mirror of https://github.com/msberends/AMR.git
255 lines
19 KiB
HTML
255 lines
19 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 for generating random MIC values and disk diffusion diameters, for AMR data analysis practice. By providing a microorganism and antimicrobial drug, the generated results will reflect reality as much as possible."><title>Random MIC Values/Disk Zones/SIR Generation — random • 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-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><link href="../deps/Fira_Code-0.4.5/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="Random MIC Values/Disk Zones/SIR Generation — random"><meta property="og:description" content="These functions can be used for generating random MIC values and disk diffusion diameters, for AMR data analysis practice. By providing a microorganism and antimicrobial drug, the generated results will reflect reality as much as possible."><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="">2.0.0.9004</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">
|
|
<a class="nav-link" href="../index.html">
|
|
<span class="fa fa-home"></span>
|
|
|
|
Home
|
|
</a>
|
|
</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--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/SPSS.html">
|
|
<span class="fa fa-file-upload"></span>
|
|
|
|
Import Data From SPSS/SAS/Stata
|
|
</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="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>
|
|
<li class="nav-item">
|
|
<a class="nav-link" href="../news/index.html">
|
|
<span class="far fa far fa-newspaper"></span>
|
|
|
|
Changelog
|
|
</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="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>Random MIC Values/Disk Zones/SIR Generation</h1>
|
|
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/random.R" class="external-link"><code>R/random.R</code></a></small>
|
|
<div class="d-none name"><code>random.Rd</code></div>
|
|
</div>
|
|
|
|
<div class="ref-description section level2">
|
|
<p>These functions can be used for generating random MIC values and disk diffusion diameters, for AMR data analysis practice. By providing a microorganism and antimicrobial drug, the generated results will reflect reality as much as possible.</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">random_mic</span><span class="op">(</span>size <span class="op">=</span> <span class="cn">NULL</span>, mo <span class="op">=</span> <span class="cn">NULL</span>, ab <span class="op">=</span> <span class="cn">NULL</span>, <span class="va">...</span><span class="op">)</span></span>
|
|
<span></span>
|
|
<span><span class="fu">random_disk</span><span class="op">(</span>size <span class="op">=</span> <span class="cn">NULL</span>, mo <span class="op">=</span> <span class="cn">NULL</span>, ab <span class="op">=</span> <span class="cn">NULL</span>, <span class="va">...</span><span class="op">)</span></span>
|
|
<span></span>
|
|
<span><span class="fu">random_sir</span><span class="op">(</span>size <span class="op">=</span> <span class="cn">NULL</span>, prob_SIR <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="fl">0.33</span>, <span class="fl">0.33</span>, <span class="fl">0.33</span><span class="op">)</span>, <span class="va">...</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>size</dt>
|
|
<dd><p>desired size of the returned vector. If used in a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> call or <code>dplyr</code> verb, will get the current (group) size if left blank.</p></dd>
|
|
|
|
|
|
<dt>mo</dt>
|
|
<dd><p>any <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> that can be coerced to a valid microorganism code with <code><a href="as.mo.html">as.mo()</a></code></p></dd>
|
|
|
|
|
|
<dt>ab</dt>
|
|
<dd><p>any <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> that can be coerced to a valid antimicrobial drug code with <code><a href="as.ab.html">as.ab()</a></code></p></dd>
|
|
|
|
|
|
<dt>...</dt>
|
|
<dd><p>ignored, only in place to allow future extensions</p></dd>
|
|
|
|
|
|
<dt>prob_SIR</dt>
|
|
<dd><p>a vector of length 3: the probabilities for "S" (1st value), "I" (2nd value) and "R" (3rd value)</p></dd>
|
|
|
|
</dl></div>
|
|
<div class="section level2">
|
|
<h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
|
|
|
|
|
|
<p>class <code>mic</code> for <code>random_mic()</code> (see <code><a href="as.mic.html">as.mic()</a></code>) and class <code>disk</code> for <code>random_disk()</code> (see <code><a href="as.disk.html">as.disk()</a></code>)</p>
|
|
</div>
|
|
<div class="section level2">
|
|
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
|
|
<p>The base <span style="R">R</span> function <code><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample()</a></code> is used for generating values.</p>
|
|
<p>Generated values are based on the EUCAST 2022 guideline as implemented in the <a href="clinical_breakpoints.html">clinical_breakpoints</a> data set. To create specific generated values per bug or drug, set the <code>mo</code> and/or <code>ab</code> argument.</p>
|
|
</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="fu">random_mic</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
|
|
<span class="r-out co"><span class="r-pr">#></span> Class 'mic'</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [1] 1 <=0.001 <=0.001 8 32 <=0.001 128 0.01 0.002 </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [10] 0.01 256 <=0.001 0.5 1 4 256 0.25 64 </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [19] 1 0.01 1 0.5 0.0625 2 0.005 </span>
|
|
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
|
|
<span class="r-out co"><span class="r-pr">#></span> Class 'disk'</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [1] 44 35 30 50 38 41 6 45 36 25 28 45 43 9 15 22 46 12 45 22 37 25 12 50 43</span>
|
|
<span class="r-in"><span><span class="fu">random_sir</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
|
|
<span class="r-out co"><span class="r-pr">#></span> Class 'sir'</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [1] S I R S S R R R R R S S S R S I R S I S S R S I I</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="co"># make the random generation more realistic by setting a bug and/or drug:</span></span></span>
|
|
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 0.0625-64</span></span></span>
|
|
<span class="r-out co"><span class="r-pr">#></span> Class 'mic'</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [1] 32 64 0.025 >=128 0.25 1 16 8 4 8 </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [11] 4 0.0625 0.25 2 0.01 8 32 >=128 1 0.002 </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [21] 16 0.025 0.002 0.01 0.0625</span>
|
|
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-16</span></span></span>
|
|
<span class="r-out co"><span class="r-pr">#></span> Class 'mic'</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [1] 32 16 2 32 4 8 4 0.5 0.5 4 1 0.5 0.5 16 4 16 2 1 0.5</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [20] 2 0.5 0.5 1 1 16 </span>
|
|
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-4</span></span></span>
|
|
<span class="r-out co"><span class="r-pr">#></span> Class 'mic'</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [1] 16 0.5 16 1 2 1 1 4 0.0625 0.025 </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [11] 16 0.0625 0.25 4 0.5 16 0.25 0.5 0.125 16 </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [21] 0.025 1 0.5 0.125 0.025 </span>
|
|
<span class="r-in"><span></span></span>
|
|
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 8-50</span></span></span>
|
|
<span class="r-out co"><span class="r-pr">#></span> Class 'disk'</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [1] 34 48 26 44 41 18 40 49 46 32 49 30 14 40 18 9 42 17 47 42 18 43 20 33 48</span>
|
|
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 11-17</span></span></span>
|
|
<span class="r-out co"><span class="r-pr">#></span> Class 'disk'</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [1] 13 17 13 14 15 14 11 14 12 16 17 17 15 11 16 13 15 11 14 15 13 17 14 17 17</span>
|
|
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 12-27</span></span></span>
|
|
<span class="r-out co"><span class="r-pr">#></span> Class 'disk'</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [1] 26 24 15 17 22 20 26 19 18 22 24 20 16 16 27 16 19 27 25 18 16 26 17 26 19</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>
|
|
|