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<!-- 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/RSI 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-5.1.3/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.1.3/bootstrap.bundle.min.js"></script><link href="../deps/Fira_Code-0.4.4/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.rawgit.com/afeld/bootstrap-toc/v1.0.1/dist/bootstrap-toc.min.js"></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/RSI 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"><m
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<img src="../logo.svg" class="logo" alt=""><h1>Random MIC Values/Disk Zones/RSI 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">
Built site for AMR: 1.8.2.9050@7ca44fb
2022-11-13 13:52:01 +01:00
<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>
Built site for AMR: 1.8.1.9020@d6676e9
2022-08-21 16:59:35 +02:00
</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_rsi</span><span class="op">(</span>size <span class="op">=</span> <span class="cn">NULL</span>, prob_RSI <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>
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<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>
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<dt>...</dt>
<dd><p>ignored, only in place to allow future extensions</p></dd>
<dt>prob_RSI</dt>
<dd><p>a vector of length 3: the probabilities for "R" (1st value), "S" (2nd value) and "I" (3rd value)</p></dd>
</dl></div>
<div class="section level2">
<h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
Built site for AMR: 1.8.2.9023@85e2fbe
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<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>
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</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="rsi_translation.html">rsi_translation</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>
Built site for AMR: 1.8.2.9023@85e2fbe
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<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
Built site for AMR: 1.8.2.9058@56dad34
2022-12-09 13:44:45 +01:00
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 8 0.25 0.01 8 128 0.025 0.5 &lt;=0.002 32 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 64 16 0.005 0.005 0.025 0.025 0.25 0.025 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 256 256 2 256 0.005 0.025 64 </span>
Built site for AMR: 1.8.1.9020@d6676e9
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<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>
Built site for AMR: 1.8.2.9034@6ad7857
2022-10-29 14:24:08 +02:00
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
Built site for AMR: 1.8.2.9058@56dad34
2022-12-09 13:44:45 +01:00
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 30 16 47 35 37 49 26 34 44 48 27 44 26 41 49 23 7 50 19 34 38 25 21 43 29</span>
Built site for AMR: 1.8.1.9020@d6676e9
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<span class="r-in"><span><span class="fu">random_rsi</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
Built site for AMR: 1.8.2.9023@85e2fbe
2022-10-19 11:58:58 +02:00
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'rsi'</span>
Built site for AMR: 1.8.2.9058@56dad34
2022-12-09 13:44:45 +01:00
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] R S S S S I S S R R R I S S S S S S S S R I R I S</span>
Built site for AMR: 1.8.1.9020@d6676e9
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<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>
Built site for AMR: 1.8.1.9045@e7af5fc
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<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>
Built site for AMR: 1.8.2.9023@85e2fbe
2022-10-19 11:58:58 +02:00
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
Built site for AMR: 1.8.2.9058@56dad34
2022-12-09 13:44:45 +01:00
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1 128 0.001 0.01 128 0.01 0.001 0.01 4 128 0.001 0.01 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] 0.002 4 16 32 1 0.25 1 2 64 16 64 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] 0.01 </span>
Built site for AMR: 1.8.1.9045@e7af5fc
2022-08-28 22:45:38 +02:00
<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>
Built site for AMR: 1.8.2.9023@85e2fbe
2022-10-19 11:58:58 +02:00
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
Built site for AMR: 1.8.2.9058@56dad34
2022-12-09 13:44:45 +01:00
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] &lt;=1 8 8 8 &lt;=1 2 4 8 &gt;=16 &gt;=16 2 4 8 &gt;=16 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [16] 4 2 &gt;=16 4 &lt;=1 2 &gt;=16 8 8 2 </span>
Built site for AMR: 1.8.1.9020@d6676e9
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<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>
Built site for AMR: 1.8.2.9023@85e2fbe
2022-10-19 11:58:58 +02:00
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
Built site for AMR: 1.8.2.9058@56dad34
2022-12-09 13:44:45 +01:00
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1 2 &gt;=16 &gt;=16 4 2 0.5 0.5 0.25 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 1 0.5 &lt;=0.125 2 4 &gt;=16 4 8 &gt;=16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 4 1 &lt;=0.125 0.5 0.5 0.5 2 </span>
Built site for AMR: 1.8.1.9020@d6676e9
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<span class="r-in"><span></span></span>
Built site for AMR: 1.8.1.9045@e7af5fc
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<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>
Built site for AMR: 1.8.2.9023@85e2fbe
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<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
Built site for AMR: 1.8.2.9058@56dad34
2022-12-09 13:44:45 +01:00
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 21 36 49 10 16 15 34 46 43 42 33 47 43 50 19 45 45 13 34 9 46 20 42 40 12</span>
Built site for AMR: 1.8.1.9045@e7af5fc
2022-08-28 22:45:38 +02:00
<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>
Built site for AMR: 1.8.2.9023@85e2fbe
2022-10-19 11:58:58 +02:00
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
Built site for AMR: 1.8.2.9058@56dad34
2022-12-09 13:44:45 +01:00
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 16 11 16 13 11 12 11 14 13 11 14 11 12 15 12 12 13 13 17 17 16 13 16 11 15</span>
Built site for AMR: 1.8.1.9020@d6676e9
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<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>
Built site for AMR: 1.8.2.9023@85e2fbe
2022-10-19 11:58:58 +02:00
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
Built site for AMR: 1.8.2.9058@56dad34
2022-12-09 13:44:45 +01:00
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 17 15 25 23 16 23 16 27 26 20 17 16 22 22 27 18 24 17 26 25 27 21 16 27 18</span>
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<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>
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