<!-- 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>Translation table for Certe — microorganisms.certe • 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" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.3.7/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" /> <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous" /> <!-- clipboard.js --> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script> <!-- sticky kit --> <script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> <script src="../pkgdown.js"></script> <!-- docsearch --> <script src="../docsearch.js"></script> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.css" integrity="sha256-QOSRU/ra9ActyXkIBbiIB144aDBdtvXBcNc3OTNuX/Q=" crossorigin="anonymous" /> <link href="../docsearch.css" rel="stylesheet"> <script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/jquery.mark.min.js" integrity="sha256-4HLtjeVgH0eIB3aZ9mLYF6E8oU5chNdjU6p6rrXpl9U=" crossorigin="anonymous"></script> <link href="../extra.css" rel="stylesheet"> <script src="../extra.js"></script> <meta property="og:title" content="Translation table for Certe — microorganisms.certe" /> <meta property="og:description" content="A data set containing all bacteria codes of Certe MMB. These codes can be joined to data with an ID from microorganisms$mo (using left_join_microorganisms). GLIMS codes can also be translated to valid MOs with guess_mo." /> <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">0.5.0.9009</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/Predict.html"> <span class="fa fa-dice"></span> Predict antimicrobial resistance </a> </li> <li> <a href="../articles/EUCAST.html"> <span class="fa fa-exchange-alt"></span> Apply EUCAST rules </a> </li> <li> <a href="../articles/mo_property.html"> <span class="fa fa-bug"></span> Get properties of a microorganism </a> </li> <li> <a href="../articles/ab_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>Translation table for Certe</h1> <div class="hidden name"><code>microorganisms.certe.Rd</code></div> </div> <div class="ref-description"> <p>A data set containing all bacteria codes of Certe MMB. These codes can be joined to data with an ID from <code><a href='microorganisms.html'>microorganisms</a>$mo</code> (using <code><a href='join.html'>left_join_microorganisms</a></code>). GLIMS codes can also be translated to valid <code>MO</code>s with <code><a href='AMR-deprecated.html'>guess_mo</a></code>.</p> </div> <pre class="usage"><span class='no'>microorganisms.certe</span></pre> <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> <p>A <code><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></code> with 2,665 observations and 2 variables:</p><dl class='dl-horizontal'> <dt><code>certe</code></dt><dd><p>Code of microorganism according to Certe MMB</p></dd> <dt><code>mo</code></dt><dd><p>Code of microorganism in <code><a href='microorganisms.html'>microorganisms</a></code></p></dd> </dl> <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><img src='figures/logo.png' height=40px style=margin-bottom:5px /> <br /> 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 omprehensive tutorial</a> about how to conduct AMR analysis and find <a href='https://msberends.gitlab.io/AMR/reference'>the complete documentation of all functions</a>, which reads a lot easier than in R.</p> <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> <div class='dont-index'><p><code><a href='as.mo.html'>as.mo</a></code> <code><a href='microorganisms.html'>microorganisms</a></code></p></div> </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="#format">Format</a></li> <li><a href="#read-more-on-our-website-">Read more on our website!</a></li> <li><a href="#see-also">See also</a></li> </ul> </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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