mirror of https://github.com/msberends/AMR.git
414 lines
43 KiB
HTML
414 lines
43 KiB
HTML
<!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 count resistant/susceptible microbial isolates. All functions support quasiquotation with pipes, can be used in summarise() from the dplyr package and also support grouped variables, see Examples.
|
||
count_resistant() should be used to count resistant isolates, count_susceptible() should be used to count susceptible isolates."><title>Count Available 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"><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-0.4.9/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.9/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/2.0.11/clipboard.min.js" integrity="sha512-7O5pXpc0oCRrxk8RUfDYFgn0nO1t+jLuIOQdOMRp4APB7uZ4vSjspzp5y6YDtDs4VzUSTbWzBFZ/LKJhnyFOKw==" crossorigin="anonymous" referrerpolicy="no-referrer"></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="Count Available 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 summarise() from the dplyr package and also support grouped variables, see Examples.
|
||
count_resistant() should be used to count resistant isolates, count_susceptible() should be used to count susceptible isolates."><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" data-bs-theme="dark"><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="">2.1.1.9022</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 & dplyr/tidyverse
|
||
</a>
|
||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||
<span class="fa fa-layer-group"></span>
|
||
|
||
AMR & data.table
|
||
</a>
|
||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||
<span class="fa fa-layer-group"></span>
|
||
|
||
AMR & tidymodels
|
||
</a>
|
||
<a class="dropdown-item" href="../articles/other_pkg.html">
|
||
<span class="fa fa-layer-group"></span>
|
||
|
||
AMR & 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>Count Available Isolates</h1>
|
||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/count.R" class="external-link"><code>R/count.R</code></a></small>
|
||
<div class="d-none name"><code>count.Rd</code></div>
|
||
</div>
|
||
|
||
<div class="ref-description section level2">
|
||
<p>These functions can be used to count resistant/susceptible microbial isolates. All functions support quasiquotation with pipes, can be used in <code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code> from the <code>dplyr</code> package and also support grouped variables, see <em>Examples</em>.</p>
|
||
<p><code>count_resistant()</code> should be used to count resistant isolates, <code>count_susceptible()</code> should be used to count susceptible isolates.</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">count_resistant</span><span class="op">(</span><span class="va">...</span>, only_all_tested <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
|
||
<span></span>
|
||
<span><span class="fu">count_susceptible</span><span class="op">(</span><span class="va">...</span>, only_all_tested <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
|
||
<span></span>
|
||
<span><span class="fu">count_R</span><span class="op">(</span><span class="va">...</span>, only_all_tested <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
|
||
<span></span>
|
||
<span><span class="fu">count_IR</span><span class="op">(</span><span class="va">...</span>, only_all_tested <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
|
||
<span></span>
|
||
<span><span class="fu">count_I</span><span class="op">(</span><span class="va">...</span>, only_all_tested <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
|
||
<span></span>
|
||
<span><span class="fu">count_SI</span><span class="op">(</span><span class="va">...</span>, only_all_tested <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
|
||
<span></span>
|
||
<span><span class="fu">count_S</span><span class="op">(</span><span class="va">...</span>, only_all_tested <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
|
||
<span></span>
|
||
<span><span class="fu">count_all</span><span class="op">(</span><span class="va">...</span>, only_all_tested <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
|
||
<span></span>
|
||
<span><span class="fu">n_sir</span><span class="op">(</span><span class="va">...</span>, only_all_tested <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
|
||
<span></span>
|
||
<span><span class="fu">count_df</span><span class="op">(</span></span>
|
||
<span> <span class="va">data</span>,</span>
|
||
<span> translate_ab <span class="op">=</span> <span class="st">"name"</span>,</span>
|
||
<span> language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
|
||
<span> combine_SI <span class="op">=</span> <span class="cn">TRUE</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>...</dt>
|
||
<dd><p>one or more vectors (or columns) with antibiotic interpretations. They will be transformed internally with <code><a href="as.sir.html">as.sir()</a></code> if needed.</p></dd>
