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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="">2.1.1.9231</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9232</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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@ -67,23 +67,23 @@
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<dl><dt id="arg-size">size<a class="anchor" aria-label="anchor" href="#arg-size"></a></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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<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 id="arg-mo">mo<a class="anchor" aria-label="anchor" href="#arg-mo"></a></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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<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 id="arg-ab">ab<a class="anchor" aria-label="anchor" href="#arg-ab"></a></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 drug code with <code><a href="as.ab.html">as.ab()</a></code></p></dd>
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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 drug code with <code><a href="as.ab.html">as.ab()</a></code></p></dd>
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<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
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<dd><p>ignored, only in place to allow future extensions</p></dd>
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<dd><p>Ignored, only in place to allow future extensions</p></dd>
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<dt id="arg-prob-sir">prob_SIR<a class="anchor" aria-label="anchor" href="#arg-prob-sir"></a></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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<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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</dl></div>
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<div class="section level2">
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@ -100,43 +100,43 @@
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<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
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<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] 0.025 2 0.25 8 4 >=256 64 0.125 1 </span>
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<span class="r-out co"><span class="r-pr">#></span> [10] 16 2 0.025 8 32 <=0.001 4 2 128 </span>
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<span class="r-out co"><span class="r-pr">#></span> [19] 0.125 4 0.01 >=256 0.25 0.25 1 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] <=0.005 0.25 1 0.0625 128 0.01 1 4 128 </span>
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<span class="r-out co"><span class="r-pr">#></span> [10] <=0.005 0.25 0.5 0.125 0.01 0.25 2 8 16 </span>
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<span class="r-out co"><span class="r-pr">#></span> [19] 0.125 0.5 >=256 >=256 >=256 0.25 16 </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>
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<span class="r-out co"><span class="r-pr">#></span> Class 'disk'</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 48 8 6 21 6 34 30 30 42 26 10 41 26 22 46 19 16 38 34 12 50 42 45 42 44</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 24 14 46 41 9 8 22 41 50 38 48 48 28 43 47 30 13 13 38 14 48 47 21 6 22</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 R S R I I R R R R R R I R S S S I I S S R R R</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] I I I I I I S R R S I S S R I R R R I S S R R I R</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>
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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] 1 16 0.025 0.001 4 4 0.125 0.002 2 0.25 0.25 64 </span>
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<span class="r-out co"><span class="r-pr">#></span> [13] 0.5 0.005 256 8 0.125 16 0.005 0.001 64 0.5 8 64 </span>
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<span class="r-out co"><span class="r-pr">#></span> [25] 0.001</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.025 4 1 0.0625 0.005 0.002 2 0.002 >=128 0.0625</span>
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<span class="r-out co"><span class="r-pr">#></span> [11] 0.125 0.5 0.002 0.01 0.001 0.002 0.01 32 64 0.005 </span>
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<span class="r-out co"><span class="r-pr">#></span> [21] 0.01 1 4 1 32 </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="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-16</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] 4 8 2 >=16 <=0.25 <=0.25 >=16 1 1 0.5 </span>
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<span class="r-out co"><span class="r-pr">#></span> [11] 8 <=0.25 2 0.5 2 <=0.25 1 4 1 <=0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> [21] >=16 4 2 1 <=0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] <=1 4 4 2 32 4 32 16 <=1 32 8 8 32 8 4 32 <=1 <=1 16 </span>
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<span class="r-out co"><span class="r-pr">#></span> [20] 8 32 8 16 4 8 </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">"Streptococcus pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-4</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] 2 8 0.0625 0.0625 0.0625 4 <=0.025 0.125 8 </span>
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<span class="r-out co"><span class="r-pr">#></span> [10] 8 0.25 0.25 0.125 <=0.025 0.25 <=0.025 0.0625 2 </span>
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<span class="r-out co"><span class="r-pr">#></span> [19] <=0.025 8 4 4 <=0.025 8 8 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.125 >=16 0.125 >=16 2 0.5 1 0.5 </span>
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<span class="r-out co"><span class="r-pr">#></span> [9] 0.125 0.5 <=0.0625 0.25 0.25 0.5 >=16 >=16 </span>
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<span class="r-out co"><span class="r-pr">#></span> [17] 1 >=16 8 0.25 8 0.25 >=16 >=16 </span>
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<span class="r-out co"><span class="r-pr">#></span> [25] 0.125 </span>
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<span class="r-in"><span></span></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="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 8-50</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> Class 'disk'</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 8 24 46 50 48 11 23 30 47 33 21 43 17 16 48 16 39 38 16 49 33 47 14 18 42</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 42 36 49 13 45 50 37 33 30 14 23 15 30 9 21 47 32 17 48 47 24 23 14 27 48</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="st">"Klebsiella pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 11-17</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> Class 'disk'</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 12 13 15 14 12 16 15 16 13 13 12 13 12 11 16 17 11 17 11 14 12 14 11 12 12</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 13 16 13 16 13 11 17 12 16 14 14 15 11 16 12 13 14 12 13 12 15 12 12 13 17</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="st">"Streptococcus pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 12-27</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> Class 'disk'</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 20 18 24 24 17 18 26 24 26 24 20 20 26 24 19 15 17 17 24 20 17 22 22 19 15</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 16 20 25 24 21 22 21 16 15 18 18 25 19 26 27 26 21 21 19 25 15 22 19 24 26</span>
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<span class="r-in"><span><span class="co"># }</span></span></span>
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</code></pre></div>
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</div>
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