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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"><title>Random MIC Values/Disk Zones/SIR Generation — random • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="96x96" href="../favicon-96x96.png"><link rel="icon" type="”image/svg+xml”" href="../favicon.svg"><link rel="apple-touch-icon" sizes="180x180" href="../apple-touch-icon.png"><link rel="icon" sizes="any" href="../favicon.ico"><link rel="manifest" href="../site.webmanifest"><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-0.4.10/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.10/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://amr-for-r.org/logo.svg"><link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.css" integrity="sha384-nB0miv6/jRmo5UMMR1wu3Gz6NLsoTkbqJghGIsx//Rlm+ZU03BU6SQNC66uf4l5+" crossorigin="anonymous"><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.js" integrity="sha384-7zkQWkzuo3B5mTepMUcHkMB5jZaolc2xDwL6VFqjFALcbeS9Ggm/Yr2r3Dy4lfFg" crossorigin="anonymous"></script><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/contrib/auto-render.min.js" integrity="sha384-43gviWU0YVjaDtb/GhzOouOXtZMP/7XUzwPTstBeZFe/+rCMvRwr4yROQP43s0Xk" crossorigin="anonymous" onload="renderMathInElement(document.body);"></script></head><body>
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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"><title>Random MIC Values/Disk Zones/SIR Generation — random • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="96x96" href="../favicon-96x96.png"><link rel="icon" type="”image/svg+xml”" href="../favicon.svg"><link rel="apple-touch-icon" sizes="180x180" href="../apple-touch-icon.png"><link rel="icon" sizes="any" href="../favicon.ico"><link rel="manifest" href="../site.webmanifest"><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-5.3.8/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.8/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.10/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.10/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://amr-for-r.org/logo.svg"><link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.css" integrity="sha384-nB0miv6/jRmo5UMMR1wu3Gz6NLsoTkbqJghGIsx//Rlm+ZU03BU6SQNC66uf4l5+" crossorigin="anonymous"><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.js" integrity="sha384-7zkQWkzuo3B5mTepMUcHkMB5jZaolc2xDwL6VFqjFALcbeS9Ggm/Yr2r3Dy4lfFg" crossorigin="anonymous"></script><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/contrib/auto-render.min.js" integrity="sha384-43gviWU0YVjaDtb/GhzOouOXtZMP/7XUzwPTstBeZFe/+rCMvRwr4yROQP43s0Xk" crossorigin="anonymous" onload="renderMathInElement(document.body);"></script></head><body>
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<a href="#main" class="visually-hidden-focusable">Skip to contents</a>
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@@ -7,7 +7,7 @@
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9057</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9061</small>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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@@ -55,11 +55,23 @@
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<div class="section level2">
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<h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
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<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>, skew <span class="op">=</span> <span class="st">"right"</span>,</span>
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<span> severity <span class="op">=</span> <span class="fl">1</span>, <span class="va">...</span><span class="op">)</span></span>
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<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">random_mic</span><span class="op">(</span></span>
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<span> size <span class="op">=</span> <span class="cn">NULL</span>,</span>
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<span> mo <span class="op">=</span> <span class="cn">NULL</span>,</span>
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<span> ab <span class="op">=</span> <span class="cn">NULL</span>,</span>
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<span> skew <span class="op">=</span> <span class="st">"right"</span>,</span>
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<span> severity <span class="op">=</span> <span class="fl">1</span>,</span>
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<span> <span class="va">...</span></span>
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<span><span class="op">)</span></span>
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<span></span>
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<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>, skew <span class="op">=</span> <span class="st">"left"</span>,</span>
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<span> severity <span class="op">=</span> <span class="fl">1</span>, <span class="va">...</span><span class="op">)</span></span>
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<span><span class="fu">random_disk</span><span class="op">(</span></span>
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<span> size <span class="op">=</span> <span class="cn">NULL</span>,</span>
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<span> mo <span class="op">=</span> <span class="cn">NULL</span>,</span>
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<span> ab <span class="op">=</span> <span class="cn">NULL</span>,</span>
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<span> skew <span class="op">=</span> <span class="st">"left"</span>,</span>
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<span> severity <span class="op">=</span> <span class="fl">1</span>,</span>
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<span> <span class="va">...</span></span>
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<span><span class="op">)</span></span>
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<span></span>
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<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>
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</div>
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@@ -111,16 +123,15 @@
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<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
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<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>
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<span class="r-out co"><span class="r-pr">#></span> Class <span style="color: #0000BB;"><mic></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.008 0.125 4 32 1 0.004 0.008 0.0002 </span>
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<span class="r-out co"><span class="r-pr">#></span> [9] 0.125 2 0.008 0.008 0.016 0.125 0.064 <=0.0001</span>
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<span class="r-out co"><span class="r-pr">#></span> [17] 0.0005 0.0002 0.5 0.002 0.002 0.25 16 <=0.0001</span>
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<span class="r-out co"><span class="r-pr">#></span> [25] 0.002 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 1 0.032 0.064 1 0.25 0.125 >=128 0.0002 32 0.25 </span>