|
||
|
||
|
||
<dt>only_all_tested</dt>
|
||
<dd><p>(for combination therapies, i.e. using more than one variable for <code>...</code>): a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate that isolates must be tested for all antibiotics, see section <em>Combination Therapy</em> below</p></dd>
|
||
|
||
|
||
<dt>data</dt>
|
||
<dd><p>a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> containing columns with class <code><a href="as.sir.html">sir</a></code> (see <code><a href="as.sir.html">as.sir()</a></code>)</p></dd>
|
||
|
||
|
||
<dt>translate_ab</dt>
|
||
<dd><p>a column name of the <a href="antibiotics.html">antibiotics</a> data set to translate the antibiotic abbreviations to, using <code><a href="ab_property.html">ab_property()</a></code></p></dd>
|
||
|
||
|
||
<dt>language</dt>
|
||
<dd><p>language of the returned text - the default is the current system language (see <code><a href="translate.html">get_AMR_locale()</a></code>) and can also be set with the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_locale</a></code>. Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></dd>
|
||
|
||
|
||
<dt>combine_SI</dt>
|
||
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether all values of S and I must be merged into one, so the output only consists of S+I vs. R (susceptible vs. resistant) - the default is <code>TRUE</code></p></dd>
|
||
|
||
</dl></div>
|
||
<div class="section level2">
|
||
<h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
|
||
|
||
|
||
<p>An <a href="https://rdrr.io/r/base/integer.html" class="external-link">integer</a></p>
|
||
|
||
|
||
</div>
|
||
<div class="section level2">
|
||
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
|
||
<p>These functions are meant to count isolates. Use the <code><a href="proportion.html">resistance()</a></code>/<code><a href="proportion.html">susceptibility()</a></code> functions to calculate microbial resistance/susceptibility.</p>
|
||
<p>The function <code>count_resistant()</code> is equal to the function <code>count_R()</code>. The function <code>count_susceptible()</code> is equal to the function <code>count_SI()</code>.</p>
|
||
<p>The function <code>n_sir()</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" class="external-link">n_distinct()</a></code>. Their function is equal to <code>count_susceptible(...) + count_resistant(...)</code>.</p>
|
||
<p>The function <code>count_df()</code> takes any variable from <code>data</code> that has an <code><a href="as.sir.html">sir</a></code> class (created with <code><a href="as.sir.html">as.sir()</a></code>) and counts the number of S's, I's and R's. It also supports grouped variables. The function <code><a href="proportion.html">sir_df()</a></code> works exactly like <code>count_df()</code>, but adds the percentage of S, I and R.</p>
|
||
</div>
|
||
<div class="section level2">
|
||
<h2 id="interpretation-of-sir">Interpretation of SIR<a class="anchor" aria-label="anchor" href="#interpretation-of-sir"></a></h2>
|
||
|
||
|
||
<p>In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R as shown below (<a href="https://www.eucast.org/newsiandr" class="external-link">https://www.eucast.org/newsiandr</a>):</p><ul><li><p><strong>S - Susceptible, standard dosing regimen</strong><br>
|
||
A microorganism is categorised as "Susceptible, standard dosing regimen", when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent.</p></li>
|
||
<li><p><strong>I - Susceptible, increased exposure</strong> <em><br>
|
||
A microorganism is categorised as "Susceptible, Increased exposure</em>" when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection.</p></li>
|
||
<li><p><strong>R = Resistant</strong><br>
|
||
A microorganism is categorised as "Resistant" when there is a high likelihood of therapeutic failure even when there is increased exposure.</p><ul><li><p><em>Exposure</em> is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection.</p></li>
|
||
</ul></li>
|
||
</ul><p>This AMR package honours this insight. Use <code><a href="proportion.html">susceptibility()</a></code> (equal to <code><a href="proportion.html">proportion_SI()</a></code>) to determine antimicrobial susceptibility and <code>count_susceptible()</code> (equal to <code>count_SI()</code>) to count susceptible isolates.</p>
|
||
</div>
|
||
<div class="section level2">
|
||
<h2 id="combination-therapy">Combination Therapy<a class="anchor" aria-label="anchor" href="#combination-therapy"></a></h2>
|
||
|
||
|
||
<p>When using more than one variable for <code>...</code> (= combination therapy), use <code>only_all_tested</code> to only count isolates that are tested for all antibiotics/variables that you test them for. See this example for two antibiotics, Drug A and Drug B, about how <code><a href="proportion.html">susceptibility()</a></code> works to calculate the %SI:</p>
|
||
<p></p><div class="sourceCode"><pre><code><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a><span class="sc">--------------------------------------------------------------------</span></span>
