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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">
<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 agent, 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_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>
<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 agent 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_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>
<p>class <code>&lt;mic&gt;</code> for <code>random_mic()</code> (see <code><a href="as.mic.html">as.mic()</a></code>) and class <code>&lt;disk&gt;</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="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>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;mic&gt;</span>
Built site for AMR: 1.8.1.9030@164886f
2022-08-26 23:31:20 +02:00
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.0625 0.5 4 16 4 0.0625 8 0.002 4 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 0.25 64 64 0.5 &lt;=0.001 0.5 &lt;=0.001 8 1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 2 0.01 0.5 0.0625 0.125 &gt;=256 0.025 </span>
Built site for AMR: 1.8.1.9020@d6676e9
2022-08-21 16:59:35 +02:00
<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">#&gt;</span> Class &lt;disk&gt;</span>
Built site for AMR: 1.8.1.9030@164886f
2022-08-26 23:31:20 +02:00
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 39 16 46 31 49 28 18 41 45 40 42 49 22 47 40 6 49 25 12 43 43 36 7 16 10</span>
Built site for AMR: 1.8.1.9020@d6676e9
2022-08-21 16:59:35 +02:00
<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>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;rsi&gt;</span>
Built site for AMR: 1.8.1.9030@164886f
2022-08-26 23:31:20 +02:00
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] S I S S R S S I S R R S S S S R S R I R R R R S R</span>
Built site for AMR: 1.8.1.9020@d6676e9
2022-08-21 16:59:35 +02:00
<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">#&gt;</span> Class &lt;mic&gt;</span>
Built site for AMR: 1.8.1.9030@164886f
2022-08-26 23:31:20 +02:00
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 8 0.002 &lt;=0.001 0.005 0.125 256 4 32 0.01 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] &lt;=0.001 0.25 1 0.025 0.125 32 32 16 0.005 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 0.5 &lt;=0.001 0.0625 0.5 256 2 64 </span>
Built site for AMR: 1.8.1.9020@d6676e9
2022-08-21 16:59:35 +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>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;mic&gt;</span>
Built site for AMR: 1.8.1.9030@164886f
2022-08-26 23:31:20 +02:00
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 32 &lt;=0.25 16 0.5 8 &lt;=0.25 8 16 8 32 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [11] 32 0.5 &lt;=0.25 32 32 32 0.5 4 8 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [21] &lt;=0.25 32 16 16 2 </span>
Built site for AMR: 1.8.1.9020@d6676e9
2022-08-21 16:59:35 +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">"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">#&gt;</span> Class &lt;mic&gt;</span>
Built site for AMR: 1.8.1.9030@164886f
2022-08-26 23:31:20 +02:00
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.25 0.25 &lt;=0.025 &gt;=16 0.0625 0.5 8 0.25 0.25 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 4 0.125 1 0.5 0.125 8 &gt;=16 0.0625 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 0.25 &gt;=16 2 &gt;=16 1 1 4 </span>
Built site for AMR: 1.8.1.9020@d6676e9
2022-08-21 16:59:35 +02:00
<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">#&gt;</span> Class &lt;disk&gt;</span>
Built site for AMR: 1.8.1.9030@164886f
2022-08-26 23:31:20 +02:00
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 47 15 40 39 45 10 36 40 47 22 12 11 44 14 45 21 17 49 24 14 11 22 44 45 11</span>
Built site for AMR: 1.8.1.9020@d6676e9
2022-08-21 16:59:35 +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>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;disk&gt;</span>
Built site for AMR: 1.8.1.9030@164886f
2022-08-26 23:31:20 +02:00
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 16 14 13 11 11 14 12 14 15 14 14 16 15 11 14 12 13 17 11 17 13 11 15 11 16</span>
Built site for AMR: 1.8.1.9020@d6676e9
2022-08-21 16:59:35 +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">"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">#&gt;</span> Class &lt;disk&gt;</span>
Built site for AMR: 1.8.1.9030@164886f
2022-08-26 23:31:20 +02:00
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 17 25 23 21 19 21 15 15 25 22 22 16 16 18 16 25 23 24 17 23 15 25 22 23 16</span>
Built site for AMR: 1.8.1.9020@d6676e9
2022-08-21 16:59:35 +02:00
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>
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