</th> <td><p>column name of an antibiotic, see Antibiotics</p></td> </tr> <tr> <th>cipr</th> <td><p>column name of an antibiotic, see Antibiotics</p></td> </tr> <tr> <th>clar</th> <td><p>column name of an antibiotic, see Antibiotics</p></td> </tr> <tr> <th>clin</th> <td><p>column name of an antibiotic, see Antibiotics</p></td> </tr> <tr> <th>clox</th> <td><p>column name of an antibiotic, see Antibiotics</p></td> </tr> <tr> <th>coli</th> <td><p>column name of an antibiotic, see Antibiotics</p></td> </tr> <tr> <th>czol</th> <td><p>column name of an antibiotic, see Antibiotics</p></td> </tr> <tr> <th>dapt</th> <td><p>column name of an antibiotic, see Antibiotics</p></td> </tr> <tr> <th>doxy</th> <td><p>column name of an antibiotic, see Antibiotics</p></td> </tr> <tr> <th>erta</th> <td><p>column name of an antibiotic, see Antibiotics</p></td> </tr> <tr> <th>eryt</th> <td><p>column name of an antibiotic, see Antibiotics</p></td> </tr> <tr> <th>fosf</th> <td><p>column name of an antibiotic, see Antibiotics</p></td> </tr> <tr> <th>fusi</th> <td><p>column name of an antibiotic, see Antibiotics</p></td> </tr> <tr> <th>gent</th> <td><p>column name of an antibiotic, see Antibiotics</p></td> </tr> <tr> <th>imip</th> <td><p>column name of an antibiotic, see Antibiotics</p></td> </tr> <tr> <th>kana</th> <td><p>column name of an antibiotic, see Antibiotics</p></td> </tr> <tr> <th>levo</th> <td><p>column name of an antibiotic, see Antibiotics</p></td> </tr> <tr> <th>linc</th> <td><p>column name of an antibiotic, see Antibiotics</p></td> </tr> <tr> <th>line</th> <td><p>column name of an antibiotic, see Antibiotics</p></td> </tr> <tr> <th>mero</th> <td><p>column name of an antibiotic, see Antibiotics</p></td> </tr> <tr> <th>metr</th> <td><p>column name of an antibiotic, see Antibiotics</p></td> </tr> <tr> <th>mino</th> <td><p>column name of an antibiotic, see Antibiotics</p></td> </tr> <tr> <th>moxi</th> <td><p>column name of an antibiotic, see Antibiotics</p></td> </tr> <tr> <th>nali</th> <td><p>column name of an antibiotic, see Antibiotics</p></td> </tr> <tr> <th>neom</th> <td><p>column name of an antibiotic, see Antibiotics</p></td> </tr> <tr> <th>neti</th> <td><p>column name of an antibiotic, see Antibiotics</p></td> </tr> <tr> <th>nitr</th> <td><p>column name of an antibiotic, see Antibiotics</p></td> </tr> <tr> <th>novo</th> <td><p>column name of an antibiotic, see Antibiotics</p></td> </tr> <tr> <th>norf</th> <td><p>column name of an antibiotic, see Antibiotics</p></td> </tr> <tr> <th>oflo</th> <td><p>column name of an antibiotic, see Antibiotics</p></td> </tr> <tr> <th>peni</th> <td><p>column name of an antibiotic, see Antibiotics</p></td> </tr> <tr> <th>pipe</th> <td><p>column name of an antibiotic, see Antibiotics</p></td> </tr> <tr> <th>pita</th> <td><p>column name of an antibiotic, see Antibiotics</p></td> </tr> <tr> <th>poly</th> <td><p>column name of an antibiotic, see Antibiotics</p></td> </tr> <tr> <th>qida</th> <td><p>column name of an antibiotic, see Antibiotics</p></td> </tr> <tr> <th>rifa</th> <td><p>column name of an antibiotic, see Antibiotics</p></td> </tr> <tr> <th>roxi</th> <td><p>column name of an antibiotic, see Antibiotics</p></td> </tr> <tr> <th>siso</th> <td><p>column name of an antibiotic, see Antibiotics</p></td> </tr> <tr> <th>teic</th> <td><p>column name of an antibiotic, see Antibiotics</p></td> </tr> <tr> <th>tetr</th> <td><p>column name of an antibiotic, see Antibiotics</p></td> </tr> <tr> <th>tica</th> <td><p>column name of an antibiotic, see Antibiotics</p></td> </tr> <tr> <th>tige</th> <td><p>column name of an antibiotic, see Antibiotics</p></td> </tr> <tr> <th>tobr</th> <td><p>column name of an antibiotic, see Antibiotics</p></td> </tr> <tr> <th>trim</th> <td><p>column name of an antibiotic, see Antibiotics</p></td> </tr> <tr> <th>trsu</th> <td><p>column name of an antibiotic, see Antibiotics</p></td> </tr> <tr> <th>vanc</th> <td><p>column name of an antibiotic, see Antibiotics</p></td> </tr> <tr> <th>...</th> <td><p>parameters that are passed on to methods</p></td> </tr> </table> <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> <p>Ordered factor with levels <code>Negative < Positive, unconfirmed < Positive</code>.