P281424
/
AMR
mirror of https://github.com/msberends/AMR.git
1
0
Fork 0
Code Releases Activity
AMR/reference/key_antimicrobials.html

338 lines
26 KiB
HTML
Raw Blame History

<!DOCTYPE html>
<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="These functions can be used to determine first weighted isolates by considering the phenotype for isolate selection (see first_isolate()). Using a phenotype-based method to determine first isolates is more reliable than methods that disregard phenotypes."><title>(Key) Antimicrobials for First Weighted Isolates — key_antimicrobials • 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"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.8/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.8/font.css" rel="stylesheet"><!-- 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"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" 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><!-- 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><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="(Key) Antimicrobials for First Weighted Isolates — key_antimicrobials"><meta property="og:description" content="These functions can be used to determine first weighted isolates by considering the phenotype for isolate selection (see first_isolate()). Using a phenotype-based method to determine first isolates is more reliable than methods that disregard phenotypes."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><meta name="twitter:card" content="summary_large_image"><meta name="twitter:creator" content="@msberends"><meta name="twitter:site" content="@msberends"><!-- 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>
<a href="#main" class="visually-hidden-focusable">Skip to contents</a>
<nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary"><div class="container">
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9015</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
<span class="navbar-toggler-icon"></span>
</button>
<div id="navbar" class="collapse navbar-collapse ms-3">
<ul class="navbar-nav me-auto"><li class="nav-item dropdown">
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--how-to">
<span class="fa fa-question-circle"></span>
How to
</a>
<div class="dropdown-menu" aria-labelledby="dropdown--how-to">
<a class="dropdown-item" href="../articles/AMR.html">
<span class="fa fa-directions"></span>
Conduct AMR Analysis
</a>
<a class="dropdown-item" href="../reference/antibiogram.html">
<span class="fa fa-file-prescription"></span>
Generate Antibiogram (Trad./Syndromic/WISCA)
</a>
<a class="dropdown-item" href="../articles/resistance_predict.html">
<span class="fa fa-dice"></span>
Predict Antimicrobial Resistance
</a>
<a class="dropdown-item" href="../articles/datasets.html">
<span class="fa fa-database"></span>
Download Data Sets for Own Use
</a>
<a class="dropdown-item" href="../reference/AMR-options.html">
<span class="fa fa-gear"></span>
Set User- Or Team-specific Package Settings
</a>
<a class="dropdown-item" href="../articles/PCA.html">
<span class="fa fa-compress"></span>
Conduct Principal Component Analysis for AMR
</a>
<a class="dropdown-item" href="../articles/MDR.html">
<span class="fa fa-skull-crossbones"></span>
Determine Multi-Drug Resistance (MDR)
</a>
<a class="dropdown-item" href="../articles/WHONET.html">
<span class="fa fa-globe-americas"></span>
Work with WHONET Data
</a>
<a class="dropdown-item" href="../articles/EUCAST.html">
<span class="fa fa-exchange-alt"></span>
Apply Eucast Rules
</a>
<a class="dropdown-item" href="../reference/mo_property.html">
<span class="fa fa-bug"></span>
Get Taxonomy of a Microorganism
</a>
<a class="dropdown-item" href="../reference/ab_property.html">
<span class="fa fa-capsules"></span>
Get Properties of an Antibiotic Drug
</a>
<a class="dropdown-item" href="../reference/av_property.html">
<span class="fa fa-capsules"></span>
Get Properties of an Antiviral Drug
</a>
</div>
</li>
<li class="nav-item dropdown">
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown--with-other-pkgs">
<span class="fa fa-layer-group"></span>
With other pkgs
</a>
<div class="dropdown-menu" aria-labelledby="dropdown--with-other-pkgs">
<a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-group"></span>
AMR &amp; dplyr/tidyverse
</a>
<a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-group"></span>
AMR &amp; data.table