|
||
<span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a> only_all_tested <span class="ot">=</span> <span class="cn">FALSE</span> only_all_tested <span class="ot">=</span> <span class="cn">TRUE</span></span>
|
||
<span id="cb1-3"><a href="#cb1-3" tabindex="-1"></a> <span class="sc">-----------------------</span> <span class="sc">-----------------------</span></span>
|
||
<span id="cb1-4"><a href="#cb1-4" tabindex="-1"></a> Drug A Drug B include as include as include as include as</span>
|
||
<span id="cb1-5"><a href="#cb1-5" tabindex="-1"></a> numerator denominator numerator denominator</span>
|
||
<span id="cb1-6"><a href="#cb1-6" tabindex="-1"></a><span class="sc">--------</span> <span class="sc">--------</span> <span class="sc">----------</span> <span class="sc">-----------</span> <span class="sc">----------</span> <span class="sc">-----------</span></span>
|
||
<span id="cb1-7"><a href="#cb1-7" tabindex="-1"></a> S or I S or I X X X X</span>
|
||
<span id="cb1-8"><a href="#cb1-8" tabindex="-1"></a> R S or I X X X X</span>
|
||
<span id="cb1-9"><a href="#cb1-9" tabindex="-1"></a> <span class="sc"><</span><span class="cn">NA</span><span class="sc">></span> S or I X X <span class="sc">-</span> <span class="sc">-</span></span>
|
||
<span id="cb1-10"><a href="#cb1-10" tabindex="-1"></a> S or I R X X X X</span>
|
||
<span id="cb1-11"><a href="#cb1-11" tabindex="-1"></a> R R <span class="sc">-</span> X <span class="sc">-</span> X</span>
|
||
<span id="cb1-12"><a href="#cb1-12" tabindex="-1"></a> <span class="sc"><</span><span class="cn">NA</span><span class="sc">></span> R <span class="sc">-</span> <span class="sc">-</span> <span class="sc">-</span> <span class="sc">-</span></span>
|
||
<span id="cb1-13"><a href="#cb1-13" tabindex="-1"></a> S or I <span class="sc"><</span><span class="cn">NA</span><span class="sc">></span> X X <span class="sc">-</span> <span class="sc">-</span></span>
|
||
<span id="cb1-14"><a href="#cb1-14" tabindex="-1"></a> R <span class="sc"><</span><span class="cn">NA</span><span class="sc">></span> <span class="sc">-</span> <span class="sc">-</span> <span class="sc">-</span> <span class="sc">-</span></span>
|
||
<span id="cb1-15"><a href="#cb1-15" tabindex="-1"></a> <span class="er"><</span><span class="cn">NA</span><span class="sc">></span> <span class="er"><</span><span class="cn">NA</span><span class="sc">></span> <span class="sc">-</span> <span class="sc">-</span> <span class="sc">-</span> <span class="sc">-</span></span>
|
||
<span id="cb1-16"><a href="#cb1-16" tabindex="-1"></a><span class="sc">--------------------------------------------------------------------</span></span></code></pre><p></p></div>
|
||
<p>Please note that, in combination therapies, for <code>only_all_tested = TRUE</code> applies that:</p>
|
||
<p></p><div class="sourceCode"><pre><code><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a> <span class="fu">count_S</span>() <span class="sc">+</span> <span class="fu">count_I</span>() <span class="sc">+</span> <span class="fu">count_R</span>() <span class="ot">=</span> <span class="fu">count_all</span>()</span>
|
||
<span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a> <span class="fu">proportion_S</span>() <span class="sc">+</span> <span class="fu">proportion_I</span>() <span class="sc">+</span> <span class="fu">proportion_R</span>() <span class="ot">=</span> <span class="dv">1</span></span></code></pre><p></p></div>
|
||
<p>and that, in combination therapies, for <code>only_all_tested = FALSE</code> applies that:</p>
|
||
<p></p><div class="sourceCode"><pre><code><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a> <span class="fu">count_S</span>() <span class="sc">+</span> <span class="fu">count_I</span>() <span class="sc">+</span> <span class="fu">count_R</span>() <span class="sc">>=</span> <span class="fu">count_all</span>()</span>
|
||
<span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a> <span class="fu">proportion_S</span>() <span class="sc">+</span> <span class="fu">proportion_I</span>() <span class="sc">+</span> <span class="fu">proportion_R</span>() <span class="sc">>=</span> <span class="dv">1</span></span></code></pre><p></p></div>
|
||
<p>Using <code>only_all_tested</code> has no impact when only using one antibiotic as input.</p>
|
||
</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="proportion.html">proportion_*</a></code> to calculate microbial resistance and susceptibility.</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"># run ?example_isolates for more info.</span></span></span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span><span class="co"># base R ------------------------------------------------------------</span></span></span>
|
||
<span class="r-in"><span><span class="fu">count_resistant</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span> <span class="co"># counts "R"</span></span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] 804</span>
|
||
