mirror of
https://github.com/msberends/AMR.git
synced 2024-12-26 06:46:11 +01:00
161 lines
17 KiB
HTML
161 lines
17 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"><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-5.3.1/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"><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></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 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."><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"></head><body>
|
|
<a href="#main" class="visually-hidden-focusable">Skip to contents</a>
|
|
|
|
|
|
<nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><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="">2.1.1.9120</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">
|
|
<button class="nav-link dropdown-toggle" type="button" id="dropdown-how-to" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true"><span class="fa fa-question-circle"></span> How to</button>
|
|
<ul class="dropdown-menu" aria-labelledby="dropdown-how-to"><li><a class="dropdown-item" href="../articles/AMR.html"><span class="fa fa-directions"></span> Conduct AMR Analysis</a></li>
|
|
<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
|
|
<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
|
|
<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
|
|
<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
|
|
<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
|
|
<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>
|
|
<li><a class="dropdown-item" href="../articles/WHONET.html"><span class="fa fa-globe-americas"></span> Work with WHONET Data</a></li>
|
|
<li><a class="dropdown-item" href="../articles/EUCAST.html"><span class="fa fa-exchange-alt"></span> Apply Eucast Rules</a></li>
|
|
<li><a class="dropdown-item" href="../reference/mo_property.html"><span class="fa fa-bug"></span> Get Taxonomy of a Microorganism</a></li>
|
|
<li><a class="dropdown-item" href="../reference/ab_property.html"><span class="fa fa-capsules"></span> Get Properties of an Antibiotic Drug</a></li>
|
|
<li><a class="dropdown-item" href="../reference/av_property.html"><span class="fa fa-capsules"></span> Get Properties of an Antiviral Drug</a></li>
|
|
</ul></li>
|
|
<li class="nav-item"><a class="nav-link" href="../articles/AMR_for_Python.html"><span class="fa fab fa-python"></span> AMR for Python</a></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><ul class="navbar-nav"><li class="nav-item"><a class="nav-link" href="../news/index.html"><span class="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="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/main/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 id="arg-size">size<a class="anchor" aria-label="anchor" href="#arg-size"></a></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 id="arg-mo">mo<a class="anchor" aria-label="anchor" href="#arg-mo"></a></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 id="arg-ab">ab<a class="anchor" aria-label="anchor" href="#arg-ab"></a></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 id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
|
|
<dd><p>ignored, only in place to allow future extensions</p></dd>
|
|
|
|
|
|
<dt id="arg-prob-sir">prob_SIR<a class="anchor" aria-label="anchor" href="#arg-prob-sir"></a></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 2024 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] 0.025 8 0.002 0.005 0.25 >=256 0.01 0.002 64 </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [10] 0.5 4 32 0.002 16 >=256 0.01 0.002 0.0625 </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [19] 0.002 64 8 8 2 <=0.001 0.125 </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] 43 7 48 40 19 50 50 20 44 14 16 33 31 17 30 6 38 7 6 12 16 11 43 43 45</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] R S R R S S R I S R S S R I I R S I R R R R I R S</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] 0.025 0.25 16 8 0.001 4 16 0.025 0.25 8 </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [11] 0.5 0.005 0.0625 2 0.125 0.002 1 16 16 0.005 </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [21] 0.001 >=32 0.002 0.0625 0.125 </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] 4 8 2 8 8 16 8 8 1 0.5 1 >=32 2 4 1 </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [16] >=32 4 2 4 4 2 16 4 16 2 </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] <=0.0625 <=0.0625 <=0.0625 0.5 0.125 0.25 0.5 2 </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [9] 0.125 0.125 0.5 4 <=0.0625 2 0.25 4 </span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [17] 2 0.25 1 2 2 <=0.0625 2 <=0.0625</span>
|
|
<span class="r-out co"><span class="r-pr">#></span> [25] 0.5 </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] 30 43 22 49 40 8 14 36 49 23 12 9 17 25 43 46 30 49 34 22 50 24 39 38 46</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] 17 15 16 14 17 14 12 13 13 17 17 12 14 16 15 14 16 14 16 13 11 16 17 13 13</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] 25 22 21 23 19 20 21 25 20 19 21 19 27 22 26 25 27 21 17 26 18 23 23 26 27</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" aria-label="Table of contents"><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/assets/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/assets/logo_umcg.svg" style="max-width: 150px;"></a></p>
|
|
</div>
|
|
|
|
</footer></div>
|
|
|
|
|
|
|
|
|
|
|
|
</body></html>
|
|
|