</a>
<a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-group"></span>
AMR &amp; tidymodels
</a>
<a class="dropdown-item" href="../articles/other_pkg.html">
<span class="fa fa-layer-group"></span>
AMR &amp; base R
</a>
</div>
</li>
<li class="active nav-item">
<a class="nav-link" href="../reference/index.html">
<span class="fa fa-book-open"></span>
Manual
</a>
</li>
<li class="nav-item">
<a class="nav-link" href="../authors.html">
<span class="fa fa-users"></span>
Authors
</a>
</li>
</ul><form class="form-inline my-2 my-lg-0" role="search">
<input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
<ul class="navbar-nav"><li class="nav-item">
<a class="nav-link" href="../news/index.html">
<span class="far fa far fa-newspaper"></span>
Changelog
</a>
</li>
<li class="nav-item">
<a class="external-link nav-link" href="https://github.com/msberends/AMR">
<span class="fab fa fab fa-github"></span>
Source Code
</a>
</li>
</ul></div>
</div>
</nav><div class="container template-reference-topic">
<div class="row">
<main id="main" class="col-md-9"><div class="page-header">
<img src="../logo.svg" class="logo" alt=""><h1>(Key) Antimicrobials for First Weighted Isolates</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/key_antimicrobials.R" class="external-link"><code>R/key_antimicrobials.R</code></a></small>
<div class="d-none name"><code>key_antimicrobials.Rd</code></div>
</div>
<div class="ref-description section level2">
<p>These functions can be used to determine first weighted isolates by considering the phenotype for isolate selection (see <code><a href="first_isolate.html">first_isolate()</a></code>). Using a phenotype-based method to determine first isolates is more reliable than methods that disregard phenotypes.</p>
</div>
<div class="section level2">
<h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">key_antimicrobials</span><span class="op">(</span></span>
<span> x <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> col_mo <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> universal <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"ampicillin"</span>, <span class="st">"amoxicillin/clavulanic acid"</span>, <span class="st">"cefuroxime"</span>,</span>
<span> <span class="st">"piperacillin/tazobactam"</span>, <span class="st">"ciprofloxacin"</span>, <span class="st">"trimethoprim/sulfamethoxazole"</span><span class="op">)</span>,</span>
<span> gram_negative <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"gentamicin"</span>, <span class="st">"tobramycin"</span>, <span class="st">"colistin"</span>, <span class="st">"cefotaxime"</span>, <span class="st">"ceftazidime"</span>,</span>
<span> <span class="st">"meropenem"</span><span class="op">)</span>,</span>
<span> gram_positive <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"vancomycin"</span>, <span class="st">"teicoplanin"</span>, <span class="st">"tetracycline"</span>, <span class="st">"erythromycin"</span>,</span>
<span> <span class="st">"oxacillin"</span>, <span class="st">"rifampin"</span><span class="op">)</span>,</span>
<span> antifungal <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"anidulafungin"</span>, <span class="st">"caspofungin"</span>, <span class="st">"fluconazole"</span>, <span class="st">"miconazole"</span>, <span class="st">"nystatin"</span>,</span>
<span> <span class="st">"voriconazole"</span><span class="op">)</span>,</span>
<span> only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span> <span class="va">...</span></span>
<span><span class="op">)</span></span>
<span></span>
<span><span class="fu">all_antimicrobials</span><span class="op">(</span>x <span class="op">=</span> <span class="cn">NULL</span>, only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">antimicrobials_equal</span><span class="op">(</span></span>
<span> <span class="va">y</span>,</span>
<span> <span class="va">z</span>,</span>
<span> type <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"points"</span>, <span class="st">"keyantimicrobials"</span><span class="op">)</span>,</span>
<span> ignore_I <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span> points_threshold <span class="op">=</span> <span class="fl">2</span>,</span>
<span> <span class="va">...</span></span>
<span><span class="op">)</span></span></code></pre></div>
</div>
<div class="section level2">
<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
