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<h1>Random MIC Values/Disk Zones/RSI Generation</h1>
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<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="hidden name"><code>random.Rd</code></div>
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</div>
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<div class="ref-description">
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<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>
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</div>
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<div id="ref-usage">
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<div class="sourceCode"><pre class="sourceCode r"><code><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>
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<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>
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<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></code></pre></div>
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</div>
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<div id="arguments">
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<h2>Arguments</h2>
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<dl><dt>size</dt>
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<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>
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<dt>mo</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 microorganism code with <code><a href="as.mo.html">as.mo()</a></code></p></dd>
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<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 agent code with <code><a href="as.ab.html">as.ab()</a></code></p></dd>
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<dt>...</dt>
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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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</dl></div>
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<div id="value">
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<h2>Value</h2>
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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>
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<div id="details">
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<h2>Details</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>
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<p>Generated values are based on the latest EUCAST guideline 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>
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</div>
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<div id="stable-lifecycle">
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<h2>Stable Lifecycle</h2>
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<p><img src="figures/lifecycle_stable.svg" style='margin-bottom:"5"'><br>
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The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
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<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
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</div>
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<div id="read-more-on-our-website-">
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<h2>Read more on Our Website!</h2>
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<p>On our website <a href="https://msberends.github.io/AMR/">https://msberends.github.io/AMR/</a> you can find <a href="https://msberends.github.io/AMR/articles/AMR.html">a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href="https://msberends.github.io/AMR/reference/">complete documentation of all functions</a> and <a href="https://msberends.github.io/AMR/articles/WHONET.html">an example analysis using WHONET data</a>.</p>
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</div>
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<div id="ref-examples">
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<h2>Examples</h2>
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<div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">random_mic</span><span class="op">(</span><span class="fl">100</span><span class="op">)</span>
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<span class="fu">random_disk</span><span class="op">(</span><span class="fl">100</span><span class="op">)</span>
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<span class="fu">random_rsi</span><span class="op">(</span><span class="fl">100</span><span class="op">)</span>
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<span class="co"># \donttest{</span>
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<span class="co"># make the random generation more realistic by setting a bug and/or drug:</span>
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<span class="fu">random_mic</span><span class="op">(</span><span class="fl">100</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 0.0625-64</span>
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<span class="fu">random_mic</span><span class="op">(</span><span class="fl">100</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-16</span>
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<span class="fu">random_mic</span><span class="op">(</span><span class="fl">100</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-4</span>
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<span class="fu">random_disk</span><span class="op">(</span><span class="fl">100</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 8-50</span>
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<span class="fu">random_disk</span><span class="op">(</span><span class="fl">100</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 11-17</span>
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<span class="fu">random_disk</span><span class="op">(</span><span class="fl">100</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 12-27</span>
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<span class="co"># }</span>
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</code></pre></div>
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<p></p><p>Developed by Matthijs S. Berends, Christian F. Luz, Dennis Souverein,
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Erwin E. A. Hassing.</p>
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