P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2024-12-26 08:46:11 +01:00
Code Releases Activity
9e20ade0a7
AMR/docs/reference/count.html

426 lines
21 KiB
HTML
Raw Blame History

<!-- 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>Count isolates — count • 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="Count isolates — count" />
<meta property="og:description" content="These functions can be used to count resistant/susceptible microbial isolates. All functions support quasiquotation with pipes, can be used in dplyrs summarise and support grouped variables, see Examples.
count_R and count_IR can be used to count resistant isolates, count_S and count_SI can be used to count susceptible 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">0.6.1.9002</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>Count isolates</h1>
<div class="hidden name"><code>count.Rd</code></div>
</div>
<div class="ref-description">
<p>These functions can be used to count resistant/susceptible microbial isolates. All functions support quasiquotation with pipes, can be used in <code>dplyr</code>s <code><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></code> and support grouped variables, see <em>Examples</em>.</p>
<p><code>count_R</code> and <code>count_IR</code> can be used to count resistant isolates, <code>count_S</code> and <code>count_SI</code> can be used to count susceptible isolates.<br /></p>
</div>
<pre class="usage"><span class='fu'>count_R</span>(<span class='no'>...</span>, <span class='kw'>also_single_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='fu'>count_IR</span>(<span class='no'>...</span>, <span class='kw'>also_single_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='fu'>count_I</span>(<span class='no'>...</span>, <span class='kw'>also_single_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='fu'>count_SI</span>(<span class='no'>...</span>, <span class='kw'>also_single_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='fu'>count_S</span>(<span class='no'>...</span>, <span class='kw'>also_single_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='fu'>count_all</span>(<span class='no'>...</span>)
<span class='fu'>n_rsi</span>(<span class='no'>...</span>)
<span class='fu'>count_df</span>(<span class='no'>data</span>, <span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/options'>getOption</a></span>(<span class='st'>"get_antibiotic_names"</span>,
<span class='st'>"official"</span>), <span class='kw'>combine_IR</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>...</th>
<td><p>one or more vectors (or columns) with antibiotic interpretations. They will be transformed internally with <code><a href='as.rsi.html'>as.rsi</a></code> if needed.</p></td>
</tr>
<tr>
<th>also_single_tested</th>
<td><p>a logical to indicate whether (in combination therapies) also observations should be included where not all antibiotics were tested, but at least one of the tested antibiotics contains a target interpretation (e.g. S in case of <code>portion_S</code> and R in case of <code>portion_R</code>). <strong>This would lead to selection bias in almost all cases.</strong></p></td>
</tr>
<tr>
<th>data</th>
<td><p>a <code>data.frame</code> containing columns with class <code>rsi</code> (see <code><a href='as.rsi.html'>as.rsi</a></code>)</p></td>
</tr>
<tr>
<th>translate_ab</th>
<td><p>a column name of the <code><a href='antibiotics.html'>antibiotics</a></code> data set to translate the antibiotic abbreviations to, using <code><a href='abname.html'>abname</a></code>. This can be set with <code><a href='https://www.rdocumentation.org/packages/base/topics/options'>getOption</a>("get_antibiotic_names")</code>.</p></td>
</tr>
<tr>
<th>combine_IR</th>
<td><p>a logical to indicate whether all values of I and R must be merged into one, so the output only consists of S vs. IR (susceptible vs. non-susceptible)</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
<p>Wickham H. <strong>Tidy Data.</strong> The Journal of Statistical Software, vol. 59, 2014. <a href='http://vita.had.co.nz/papers/tidy-data.html'>http://vita.had.co.nz/papers/tidy-data.html</a></p>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>Integer</p>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>These functions are meant to count isolates. Use the <code><a href='portion.html'>portion</a>_*</code> functions to calculate microbial resistance.</p>
<p><code>n_rsi</code> is an alias of <code>count_all</code>. They can be used to count all available isolates, i.e. where all input antibiotics have an available result (S, I or R). Their use is equal to <code><a href='https://dplyr.tidyverse.org/reference/n_distinct.html'>n_distinct</a></code>. Their function is equal to <code>count_S(...) + count_IR(...)</code>.</p>
