<!-- 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>Key antibiotics for first <em>weighted</em> isolates — key_antibiotics • 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="Key antibiotics for first <em>weighted</em> isolates — key_antibiotics" /> <meta property="og:description" content="These function can be used to determine first isolates (see first_isolate). Using key antibiotics to determine first isolates is more reliable than without key antibiotics. These selected isolates will then be called first weighted isolates." /> <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">0.6.0</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/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>Key antibiotics for first <em>weighted</em> isolates</h1> <div class="hidden name"><code>key_antibiotics.Rd</code></div> </div> <div class="ref-description"> <p>These function can be used to determine first isolates (see <code><a href='first_isolate.html'>first_isolate</a></code>). Using key antibiotics to determine first isolates is more reliable than without key antibiotics. These selected isolates will then be called first <em>weighted</em> isolates.</p> </div> <pre class="usage"><span class='fu'>key_antibiotics</span>(<span class='no'>tbl</span>, <span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>universal_1</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>tbl</span>, <span class='st'>"amox"</span>), <span class='kw'>universal_2</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>tbl</span>, <span class='st'>"amcl"</span>), <span class='kw'>universal_3</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>tbl</span>, <span class='st'>"cfur"</span>), <span class='kw'>universal_4</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>tbl</span>, <span class='st'>"pita"</span>), <span class='kw'>universal_5</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>tbl</span>, <span class='st'>"cipr"</span>), <span class='kw'>universal_6</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>tbl</span>, <span class='st'>"trsu"</span>), <span class='kw'>GramPos_1</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>tbl</span>, <span class='st'>"vanc"</span>), <span class='kw'>GramPos_2</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>tbl</span>, <span class='st'>"teic"</span>), <span class='kw'>GramPos_3</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>tbl</span>, <span class='st'>"tetr"</span>), <span class='kw'>GramPos_4</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>tbl</span>, <span class='st'>"eryt"</span>), <span class='kw'>GramPos_5</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>tbl</span>, <span class='st'>"oxac"</span>), <span class='kw'>GramPos_6</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>tbl</span>, <span class='st'>"rifa"</span>), <span class='kw'>GramNeg_1</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>tbl</span>, <span class='st'>"gent"</span>), <span class='kw'>GramNeg_2</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>tbl</span>, <span class='st'>"tobr"</span>), <span class='kw'>GramNeg_3</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>tbl</span>, <span class='st'>"coli"</span>), <span class='kw'>GramNeg_4</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>tbl</span>, <span class='st'>"cfot"</span>), <span class='kw'>GramNeg_5</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>tbl</span>, <span class='st'>"cfta"</span>), <span class='kw'>GramNeg_6</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>tbl</span>, <span class='st'>"mero"</span>), <span class='kw'>warnings</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>) <span class='fu'>key_antibiotics_equal</span>(<span class='no'>x</span>, <span class='no'>y</span>, <span class='kw'>type</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"keyantibiotics"</span>, <span class='st'>"points"</span>), <span class='kw'>ignore_I</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>points_threshold</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>info</span> <span class='kw'>=</span> <span class='fl'>FALSE</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 antibiotics coloms, like <code>amox</code> and <code>amcl</code>.</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>universal_1, universal_2, universal_3, universal_4, universal_5, universal_6</th> <td><p>column names of <strong>broad-spectrum</strong> antibiotics, case-insensitive. At default, the columns containing these antibiotics will be guessed with <code><a href='guess_ab_col.html'>guess_ab_col</a></code>.</p></td> </tr> <tr> <th>GramPos_1, GramPos_2, GramPos_3, GramPos_4, GramPos_5, GramPos_6</th> <td><p>column names of antibiotics for <strong>Gram positives</strong>, case-insensitive. At default, the columns containing these antibiotics will be guessed with <code><a href='guess_ab_col.html'>guess_ab_col</a></code>.</p></td> </tr> <tr> <th>GramNeg_1, GramNeg_2, GramNeg_3, GramNeg_4, GramNeg_5, GramNeg_6</th> <td><p>column names of antibiotics for <strong>Gram negatives</strong>, case-insensitive. At default, the columns containing these antibiotics will be guessed with <code><a href='guess_ab_col.html'>guess_ab_col</a></code>.</p></td> </tr> <tr> <th>warnings</th> <td><p>give warning about missing antibiotic columns, they will anyway be ignored</p></td> </tr> <tr> <th>...