<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> <html lang="en"> <head> <meta charset="utf-8"> <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> <title>Create Identifier of an Isolate — isolate_identifier • AMR (for R)</title> <!-- favicons --> <link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"> <link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"> <link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png" /> <link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png" /> <link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png" /> <link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png" /> <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" /> <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script> <!-- bootstrap-toc --> <link rel="stylesheet" href="../bootstrap-toc.css"> <script src="../bootstrap-toc.js"></script> <!-- Font Awesome icons --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" /> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" /> <!-- clipboard.js --> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script> <!-- headroom.js --> <script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> <script src="../pkgdown.js"></script> <link href="../extra.css" rel="stylesheet"> <script src="../extra.js"></script> <meta property="og:title" content="Create Identifier of an Isolate — isolate_identifier" /> <meta property="og:description" content="This function will paste the microorganism code with all antimicrobial results into one string for each row in a data set. This is useful to compare isolates, e.g. between institutions or regions, when there is no genotyping available." /> <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">1.5.0.9016</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> <a href="../index.html"> <span class="fas fa-home"></span> Home </a> </li> <li class="dropdown"> <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> <span class="fas fa-question-circle"></span> How to <span class="caret"></span> </a> <ul class="dropdown-menu" role="menu"> <li> <a href="../articles/AMR.html"> <span class="fas fa-directions"></span> Conduct AMR analysis </a> </li> <li> <a href="../articles/resistance_predict.html"> <span class="fas fa-dice"></span> Predict antimicrobial resistance </a> </li> <li> <a href="../articles/datasets.html"> <span class="fas fa-database"></span> Data sets for download / own use </a> </li> <li> <a href="../articles/PCA.html"> <span class="fas fa-compress"></span> Conduct principal component analysis for AMR </a> </li> <li> <a href="../articles/MDR.html"> <span class="fas fa-skull-crossbones"></span> Determine multi-drug resistance (MDR) </a> </li> <li> <a href="../articles/WHONET.html"> <span class="fas fa-globe-americas"></span> Work with WHONET data </a> </li> <li> <a href="../articles/SPSS.html"> <span class="fas fa-file-upload"></span> Import data from SPSS/SAS/Stata </a> </li> <li> <a href="../articles/EUCAST.html"> <span class="fas fa-exchange-alt"></span> Apply EUCAST rules </a> </li> <li> <a href="../reference/mo_property.html"> <span class="fas fa-bug"></span> Get properties of a microorganism </a> </li> <li> <a href="../reference/ab_property.html"> <span class="fas fa-capsules"></span> Get properties of an antibiotic </a> </li> <li> <a href="../articles/benchmarks.html"> <span class="fas fa-shipping-fast"></span> Other: benchmarks </a> </li> </ul> </li> <li> <a href="../reference/index.html"> <span class="fas fa-book-open"></span> Manual </a> </li> <li> <a href="../authors.html"> <span class="fas fa-users"></span> Authors </a> </li> <li> <a href="../news/index.html"> <span class="far fa-newspaper"></span> Changelog </a> </li> </ul> <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/msberends/AMR"> <span class="fab fa-github"></span> Source Code </a> </li> <li> <a href="../survey.html"> <span class="fas fa-clipboard-list"></span> Survey </a> </li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> </header> <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Create Identifier of an Isolate</h1> <small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/isolate_identifier.R'><code>R/isolate_identifier.R</code></a></small> <div class="hidden name"><code>isolate_identifier.Rd</code></div> </div> <div class="ref-description"> <p>This function will paste the microorganism code with all antimicrobial results into one string for each row in a data set. This is useful to compare isolates, e.g. between institutions or regions, when there is no genotyping available.</p> </div> <pre class="usage"><span class='fu'>isolate_identifier</span><span class='op'>(</span><span class='va'>x</span>, col_mo <span class='op'>=</span> <span class='cn'>NULL</span>, cols_ab <span class='op'>=</span> <span class='cn'>NULL</span><span class='op'>)</span> <span class='co'># S3 method for isolate_identifier</span> <span class='fu'><a href='https://rdrr.io/r/base/all.equal.html'>all.equal</a></span><span class='op'>(</span><span class='va'>target</span>, <span class='va'>current</span>, ignore_empty_results <span class='op'>=</span> <span class='cn'>TRUE</span>, <span class='va'>...</span><span class='op'>)</span></pre> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> <th>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>cols_ab</th> <td><p>a character vector of column names of <code>x</code>, or (a combination with) an <a href='[ab_class()]'>antibiotic selector function</a>, such as <code><a href='antibiotic_class_selectors.html'>carbapenems()</a></code> and <code><a href='antibiotic_class_selectors.html'>aminoglycosides()</a></code></p></td> </tr> <tr> <th>target</th> <td><p><span style="R">R</span> object.</p></td> </tr> <tr> <th>current</th> <td><p>other <span style="R">R</span> object, to be compared with <code>target</code>.</p></td> </tr> <tr> <th>ignore_empty_results</th> <td><p>a logical to indicate whether empty results must be ignored, so that only values R, S and I will be compared</p></td> </tr> <tr> <th>...</th> <td><p>column name of an antibiotic, see section <em>Antibiotics</em> below</p></td> </tr> </table> <h2 class="hasAnchor" id="experimental-lifecycle"><a class="anchor" href="#experimental-lifecycle"></a>Experimental Lifecycle</h2> <p><img src='figures/lifecycle_experimental.svg' style=margin-bottom:5px /> <br /> The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>experimental</strong>. An experimental function is in early stages of development. The unlying code might be changing frequently. Experimental functions might be removed without deprecation, so you are generally best off waiting until a function is more mature before you use it in production code. Experimental functions are only available in development versions of this <code>AMR</code> package and will thus not be included in releases that are submitted to CRAN, since such functions have not yet matured enough.</p> <h2 class="hasAnchor" id="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>. 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'># automatic selection of microorganism and antibiotics (i.e., all <rsi> columns, see ?as.rsi)</span> <span class='va'>x</span> <span class='op'><-</span> <span class='fu'>isolate_identifier</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>)</span> <span class='co'># ignore microorganism codes, only use antimicrobial results</span> <span class='va'>x</span> <span class='op'><-</span> <span class='fu'>isolate_identifier</span><span class='op'>(</span><span class='va'>example_isolates</span>, col_mo <span class='op'>=</span> <span class='cn'>FALSE</span>, cols_ab <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'>"AMX"</span>, <span class='st'>"TZP"</span>, <span class='st'>"GEN"</span>, <span class='st'>"TOB"</span><span class='op'>)</span><span class='op'>)</span> <span class='co'># select antibiotics from certain antibiotic classes</span> <span class='va'>x</span> <span class='op'><-</span> <span class='fu'>isolate_identifier</span><span class='op'>(</span><span class='va'>example_isolates</span>, cols_ab <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='fu'><a href='antibiotic_class_selectors.html'>carbapenems</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='fu'><a href='antibiotic_class_selectors.html'>aminoglycosides</a></span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</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. 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