<span class="r-in"><span><span class="fu">count_susceptible</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span> <span class="co"># counts "S" and "I"</span></span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] 546</span>
|
||
<span class="r-in"><span><span class="fu">count_all</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span> <span class="co"># counts "S", "I" and "R"</span></span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] 1350</span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span><span class="co"># be more specific</span></span></span>
|
||
<span class="r-in"><span><span class="fu">count_S</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span></span></span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> Using count_S() is discouraged; use count_susceptible() instead to also</span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> consider "I" being susceptible. This note will be shown once for this</span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> session.</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] 543</span>
|
||
<span class="r-in"><span><span class="fu">count_SI</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span></span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] 546</span>
|
||
<span class="r-in"><span><span class="fu">count_I</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span></span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] 3</span>
|
||
<span class="r-in"><span><span class="fu">count_IR</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span></span></span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> Using count_IR() is discouraged; use count_resistant() instead to not</span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> consider "I" being resistant. This note will be shown once for this</span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> session.</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] 807</span>
|
||
<span class="r-in"><span><span class="fu">count_R</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span></span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] 804</span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span><span class="co"># Count all available isolates</span></span></span>
|
||
<span class="r-in"><span><span class="fu">count_all</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span></span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] 1350</span>
|
||
<span class="r-in"><span><span class="fu">n_sir</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span></span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] 1350</span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span><span class="co"># n_sir() is an alias of count_all().</span></span></span>
|
||
<span class="r-in"><span><span class="co"># Since it counts all available isolates, you can</span></span></span>
|
||
<span class="r-in"><span><span class="co"># calculate back to count e.g. susceptible isolates.</span></span></span>
|
||
<span class="r-in"><span><span class="co"># These results are the same:</span></span></span>
|
||
<span class="r-in"><span><span class="fu">count_susceptible</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span></span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] 546</span>
|
||
<span class="r-in"><span><span class="fu"><a href="proportion.html">susceptibility</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span> <span class="op">*</span> <span class="fu">n_sir</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span></span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] 546</span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span><span class="co"># dplyr -------------------------------------------------------------</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="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">ward</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise</a></span><span class="op">(</span></span></span>
|
||
<span class="r-in"><span> R <span class="op">=</span> <span class="fu">count_R</span><span class="op">(</span><span class="va">CIP</span><span class="op">)</span>,</span></span>
|
||
<span class="r-in"><span> I <span class="op">=</span> <span class="fu">count_I</span><span class="op">(</span><span class="va">CIP</span><span class="op">)</span>,</span></span>
|
||
<span class="r-in"><span> S <span class="op">=</span> <span class="fu">count_S</span><span class="op">(</span><span class="va">CIP</span><span class="op">)</span>,</span></span>
|
||
<span class="r-in"><span> n1 <span class="op">=</span> <span class="fu">count_all</span><span class="op">(</span><span class="va">CIP</span><span class="op">)</span>, <span class="co"># the actual total; sum of all three</span></span></span>
|
||
<span class="r-in"><span> n2 <span class="op">=</span> <span class="fu">n_sir</span><span class="op">(</span><span class="va">CIP</span><span class="op">)</span>, <span class="co"># same - analogous to n_distinct</span></span></span>