<p><code>count_df</code> takes any variable from <code>data</code> that has an <code>"rsi"</code> class (created with <code><a href='as.rsi.html'>as.rsi</a></code>) and counts the amounts of R, I and S. The resulting <em>tidy data</em> (see Source) <code>data.frame</code> will have three rows (S/I/R) and a column for each variable with class <code>"rsi"</code>.</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='portion.html'>portion</a>_*</code> to calculate microbial resistance and susceptibility.</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 data set available in the AMR package. It is true, genuine data.</span>
?<span class='no'>septic_patients</span>
<span class='co'># Count resistant isolates</span>
<span class='fu'>count_R</span>(<span class='no'>septic_patients</span>$<span class='no'>amox</span>)
<span class='fu'>count_IR</span>(<span class='no'>septic_patients</span>$<span class='no'>amox</span>)
<span class='co'># Or susceptible isolates</span>
<span class='fu'>count_S</span>(<span class='no'>septic_patients</span>$<span class='no'>amox</span>)
<span class='fu'>count_SI</span>(<span class='no'>septic_patients</span>$<span class='no'>amox</span>)
<span class='co'># Count all available isolates</span>
<span class='fu'>count_all</span>(<span class='no'>septic_patients</span>$<span class='no'>amox</span>)
<span class='fu'>n_rsi</span>(<span class='no'>septic_patients</span>$<span class='no'>amox</span>)
<span class='co'># Since n_rsi counts available isolates, you can</span>
<span class='co'># calculate back to count e.g. non-susceptible isolates.</span>
<span class='co'># This results in the same:</span>
<span class='fu'>count_IR</span>(<span class='no'>septic_patients</span>$<span class='no'>amox</span>)
<span class='fu'><a href='portion.html'>portion_IR</a></span>(<span class='no'>septic_patients</span>$<span class='no'>amox</span>) * <span class='fu'>n_rsi</span>(<span class='no'>septic_patients</span>$<span class='no'>amox</span>)
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>R</span> <span class='kw'>=</span> <span class='fu'>count_R</span>(<span class='no'>cipr</span>),
<span class='kw'>I</span> <span class='kw'>=</span> <span class='fu'>count_I</span>(<span class='no'>cipr</span>),
<span class='kw'>S</span> <span class='kw'>=</span> <span class='fu'>count_S</span>(<span class='no'>cipr</span>),
<span class='kw'>n1</span> <span class='kw'>=</span> <span class='fu'>count_all</span>(<span class='no'>cipr</span>), <span class='co'># the actual total; sum of all three</span>
<span class='kw'>n2</span> <span class='kw'>=</span> <span class='fu'>n_rsi</span>(<span class='no'>cipr</span>), <span class='co'># same - analogous to n_distinct</span>
<span class='kw'>total</span> <span class='kw'>=</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/n.html'>n</a></span>()) <span class='co'># NOT the number of tested isolates!</span>
<span class='co'># Count co-resistance between amoxicillin/clav acid and gentamicin,</span>
<span class='co'># so we can see that combination therapy does a lot more than mono therapy.</span>
<span class='co'># Please mind that `portion_S` calculates percentages right away instead.</span>
<span class='fu'>count_S</span>(<span class='no'>septic_patients</span>$<span class='no'>amcl</span>) <span class='co'># S = 1342 (71.4%)</span>
<span class='fu'>count_all</span>(<span class='no'>septic_patients</span>$<span class='no'>amcl</span>) <span class='co'># n = 1879</span>
<span class='fu'>count_S</span>(<span class='no'>septic_patients</span>$<span class='no'>gent</span>) <span class='co'># S = 1372 (74.0%)</span>
<span class='fu'>count_all</span>(<span class='no'>septic_patients</span>$<span class='no'>gent</span>) <span class='co'># n = 1855</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/with'>with</a></span>(<span class='no'>septic_patients</span>,
<span class='fu'>count_S</span>(<span class='no'>amcl</span>, <span class='no'>gent</span>)) <span class='co'># S = 1660 (92.3%)</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/with'>with</a></span>(<span class='no'>septic_patients</span>, <span class='co'># n = 1798</span>
<span class='fu'>n_rsi</span>(<span class='no'>amcl</span>, <span class='no'>gent</span>))
<span class='co'># Get portions S/I/R immediately of all rsi columns</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>amox</span>, <span class='no'>cipr</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>count_df</span>(<span class='kw'>translate</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='co'># It also supports grouping variables</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>hospital_id</span>, <span class='no'>amox</span>, <span class='no'>cipr</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>count_df</span>(<span class='kw'>translate</span> <span class='kw'>=</span> <span class='fl'>FALSE</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="#source">Source</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</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. 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>
View Git Blame Copy Permalink