<!-- 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>Class 'rsi' — as.rsi • 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="Class 'rsi' — as.rsi" /> <meta property="og:description" content="This transforms a vector to a new class rsi, which is an ordered factor with levels S &lt; I &lt; R. Invalid antimicrobial interpretations will be translated as NA with a warning." /> <meta property="og:image" content="https://msberends.gitlab.io/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">0.5.0.9008</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> <a href="../articles/AMR.html"> <span class="fa fa-directions"></span> Get Started </a> </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> <li> <a href="https://gitlab.com/msberends/AMR"> <span class="fab fa fab fa-gitlab"></span> Source Code </a> </li> </ul> <ul class="nav navbar-nav navbar-right"> <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>Class 'rsi'</h1> <div class="hidden name"><code>as.rsi.Rd</code></div> </div> <div class="ref-description"> <p>This transforms a vector to a new class <code>rsi</code>, which is an ordered factor with levels <code>S < I < R</code>. Invalid antimicrobial interpretations will be translated as <code>NA</code> with a warning.</p> </div> <pre class="usage"><span class='fu'>as.rsi</span>(<span class='no'>x</span>) <span class='fu'>is.rsi</span>(<span class='no'>x</span>) <span class='fu'>is.rsi.eligible</span>(<span class='no'>x</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>vector</p></td> </tr> </table> <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> <p>Ordered factor with new class <code>rsi</code></p> <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> <p>The function <code>is.rsi.eligible</code> returns <code>TRUE</code> when a columns contains only valid antimicrobial interpretations (S and/or I and/or R), and <code>FALSE</code> otherwise.</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.mic.html'>as.mic</a></code></p></div> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><span class='co'># NOT RUN {</span> <span class='no'>rsi_data</span> <span class='kw'><-</span> <span class='fu'>as.rsi</span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/rep'>rep</a></span>(<span class='st'>"S"</span>, <span class='fl'>474</span>), <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/rep'>rep</a></span>(<span class='st'>"I"</span>, <span class='fl'>36</span>), <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/rep'>rep</a></span>(<span class='st'>"R"</span>, <span class='fl'>370</span>))) <span class='no'>rsi_data</span> <span class='kw'><-</span> <span class='fu'>as.rsi</span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/rep'>rep</a></span>(<span class='st'>"S"</span>, <span class='fl'>474</span>), <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/rep'>rep</a></span>(<span class='st'>"I"</span>, <span class='fl'>36</span>), <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/rep'>rep</a></span>(<span class='st'>"R"</span>, <span class='fl'>370</span>), <span class='st'>"A"</span>, <span class='st'>"B"</span>, <span class='st'>"C"</span>)) <span class='fu'>is.rsi</span>(<span class='no'>rsi_data</span>) <span class='co'># this can also coerce combined MIC/RSI values:</span> <span class='fu'>as.rsi</span>(<span class='st'>"<= 0.002; S"</span>) <span class='co'># will return S</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>rsi_data</span>) <span class='co'># for percentages</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/barplot'>barplot</a></span>(<span class='no'>rsi_data</span>) <span class='co'># for frequencies</span> <span class='fu'><a href='freq.html'>freq</a></span>(<span class='no'>rsi_data</span>) <span class='co'># frequency table with informative header</span> <span class='co'># using dplyr's mutate</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='http://dplyr.tidyverse.org/reference/summarise_all.html'>mutate_at</a></span>(<span class='fu'><a href='http://dplyr.tidyverse.org/reference/vars.html'>vars</a></span>(<span class='no'>peni</span>:<span class='no'>rifa</span>), <span class='no'>as.rsi</span>) <span class='co'># fastest way to transform all columns with already valid AB results to class `rsi`:</span> <span class='no'>septic_patients</span> <span class='kw'>%>%</span> <span class='fu'><a href='http://dplyr.tidyverse.org/reference/summarise_all.html'>mutate_if</a></span>(<span class='no'>is.rsi.eligible</span>, <span class='no'>as.rsi</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="#see-also">See also</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>