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<![endif]--></head><body>
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@ -10,7 +10,7 @@
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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="">1.8.2.9095</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9096</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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@ -127,7 +127,7 @@
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</nav><div class="container template-reference-topic">
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<div class="row">
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<main id="main" class="col-md-9"><div class="page-header">
|
||||
<img src="../logo.svg" class="logo" alt=""><h1>Random MIC Values/Disk Zones/RSI Generation</h1>
|
||||
<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>
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<div class="d-none name"><code>random.Rd</code></div>
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</div>
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@ -142,7 +142,7 @@
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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>, <span class="va">...</span><span class="op">)</span></span>
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<span></span>
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<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>
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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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<div class="section level2">
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@ -163,8 +163,8 @@
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<dd><p>ignored, only in place to allow future extensions</p></dd>
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<dt>prob_RSI</dt>
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<dd><p>a vector of length 3: the probabilities for "R" (1st value), "S" (2nd value) and "I" (3rd value)</p></dd>
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<dt>prob_SIR</dt>
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<dd><p>a vector of length 3: the probabilities for "S" (1st value), "I" (2nd value) and "R" (3rd value)</p></dd>
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||||
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</dl></div>
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<div class="section level2">
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@ -176,49 +176,49 @@
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<div class="section level2">
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||||
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
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||||
<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>
|
||||
<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>
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</div>
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||||
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<div class="section level2">
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||||
<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>
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<span class="r-out co"><span class="r-pr">#></span> Class 'mic'</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.5 0.125 64 0.025 4 32 0.5 0.5 1 0.001 </span>
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<span class="r-out co"><span class="r-pr">#></span> [11] 0.005 0.001 16 2 0.0625 1 0.005 0.001 0.002 64 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [21] 0.125 0.001 0.25 256 0.25 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.01 0.25 64 4 8 0.125 16 0.125 128 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [10] 4 64 2 2 1 0.005 0.0625 2 0.125 </span>
|
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<span class="r-out co"><span class="r-pr">#></span> [19] <=0.001 0.025 256 8 2 128 0.5 </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>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'disk'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 22 17 48 24 33 35 46 9 46 34 48 48 30 42 8 44 15 41 34 27 42 47 19 32 29</span>
|
||||
<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>
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<span class="r-out co"><span class="r-pr">#></span> Class 'rsi'</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [1] S S R S R S R S I R I I R S R S S I R I S I S S S</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [1] 39 21 49 46 49 48 32 49 18 43 8 14 50 31 38 18 36 47 42 50 18 47 50 17 13</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 'sir'</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [1] I R S R R I R I R I I R I S R S R S S S I I I R 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"># \donttest{</span></span></span>
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||||
<span class="r-in"><span><span class="co"># make the random generation more realistic by setting a bug and/or drug:</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>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'mic'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.125 8 0.25 0.01 4 0.5 0.005 0.01 256 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [10] 16 2 0.0625 0.5 0.002 0.125 32 32 0.002 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [19] <=0.001 4 0.005 0.002 <=0.001 256 0.125 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.01 0.001 0.025 32 4 8 0.002 1 0.002 0.002 1 0.005</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [13] 4 0.025 >=128 4 8 0.002 0.001 0.5 0.01 >=128 0.001 >=128</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [25] 4 </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 4 8 16 2 16 <=1 8 2 16 8 <=1 64 2 4 2 2 2 2 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [20] 64 8 8 4 32 4 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] <=1 <=1 2 4 4 4 <=1 8 8 8 <=1 <=1 4 4 8 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [16] 2 <=1 2 4 4 <=1 8 >=16 4 8 </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] 1 0.025 0.0625 >=4 0.5 0.5 0.5 0.5 >=4 >=4 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [11] 0.25 0.025 0.025 0.125 >=4 1 >=4 1 1 0.5 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [21] 2 0.25 1 1 1 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 0.125 1 0.25 0.5 0.125 4 0.025 4 0.025 0.125 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [11] 0.025 0.25 4 >=8 0.5 0.125 0.025 0.025 0.5 0.25 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [21] 0.0625 0.125 2 0.0625 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] 46 27 10 49 45 44 27 26 10 43 35 37 42 42 46 37 19 18 41 17 29 50 10 23 50</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 39 45 17 46 43 35 44 42 26 40 9 14 49 40 46 48 8 43 31 47 47 39 40 13 42</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] 11 17 11 14 14 12 14 11 14 15 14 11 12 15 16 11 13 13 16 12 15 14 14 17 15</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 14 16 17 12 13 12 11 16 11 13 17 15 14 17 14 13 16 16 11 12 13 14 14 14 16</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] 27 27 20 21 24 17 21 21 22 18 16 27 27 22 19 25 25 21 15 19 27 21 18 21 17</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 22 26 18 15 21 26 23 22 16 22 27 25 15 24 16 23 20 19 18 23 24 15 27 18 17</span>
|
||||
<span class="r-in"><span><span class="co"># }</span></span></span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
|
||||
Reference in New Issue
Block a user