</p> <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> <p>When <code>country</code> will be left blank, guidelines will be taken from EUCAST Expert Rules Version 3.1 "Intrinsic Resistance and Exceptional Phenotypes Tables" (<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> <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>tica = NULL</code>). Non-existing columns will anyway be skipped with a warning.</p> <p>Abbrevations of the column containing antibiotics in the form: <strong>abbreviation</strong>: generic name (<em>ATC code</em>)</p> <p><strong>amcl</strong>: amoxicillin+clavulanic acid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CR02'>J01CR02</a>), <strong>amik</strong>: amikacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB06'>J01GB06</a>), <strong>amox</strong>: amoxicillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA04'>J01CA04</a>), <strong>ampi</strong>: ampicillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA01'>J01CA01</a>), <strong>azit</strong>: azithromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA10'>J01FA10</a>), <strong>azlo</strong>: azlocillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA09'>J01CA09</a>), <strong>aztr</strong>: aztreonam (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DF01'>J01DF01</a>), <strong>cefa</strong>: cefaloridine (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DB02'>J01DB02</a>), <strong>cfep</strong>: cefepime (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DE01'>J01DE01</a>), <strong>cfot</strong>: cefotaxime (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DD01'>J01DD01</a>), <strong>cfox</strong>: cefoxitin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DC01'>J01DC01</a>), <strong>cfra</strong>: cefradine (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DB09'>J01DB09</a>), <strong>cfta</strong>: ceftazidime (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DD02'>J01DD02</a>), <strong>cftr</strong>: ceftriaxone (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DD04'>J01DD04</a>), <strong>cfur</strong>: cefuroxime (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DC02'>J01DC02</a>), <strong>chlo</strong>: chloramphenicol (<a href='https://www.whocc.no/atc_ddd_index/?code=J01BA01'>J01BA01</a>), <strong>cipr</strong>: ciprofloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA02'>J01MA02</a>), <strong>clar</strong>: clarithromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA09'>J01FA09</a>), <strong>clin</strong>: clindamycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FF01'>J01FF01</a>), <strong>clox</strong>: flucloxacillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CF05'>J01CF05</a>), <strong>coli</strong>: colistin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XB01'>J01XB01</a>), <strong>czol</strong>: cefazolin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DB04'>J01DB04</a>), <strong>dapt</strong>: daptomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XX09'>J01XX09</a>), <strong>doxy</strong>: doxycycline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01AA02'>J01AA02</a>), <strong>erta</strong>: ertapenem (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DH03'>J01DH03</a>), <strong>eryt</strong>: erythromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA01'>J01FA01</a>), <strong>fosf</strong>: fosfomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XX01'>J01XX01</a>), <strong>fusi</strong>: fusidic acid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XC01'>J01XC01</a>), <strong>gent</strong>: gentamicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB03'>J01GB03</a>), <strong>imip</strong>: imipenem (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DH51'>J01DH51</a>), <strong>kana</strong>: kanamycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB04'>J01GB04</a>), <strong>levo</strong>: levofloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA12'>J01MA12</a>), <strong>linc</strong>: lincomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FF02'>J01FF02</a>), <strong>line</strong>: linezolid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XX08'>J01XX08</a>), <strong>mero</strong>: meropenem (<a href='https://www.whocc.no/atc_ddd_index/?code=J01DH02'>J01DH02</a>), <strong>mezl</strong>: mezlocillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA10'>J01CA10</a>), <strong>mino</strong>: minocycline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01AA08'>J01AA08</a>), <strong>moxi</strong>: moxifloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA14'>J01MA14</a>), <strong>nali</strong>: nalidixic acid (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MB02'>J01MB02</a>), <strong>neom</strong>: neomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB05'>J01GB05</a>), <strong>neti</strong>: netilmicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB07'>J01GB07</a>), <strong>nitr</strong>: nitrofurantoin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XE01'>J01XE01</a>), <strong>norf</strong>: norfloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA06'>J01MA06</a>), <strong>novo</strong>: novobiocin (an ATCvet code: <a href='https://www.whocc.no/atc_ddd_index/?code=QJ01XX95'>QJ01XX95</a>), <strong>oflo</strong>: ofloxacin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01MA01'>J01MA01</a>), <strong>peni</strong>: (benzyl)penicillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CE01'>J01CE01</a>), <strong>pipe</strong>: piperacillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA12'>J01CA12</a>), <strong>pita</strong>: piperacillin+tazobactam (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CR05'>J01CR05</a>), <strong>poly</strong>: polymyxin B (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XB02'>J01XB02</a>), <strong>pris</strong>: pristinamycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FG01'>J01FG01</a>), <strong>qida</strong>: quinupristin/dalfopristin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FG02'>J01FG02</a>), <strong>rifa</strong>: rifampicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J04AB02'>J04AB02</a>), <strong>roxi</strong>: roxithromycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01FA06'>J01FA06</a>), <strong>siso</strong>: sisomicin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB08'>J01GB08</a>), <strong>teic</strong>: teicoplanin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XA02'>J01XA02</a>), <strong>tetr</strong>: tetracycline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01AA07'>J01AA07</a>), <strong>tica</strong>: ticarcillin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01CA13'>J01CA13</a>), <strong>tige</strong>: tigecycline (<a href='https://www.whocc.no/atc_ddd_index/?code=J01AA12'>J01AA12</a>), <strong>tobr</strong>: tobramycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01GB01'>J01GB01</a>), <strong>trim</strong>: trimethoprim (<a href='https://www.whocc.no/atc_ddd_index/?code=J01EA01'>J01EA01</a>), <strong>trsu</strong>: sulfamethoxazole and trimethoprim (<a href='https://www.whocc.no/atc_ddd_index/?code=J01EE01'>J01EE01</a>), <strong>vanc</strong>: vancomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XA01'>J01XA01</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.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.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'># NOT RUN {</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>) <span class='no'>septic_patients</span> <span class='kw'>%>%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>EUCAST</span> <span class='kw'>=</span> <span class='fu'>mdro</span>(<span class='no'>.</span>), <span class='kw'>BRMO</span> <span class='kw'>=</span> <span class='fu'>brmo</span>(<span class='no'>.</span>)) <span class='co'># }</span></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> <li><a href="#arguments">Arguments</a></li> <li><a href="#value">Value</a></li> <li><a href="#details">Details</a></li> <li><a href="#antibiotics">Antibiotics</a></li> <li><a href="#read-more-on-our-website-">Read more on our website!</a></li> <li><a href="#examples">Examples</a></li> </ul> </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/c.glasner/'>Corinna Glasner</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>.</p> </div> <div class="pkgdown"> <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> </div> </footer> </div> <script src="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.js" integrity="sha256-GKvGqXDznoRYHCwKXGnuchvKSwmx9SRMrZOTh2g4Sb0=" crossorigin="anonymous"></script> <script> docsearch({ apiKey: 'f737050abfd4d726c63938e18f8c496e', indexName: 'amr', inputSelector: 'input#search-input.form-control', transformData: function(hits) { return hits.map(function (hit) { hit.url = updateHitURL(hit); return hit; }); } }); </script> </body> </html>