</th> <td><p>other parameters passed on to function</p></td> </tr> <tr> <th>x, y</th> <td><p>characters to compare</p></td> </tr> <tr> <th>type</th> <td><p>type to determine weighed isolates; can be <code>"keyantibiotics"</code> or <code>"points"</code>, see Details</p></td> </tr> <tr> <th>ignore_I</th> <td><p>logical to determine whether antibiotic interpretations with <code>"I"</code> will be ignored when <code>type = "keyantibiotics"</code>, see Details</p></td> </tr> <tr> <th>points_threshold</th> <td><p>points until the comparison of key antibiotics will lead to inclusion of an isolate when <code>type = "points"</code>, see Details</p></td> </tr> <tr> <th>info</th> <td><p>print progress</p></td> </tr> </table> <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> <p>The function <code>key_antibiotics</code> returns a character vector with 12 antibiotic results for every isolate. These isolates can then be compared using <code>key_antibiotics_equal</code>, to check if two isolates have generally the same antibiogram. Missing and invalid values are replaced with a dot (<code>"."</code>). The <code><a href='first_isolate.html'>first_isolate</a></code> function only uses this function on the same microbial species from the same patient. Using this, an MRSA will be included after a susceptible <em>S. aureus</em> (MSSA) found within the same episode (see <code>episode</code> parameter of <code><a href='first_isolate.html'>first_isolate</a></code>). Without key antibiotic comparison it would not.</p> <p>At default, the antibiotics that are used for <strong>Gram positive bacteria</strong> are (colum names): <br /> <code>"amox"</code>, <code>"amcl"</code>, <code>"cfur"</code>, <code>"pita"</code>, <code>"cipr"</code>, <code>"trsu"</code> (until here is universal), <code>"vanc"</code>, <code>"teic"</code>, <code>"tetr"</code>, <code>"eryt"</code>, <code>"oxac"</code>, <code>"rifa"</code>.</p> <p>At default, the antibiotics that are used for <strong>Gram negative bacteria</strong> are (colum names): <br /> <code>"amox"</code>, <code>"amcl"</code>, <code>"cfur"</code>, <code>"pita"</code>, <code>"cipr"</code>, <code>"trsu"</code> (until here is universal), <code>"gent"</code>, <code>"tobr"</code>, <code>"coli"</code>, <code>"cfot"</code>, <code>"cfta"</code>, <code>"mero"</code>.</p> <p>The function <code>key_antibiotics_equal</code> checks the characters returned by <code>key_antibiotics</code> for equality, and returns a logical vector.</p> <h2 class="hasAnchor" id="key-antibiotics"><a class="anchor" href="#key-antibiotics"></a>Key antibiotics</h2> <p>There are two ways to determine whether isolates can be included as first <em>weighted</em> isolates which will give generally the same results: <br /></p> <p><strong>1. Using</strong> <code>type = "keyantibiotics"</code> <strong>and parameter</strong> <code>ignore_I</code> <br /> Any difference from S to R (or vice versa) will (re)select an isolate as a first weighted isolate. With <code>ignore_I = FALSE</code>, also differences from I to S|R (or vice versa) will lead to this. This is a reliable method and 30-35 times faster than method 2. <br /></p> <p><strong>2. Using</strong> <code>type = "points"</code> <strong>and parameter</strong> <code>points_threshold</code> <br /> A difference from I to S|R (or vice versa) means 0.5 points, a difference from S to R (or vice versa) means 1 point. When the sum of points exceeds <code>points_threshold</code>, an isolate will be (re)selected as a first weighted isolate.</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="see-also"><a class="anchor" href="#see-also"></a>See also</h2> <div class='dont-index'><p><code><a href='first_isolate.html'>first_isolate</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='co'># septic_patients is a dataset available in the AMR package</span> ?<span class='no'>septic_patients</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>) <span class='co'># set key antibiotics to a new variable</span> <span class='no'>my_patients</span> <span class='kw'><-</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'>keyab</span> <span class='kw'>=</span> <span class='fu'>key_antibiotics</span>(<span class='no'>.</span>)) <span class='kw'>%>%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>( <span class='co'># now calculate first isolates</span> <span class='kw'>first_regular</span> <span class='kw'>=</span> <span class='fu'><a href='first_isolate.html'>first_isolate</a></span>(<span class='no'>.</span>, <span class='kw'>col_keyantibiotics</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>), <span class='co'># and first WEIGHTED isolates</span> <span class='kw'>first_weighted</span> <span class='kw'>=</span> <span class='fu'><a href='first_isolate.html'>first_isolate</a></span>(<span class='no'>.</span>, <span class='kw'>col_keyantibiotics</span> <span class='kw'>=</span> <span class='st'>"keyab"</span>) ) <span class='co'># Check the difference, in this data set it results in 7% more isolates:</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/sum'>sum</a></span>(<span class='no'>my_patients</span>$<span class='no'>first_regular</span>, <span class='kw'>na.rm</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/sum'>sum</a></span>(<span class='no'>my_patients</span>$<span class='no'>first_weighted</span>, <span class='kw'>na.rm</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='co'># output of the `key_antibiotics` function could be like this:</span> <span class='no'>strainA</span> <span class='kw'><-</span> <span class='st'>"SSSRR.S.R..S"</span> <span class='no'>strainB</span> <span class='kw'><-</span> <span class='st'>"SSSIRSSSRSSS"</span> <span class='fu'>key_antibiotics_equal</span>(<span class='no'>strainA</span>, <span class='no'>strainB</span>) <span class='co'># TRUE, because I is ignored (as well as missing values)</span> <span class='fu'>key_antibiotics_equal</span>(<span class='no'>strainA</span>, <span class='no'>strainB</span>, <span class='kw'>ignore_I</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>) <span class='co'># FALSE, because I is not ignored and so the 4th value differs</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="#details">Details</a></li> <li><a href="#key-antibiotics">Key antibiotics</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> <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. 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