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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/SIR Generation</h1>
      <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/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 drug, 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_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>
    </div>

    <div class="section level2">
    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>


<dl><dt id="arg-size">size<a class="anchor" aria-label="anchor" href="#arg-size"></a></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 id="arg-mo">mo<a class="anchor" aria-label="anchor" href="#arg-mo"></a></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 id="arg-ab">ab<a class="anchor" aria-label="anchor" href="#arg-ab"></a></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 drug code with <code><a href="as.ab.html">as.ab()</a></code>.</p></dd>


<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
<dd><p>Ignored, only in place to allow future extensions.</p></dd>


<dt id="arg-prob-sir">prob_SIR<a class="anchor" aria-label="anchor" href="#arg-prob-sir"></a></dt>
<dd><p>A vector of length 3: the probabilities for "S" (1st value), "I" (2nd value) and "R" (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>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>
    </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 2025 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>
    </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 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 0.125   8       1       4       0.01    0.002   64      &lt;=0.001 0.01   </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 1       &gt;=256   &gt;=256   2       0.025   0.01    64      4       0.5    </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 0.025   8       0.005   &gt;=256   8       &lt;=0.001 8      </span>
<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 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  [1]  7 45 30 48 23 12 45 40 47  9 20 20 23  9 32 20 50 26 42 30 47 11 24 34 46</span>
<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>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] I R I S S I S S I S S R I S I I R S R S R R S I I</span>
<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 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 32      0.0625  16      0.005   0.01    0.25    0.5     4       0.5    </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 0.125   0.125   0.25    &gt;=64    &gt;=64    2       0.025   0.0625  0.025  </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 2       0.125   0.01    8       &lt;=0.001 0.0625  0.5    </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">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 1      8      1      0.5    4      4      2      4      8      2     </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [11] 8      &lt;=0.25 16     2      2      2      16     4      0.5    8     </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [21] 8      &lt;=0.25 2      8      1     </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">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 0.25    1       0.25    &gt;=8     2       1       &lt;=0.125 0.25    2      </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 2       1       4       0.5     &lt;=0.125 2       2       &lt;=0.125 0.5    </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 0.5     &gt;=8     2       0.5     2       &gt;=8     &gt;=8    </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">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 39 14 27 41 44 37 46 17 16 13 23 31 19 22 42 15 40 44 40 40 30 34 34 43 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">"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 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 12 15 17 17 12 13 16 14 15 12 15 16 11 15 11 17 15 13 14 11 13 17 11 17 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">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 16 26 21 26 20 22 25 18 26 27 18 25 17 23 21 16 20 23 21 15 21 22 20 19 17</span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>
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