<dl><dt>x</dt>
<dd><p>a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> with antibiotics columns, like <code>AMX</code> or <code>amox</code>. Can be left blank to determine automatically</p></dd>
<dt>col_mo</dt>
<dd><p>column name of the names or codes of the microorganisms (see <code><a href="as.mo.html">as.mo()</a></code>) - the default is 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></dd>
<dt>universal</dt>
<dd><p>names of <strong>broad-spectrum</strong> antimicrobial drugs, case-insensitive. Set to <code>NULL</code> to ignore. See <em>Details</em> for the default antimicrobial drugs</p></dd>
<dt>gram_negative</dt>
<dd><p>names of antibiotic drugs for <strong>Gram-positives</strong>, case-insensitive. Set to <code>NULL</code> to ignore. See <em>Details</em> for the default antibiotic drugs</p></dd>
<dt>gram_positive</dt>
<dd><p>names of antibiotic drugs for <strong>Gram-negatives</strong>, case-insensitive. Set to <code>NULL</code> to ignore. See <em>Details</em> for the default antibiotic drugs</p></dd>
<dt>antifungal</dt>
<dd><p>names of antifungal drugs for <strong>fungi</strong>, case-insensitive. Set to <code>NULL</code> to ignore. See <em>Details</em> for the default antifungal drugs</p></dd>
<dt>only_sir_columns</dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether only columns must be included that were transformed to class <code>sir</code> (see <code><a href="as.sir.html">as.sir()</a></code>) on beforehand (default is <code>FALSE</code>)</p></dd>
<dt>...</dt>
<dd><p>ignored, only in place to allow future extensions</p></dd>
<dt>y, z</dt>
<dd><p><a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> vectors to compare</p></dd>
<dt>type</dt>
<dd><p>type to determine weighed isolates; can be <code>"keyantimicrobials"</code> or <code>"points"</code>, see <em>Details</em></p></dd>
<dt>ignore_I</dt>
<dd><p><a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether antibiotic interpretations with <code>"I"</code> will be ignored when <code>type = "keyantimicrobials"</code>, see <em>Details</em></p></dd>
<dt>points_threshold</dt>
<dd><p>minimum number of points to require before differences in the antibiogram will lead to inclusion of an isolate when <code>type = "points"</code>, see <em>Details</em></p></dd>
</dl></div>
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<p>The <code>key_antimicrobials()</code> and <code>all_antimicrobials()</code> functions are context-aware. This means that the <code>x</code> argument can be left blank if used inside a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> call, see <em>Examples</em>.</p>
<p>The function <code>key_antimicrobials()</code> returns a <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> vector with 12 antimicrobial results for every isolate. The function <code>all_antimicrobials()</code> returns a <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> vector with all antimicrobial drug results for every isolate. These vectors can then be compared using <code>antimicrobials_equal()</code>, to check if two isolates have generally the same antibiogram. Missing and invalid values are replaced with a dot (<code>"."</code>) by <code>key_antimicrobials()</code> and ignored by <code>antimicrobials_equal()</code>.</p>
<p>Please see the <code><a href="first_isolate.html">first_isolate()</a></code> function how these important functions enable the 'phenotype-based' method for determination of first isolates.</p>
<p>The default antimicrobial drugs used for <strong>all rows</strong> (set in <code>universal</code>) are:</p><ul><li><p>Ampicillin</p></li>
<li><p>Amoxicillin/clavulanic acid</p></li>
<li><p>Cefuroxime</p></li>
<li><p>Ciprofloxacin</p></li>
<li><p>Piperacillin/tazobactam</p></li>
<li><p>Trimethoprim/sulfamethoxazole</p></li>
</ul><p>The default antimicrobial drugs used for <strong>Gram-negative bacteria</strong> (set in <code>gram_negative</code>) are:</p><ul><li><p>Cefotaxime</p></li>
<li><p>Ceftazidime</p></li>
<li><p>Colistin</p></li>
<li><p>Gentamicin</p></li>
<li><p>Meropenem</p></li>
<li><p>Tobramycin</p></li>
</ul><p>The default antimicrobial drugs used for <strong>Gram-positive bacteria</strong> (set in <code>gram_positive</code>) are:</p><ul><li><p>Erythromycin</p></li>
<li><p>Oxacillin</p></li>
<li><p>Rifampin</p></li>
<li><p>Teicoplanin</p></li>
<li><p>Tetracycline</p></li>
<li><p>Vancomycin</p></li>
