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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="">1.8.2.9103</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</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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@ -42,6 +42,11 @@
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Conduct AMR Analysis
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</a>
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<a class="dropdown-item" href="../reference/antibiogram.html">
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<span class="fa fa-file-prescription"></span>
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Generate Antibiogram (Trad./Syndromic/WISCA)
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</a>
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<a class="dropdown-item" href="../articles/resistance_predict.html">
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<span class="fa fa-dice"></span>
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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] 16 0.01 0.025 0.25 0.01 0.0625 0.001 16 0.01 128 </span>
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<span class="r-out co"><span class="r-pr">#></span> [11] 16 64 0.01 0.5 0.005 4 64 0.002 0.125 0.01 </span>
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<span class="r-out co"><span class="r-pr">#></span> [21] 0.0625 0.001 0.025 0.5 >=256 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 4 0.25 0.002 0.25 0.125 8 0.5 0.125 32 256 </span>
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<span class="r-out co"><span class="r-pr">#></span> [11] 256 8 0.0625 2 0.5 8 0.001 128 256 0.005 </span>
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<span class="r-out co"><span class="r-pr">#></span> [21] 0.01 128 0.002 0.01 0.001 </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] 41 50 9 45 7 8 44 29 22 7 44 30 28 20 38 50 38 40 18 12 13 35 50 8 12</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 28 47 9 12 25 45 46 47 21 41 31 50 48 49 30 37 42 41 35 28 48 40 44 44 29</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] S I S R S I S R S R S R I I S S I S S I I S S S R</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] S S I R R I I I R R R R S S R R I I R S I R R I 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"># \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] 32 0.01 0.5 8 2 16 0.01 0.005 >=64 0.025 </span>
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<span class="r-out co"><span class="r-pr">#></span> [11] 0.01 0.0625 >=64 2 0.025 16 8 0.001 0.01 >=64 </span>
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<span class="r-out co"><span class="r-pr">#></span> [21] 1 32 2 >=64 0.25 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.01 1 4 0.025 16 0.0625 2 16 0.25 </span>
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<span class="r-out co"><span class="r-pr">#></span> [10] 8 0.0625 1 4 16 32 0.125 4 16 </span>
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<span class="r-out co"><span class="r-pr">#></span> [19] 0.5 1 32 16 <=0.001 0.005 >=64 </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] 8 32 >=64 8 <=1 2 2 <=1 8 8 16 2 32 4 2 </span>
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<span class="r-out co"><span class="r-pr">#></span> [16] <=1 8 <=1 <=1 32 4 4 >=64 32 16 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 16 1 4 16 8 2 1 8 8 16 8 1 1 4 4 4 2 16 1 1 2 4 8 1 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] 0.25 0.25 0.5 0.25 0.125 4 8 8 </span>
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<span class="r-out co"><span class="r-pr">#></span> [9] 1 0.125 1 <=0.0625 4 <=0.0625 <=0.0625 1 </span>
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<span class="r-out co"><span class="r-pr">#></span> [17] 0.125 1 0.125 2 2 4 4 1 </span>
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<span class="r-out co"><span class="r-pr">#></span> [25] 8 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 8 1 0.25 0.0625 1 4 8 2 0.25 1 </span>
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<span class="r-out co"><span class="r-pr">#></span> [11] 8 0.25 4 0.025 0.25 0.25 16 0.125 1 16 </span>
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<span class="r-out co"><span class="r-pr">#></span> [21] 0.025 4 0.5 16 16 </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] 12 46 47 45 33 42 43 46 46 50 41 41 50 21 50 33 17 18 43 25 47 8 25 22 50</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 19 49 18 32 43 23 48 48 45 26 18 18 34 34 43 16 43 44 49 47 35 39 32 19 23</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] 11 15 16 16 16 15 16 16 11 15 15 11 12 16 16 13 15 14 17 14 17 12 15 13 15</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 16 12 16 11 14 12 13 11 13 15 17 16 14 12 12 16 15 14 13 15 17 16 15 17 14</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] 16 25 17 26 18 23 20 17 15 24 20 23 20 16 24 27 25 17 23 25 25 25 24 25 17</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 19 18 24 25 20 16 15 20 19 18 18 17 24 21 24 16 24 22 19 18 26 27 27 25 16</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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