|
||
<span class="r-in"><span> total <span class="op">=</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/context.html" class="external-link">n</a></span><span class="op">(</span><span class="op">)</span></span></span>
|
||
<span class="r-in"><span> <span class="op">)</span> <span class="co"># NOT the number of tested isolates!</span></span></span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span> <span class="co"># Number of available isolates for a whole antibiotic class</span></span></span>
|
||
<span class="r-in"><span> <span class="co"># (i.e., in this data set columns GEN, TOB, AMK, KAN)</span></span></span>
|
||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">ward</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="fu"><a href="antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">n_sir</span><span class="op">)</span><span class="op">)</span></span></span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span> <span class="co"># Count co-resistance between amoxicillin/clav acid and gentamicin,</span></span></span>
|
||
<span class="r-in"><span> <span class="co"># so we can see that combination therapy does a lot more than mono therapy.</span></span></span>
|
||
<span class="r-in"><span> <span class="co"># Please mind that `susceptibility()` calculates percentages right away instead.</span></span></span>
|
||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu">count_susceptible</span><span class="op">(</span><span class="va">AMC</span><span class="op">)</span> <span class="co"># 1433</span></span></span>
|
||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu">count_all</span><span class="op">(</span><span class="va">AMC</span><span class="op">)</span> <span class="co"># 1879</span></span></span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu">count_susceptible</span><span class="op">(</span><span class="va">GEN</span><span class="op">)</span> <span class="co"># 1399</span></span></span>
|
||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu">count_all</span><span class="op">(</span><span class="va">GEN</span><span class="op">)</span> <span class="co"># 1855</span></span></span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu">count_susceptible</span><span class="op">(</span><span class="va">AMC</span>, <span class="va">GEN</span><span class="op">)</span> <span class="co"># 1764</span></span></span>
|
||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu">count_all</span><span class="op">(</span><span class="va">AMC</span>, <span class="va">GEN</span><span class="op">)</span> <span class="co"># 1936</span></span></span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span> <span class="co"># Get number of S+I vs. R immediately of selected columns</span></span></span>
|
||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">AMX</span>, <span class="va">CIP</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||
<span class="r-in"><span> <span class="fu">count_df</span><span class="op">(</span>translate <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span> <span class="co"># It also supports grouping variables</span></span></span>
|
||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">ward</span>, <span class="va">AMX</span>, <span class="va">CIP</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">ward</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||
<span class="r-in"><span> <span class="fu">count_df</span><span class="op">(</span>translate <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span>
|
||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'</span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 12 × 4</span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> ward antibiotic interpretation value</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><ord></span> <span style="color: #949494; font-style: italic;"><int></span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> Clinical AMX SI 357</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> Clinical AMX R 487</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> Clinical CIP SI 741</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> Clinical CIP R 128</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> ICU AMX SI 158</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> ICU AMX R 270</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> ICU CIP SI 362</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> ICU CIP R 85</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> Outpatient AMX SI 31</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> Outpatient AMX R 47</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">11</span> Outpatient CIP SI 78</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">12</span> Outpatient CIP R 15</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><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><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>
|
||
|