</ul><p>The default antimicrobial drugs used for <strong>fungi</strong> (set in <code>antifungal</code>) are:</p><ul><li><p>Anidulafungin</p></li>
<li><p>Caspofungin</p></li>
<li><p>Fluconazole</p></li>
<li><p>Miconazole</p></li>
<li><p>Nystatin</p></li>
<li><p>Voriconazole</p></li>
</ul></div>
<div class="section level2">
<h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
<div class="dont-index"><p><code><a href="first_isolate.html">first_isolate()</a></code></p></div>
</div>
<div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># `example_isolates` is a data set available in the AMR package.</span></span></span>
<span class="r-in"><span><span class="co"># See ?example_isolates.</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># output of the `key_antimicrobials()` function could be like this:</span></span></span>
<span class="r-in"><span><span class="va">strainA</span> <span class="op">&lt;-</span> <span class="st">"SSSRR.S.R..S"</span></span></span>
<span class="r-in"><span><span class="va">strainB</span> <span class="op">&lt;-</span> <span class="st">"SSSIRSSSRSSS"</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># those strings can be compared with:</span></span></span>
<span class="r-in"><span><span class="fu">antimicrobials_equal</span><span class="op">(</span><span class="va">strainA</span>, <span class="va">strainB</span>, type <span class="op">=</span> <span class="st">"keyantimicrobials"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE</span>
<span class="r-in"><span><span class="co"># TRUE, because I is ignored (as well as missing values)</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">antimicrobials_equal</span><span class="op">(</span><span class="va">strainA</span>, <span class="va">strainB</span>, type <span class="op">=</span> <span class="st">"keyantimicrobials"</span>, ignore_I <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] FALSE</span>
<span class="r-in"><span><span class="co"># FALSE, because I is not ignored and so the 4th [character] differs</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="co"># set key antibiotics to a new variable</span></span></span>
<span class="r-in"><span> <span class="va">my_patients</span> <span class="op">&lt;-</span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>keyab <span class="op">=</span> <span class="fu">key_antimicrobials</span><span class="op">(</span>antifungal <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="co"># no need to define `x`</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span></span></span>
<span class="r-in"><span> <span class="co"># now calculate first isolates</span></span></span>
<span class="r-in"><span> first_regular <span class="op">=</span> <span class="fu"><a href="first_isolate.html">first_isolate</a></span><span class="op">(</span>col_keyantimicrobials <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> <span class="co"># and first WEIGHTED isolates</span></span></span>
<span class="r-in"><span> first_weighted <span class="op">=</span> <span class="fu"><a href="first_isolate.html">first_isolate</a></span><span class="op">(</span>col_keyantimicrobials <span class="op">=</span> <span class="st">"keyab"</span><span class="op">)</span></span></span>
<span class="r-in"><span> <span class="op">)</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span> <span class="co"># Check the difference in this data set, 'weighted' results in more isolates:</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="va">my_patients</span><span class="op">$</span><span class="va">first_regular</span>, na.rm <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="va">my_patients</span><span class="op">$</span><span class="va">first_weighted</span>, na.rm <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1376</span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>
</div>
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
</nav></aside></div>
<footer><div class="pkgdown-footer-left">
<p></p><p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p>
</div>
<div class="pkgdown-footer-right">
<p></p><p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_rug.svg" style="max-width: 150px;"></a><a target="_blank" href="https://www.umcg.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_umcg.svg" style="max-width: 150px;"></a></p>
</div>
</footer></div>
</body></html>
View Git Blame Copy Permalink