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@@ -7,7 +7,7 @@
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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="">3.0.1.9004</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9007</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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@@ -111,16 +111,16 @@
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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] 0.008 0.016 0.25 0.5 0.5 1 0.002 0.002 </span>
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<span class="r-out co"><span class="r-pr">#></span> [9] 0.001 0.064 0.002 0.064 <=0.0002 1 4 0.016 </span>
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<span class="r-out co"><span class="r-pr">#></span> [17] 0.008 8 0.25 0.5 0.5 0.032 4 0.008 </span>
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<span class="r-out co"><span class="r-pr">#></span> [25] 0.004 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.125 <=0.0001 0.004 0.004 0.5 0.032 1 0.008 </span>
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<span class="r-out co"><span class="r-pr">#></span> [9] 128 0.0002 0.002 0.002 32 0.032 0.0005 0.0002 </span>
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<span class="r-out co"><span class="r-pr">#></span> [17] 0.008 0.001 0.0002 <=0.0001 0.064 0.016 0.008 4 </span>
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<span class="r-out co"><span class="r-pr">#></span> [25] 1 </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] 39 47 20 36 18 44 43 25 28 26 44 36 42 8 28 44 31 29 49 30 28 39 49 25 49</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 50 21 48 47 46 38 45 47 24 28 45 43 19 23 44 19 31 22 40 39 39 36 35 14 34</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 S R S R R S I I I S R R S I I S I I I S S R S</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] I S S R I S R I R I S S S R R R I I R R I S R R S</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="co"># add more skewedness, make more realistic by setting a bug and/or drug:</span></span></span>
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<span class="r-in"><span><span class="va">disks</span> <span class="op"><-</span> <span class="fu">random_disk</span><span class="op">(</span><span class="fl">100</span>, severity <span class="op">=</span> <span class="fl">2</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span>, ab <span class="op">=</span> <span class="st">"CIP"</span><span class="op">)</span></span></span>
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@@ -133,28 +133,28 @@
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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="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 8 0.004 4 0.032 8 0.016 8 0.001 0.0002</span>
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<span class="r-out co"><span class="r-pr">#></span> [11] 0.002 0.004 0.001 0.0005 0.0001 0.002 0.125 >=64 0.002 0.0005</span>
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<span class="r-out co"><span class="r-pr">#></span> [21] 0.001 0.0002 0.0005 0.001 0.0005</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.0001 0.0002 0.016 0.5 0.008 >=8 0.125 0.0002 0.002 0.0005</span>
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<span class="r-out co"><span class="r-pr">#></span> [11] 1 0.0001 0.25 0.0002 0.25 2 0.0005 0.064 0.5 0.004 </span>
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<span class="r-out co"><span class="r-pr">#></span> [21] 0.001 0.064 0.032 0.0005 0.125 </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] <=0.5 <=0.5 <=0.5 1 <=0.5 <=0.5 <=0.5 <=0.5 <=0.5 <=0.5 1 1 </span>
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<span class="r-out co"><span class="r-pr">#></span> [13] <=0.5 <=0.5 <=0.5 <=0.5 1 <=0.5 <=0.5 <=0.5 <=0.5 1 1 <=0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> [25] <=0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] <=2 <=2 4 <=2 <=2 4 <=2 4 <=2 4 <=2 <=2 <=2 <=2 <=2 <=2 4 4 <=2</span>
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<span class="r-out co"><span class="r-pr">#></span> [20] 4 <=2 <=2 <=2 <=2 <=2</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 1 1 1 >=2 >=2 >=2 1 >=2 1 1 >=2 1 1 1 >=2 1 1 1 </span>
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<span class="r-out co"><span class="r-pr">#></span> [20] >=2 >=2 1 1 1 1 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 2 <=0.064 1 <=0.064 <=0.064 2 <=0.064 0.25 0.25 </span>
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<span class="r-out co"><span class="r-pr">#></span> [10] 2 <=0.064 <=0.064 <=0.064 <=0.064 0.25 0.5 0.5 0.25 </span>
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<span class="r-out co"><span class="r-pr">#></span> [19] 0.125 0.125 4 0.25 1 <=0.064 <=0.064</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] 28 12 30 26 9 34 30 19 32 31 33 34 30 19 15 24 18 34 12 32 29 33 29 32 17</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 14 19 19 33 33 26 16 27 29 33 24 17 17 15 16 26 26 14 17 29 25 25 24 32 32</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] 18 15 19 13 22 20 22 13 18 14 19 13 12 22 20 21 12 20 18 19 20 22 18 17 20</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 22 15 21 11 19 20 11 14 12 12 17 16 12 10 15 22 19 21 19 17 18 19 21 17 21</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] 21 31 27 28 30 34 16 32 28 25 25 23 29 26 24 28 27 33 30 19 30 22 27 22 32</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 21 25 16 29 27 24 31 22 35 28 26 32 24 18 35 33 24 28 33 25 35 25 32 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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