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<span class="r-out co"><span class="r-pr">#></span> [11] 0.008 0.125 0.001 0.032 8 >=128 0.032 0.008 8 >=128 </span>
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<span class="r-out co"><span class="r-pr">#></span> [21] 0.125 0.0001 0.5 64 1 </span>
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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>
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<span class="r-out co"><span class="r-pr">#></span> Class <span style="color: #0000BB;"><disk></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 25 47 24 47 38 28 36 33 31 50 41 29 40 31 44 45 37 40 44 49 9 48 20 37 47</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 49 39 29 30 16 23 44 50 25 28 29 14 44 34 8 33 33 34 38 42 10 42 43 11 46</span>
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<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>
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<span class="r-out co"><span class="r-pr">#></span> Class <span style="color: #0000BB;"><sir></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] S S R R S S I S I S S I S R I I I I S I R I I I I</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] I S S S R R S R I I I I S R S I S S S R R I R S I</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="co"># add more skewedness, make more realistic by setting a bug and/or drug:</span></span></span>
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<span class="r-in"><span><span class="va">disks</span> <span class="op"><-</span> <span class="fu">random_disk</span><span class="op">(</span><span class="fl">100</span>, severity <span class="op">=</span> <span class="fl">2</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span>, ab <span class="op">=</span> <span class="st">"CIP"</span><span class="op">)</span></span></span>
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@@ -133,29 +144,30 @@
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<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
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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>
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<span class="r-out co"><span class="r-pr">#></span> Class <span style="color: #0000BB;"><mic></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 2 0.001 4 0.008 0.0005 0.0005 0.0005 0.0002 0.0002 >=64 </span>
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<span class="r-out co"><span class="r-pr">#></span> [11] 0.0002 1 0.5 0.002 0.5 0.002 0.001 0.032 0.008 0.004 </span>
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<span class="r-out co"><span class="r-pr">#></span> [21] 0.032 0.0002 0.0005 0.002 0.001 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 256 <=0.0001 <=0.0001 0.016 1 0.016 2 8 </span>
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<span class="r-out co"><span class="r-pr">#></span> [9] 0.5 0.004 0.032 0.004 0.001 0.001 0.064 0.002 </span>
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<span class="r-out co"><span class="r-pr">#></span> [17] 0.032 0.004 0.008 16 0.125 <=0.0001 0.001 0.008 </span>
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<span class="r-out co"><span class="r-pr">#></span> [25] 0.001 </span>
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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="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-16</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> Class <span style="color: #0000BB;"><mic></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] <=0.5 <=0.5 2 <=0.5 1 <=0.5 <=0.5 <=0.5 <=0.5 1 <=0.5 <=0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> [13] <=0.5 1 <=0.5 1 <=0.5 <=0.5 <=0.5 <=0.5 <=0.5 <=0.5 2 1 </span>
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<span class="r-out co"><span class="r-pr">#></span> [25] 2 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.5 <=0.25 0.5 4 1 1 0.5 0.5 0.5 <=0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> [11] 0.5 0.5 2 1 <=0.25 <=0.25 8 <=0.25 1 1 </span>
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<span class="r-out co"><span class="r-pr">#></span> [21] <=0.25 0.5 16 2 0.5 </span>
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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>
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<span class="r-out co"><span class="r-pr">#></span> Class <span style="color: #0000BB;"><mic></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.125 0.125 1 0.25 0.5 0.125 0.125 0.125 0.125 0.125 0.125 0.125</span>
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<span class="r-out co"><span class="r-pr">#></span> [13] 1 0.125 0.5 1 0.125 0.25 0.5 0.25 0.5 0.5 0.5 0.125</span>
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<span class="r-out co"><span class="r-pr">#></span> [25] 0.25 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.125 0.125 0.125 0.125 0.125 >=0.25 0.125 0.125 0.125 0.125 </span>
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<span class="r-out co"><span class="r-pr">#></span> [11] >=0.25 0.125 >=0.25 0.125 0.125 0.125 >=0.25 0.125 >=0.25 >=0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> [21] >=0.25 0.125 0.125 0.125 >=0.25</span>
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<span class="r-in"><span></span></span>
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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>
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<span class="r-out co"><span class="r-pr">#></span> Class <span style="color: #0000BB;"><disk></span></span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [1] 32 21 23 21 14 22 25 29 29 28 34 34 34 33 13 28 33 34 32 25 18 26 13 21 33</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [1] 18 32 21 19 23 10 30 18 22 34 19 32 28 18 25 7 27 23 28 17 29 18 22 28 23</span>
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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="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 11-17</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> Class <span style="color: #0000BB;"><disk></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 20 21 15 22 16 22 16 14 21 17 15 19 20 17 18 21 16 20 11 22 19 18 19 11 21</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 22 18 13 22 17 12 20 20 16 20 22 22 18 20 20 22 22 16 13 17 15 17 16 22 15</span>
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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>
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<span class="r-out co"><span class="r-pr">#></span> Class <span style="color: #0000BB;"><disk></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 29 25 31 17 29 21 31 34 33 31 29 30 23 20 33 20 34 32 35 26 26 26 34 30 33</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 31 30 30 28 24 35 28 34 28 29 27 29 24 21 13 16 34 19 26 20 27 32 32 24 26</span>
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<span class="r-in"><span><span class="co"># }</span></span></span>
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</code></pre></div>
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</div>
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