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<h1>Random MIC Values/Disk Zones/RSI Generation</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/main/R/random.R'><code>R/random.R</code></a></small>
<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="hidden name"><code>random.Rd</code></div>
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@ -246,100 +161,88 @@
<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="ref-usage 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>
<div id="ref-usage">Usage,<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>
<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 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 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'>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>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>size</th>
<td><p>desired size of the returned vector. If used in a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> call or <code>dplyr</code> verb, will get the current (group) size if left blank.</p></td>
</tr>
<tr>
<th>mo</th>
<td><p>any <a href='https://rdrr.io/r/base/character.html'>character</a> that can be coerced to a valid microorganism code with <code><a href='as.mo.html'>as.mo()</a></code></p></td>
</tr>
<tr>
<th>ab</th>
<td><p>any <a href='https://rdrr.io/r/base/character.html'>character</a> that can be coerced to a valid antimicrobial agent code with <code><a href='as.ab.html'>as.ab()</a></code></p></td>
</tr>
<tr>
<th>...</th>
<td><p>ignored, only in place to allow future extensions</p></td>
</tr>
<tr>
<th>prob_RSI</th>
<td><p>a vector of length 3: the probabilities for "R" (1st value), "S" (2nd value) and "I" (3rd value)</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</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>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>The base <span style="R">R</span> function <code><a href='https://rdrr.io/r/base/sample.html'>sample()</a></code> is used for generating values.</p>
<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>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable Lifecycle</h2>
<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></div>
<div id="arguments">
<h2>Arguments</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 id="value">
<h2>Value</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 id="details">
<h2>Details</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 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>
</div>
<div id="stable-lifecycle">
<h2>Stable Lifecycle</h2>
<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
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>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a argument will be deprecated and first continue to work, but will emit an 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>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on Our Website!</h2>
<p><img src="figures/lifecycle_stable.svg" style="margin-bottom:5px"><br>
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>
<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 an 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>
</div>
<div id="read-more-on-our-website-">
<h2>Read more on Our Website!</h2>
<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>
<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>
</div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<div class="ref-examples 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>
<span class='fu'>random_disk</span><span class='op'>(</span><span class='fl'>100</span><span class='op'>)</span>
<span class='fu'>random_rsi</span><span class='op'>(</span><span class='fl'>100</span><span class='op'>)</span>
<div id="ref-examples">
<h2>Examples</h2>
<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>
<span class="fu">random_disk</span><span class="op">(</span><span class="fl">100</span><span class="op">)</span>
<span class="fu">random_rsi</span><span class="op">(</span><span class="fl">100</span><span class="op">)</span>
<span class='co'># \donttest{</span>
<span class='co'># make the random generation more realistic by setting a bug and/or drug:</span>
<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>
<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>
<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>
<span class="co"># \donttest{</span>
<span class="co"># make the random generation more realistic by setting a bug and/or drug:</span>
<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>
<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>
<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>
<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>
<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>
<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>
<span class='co'># }</span>
<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>
<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>
<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>
<span class="co"># }</span>
</code></pre></div>
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