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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="">3.0.1.9063</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9065</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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@@ -123,15 +123,15 @@
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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 <span style="color: #0000BB;"><mic></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 1 0.032 0.064 1 0.25 0.125 >=128 0.0002 32 0.25 </span>
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<span class="r-out co"><span class="r-pr">#></span> [11] 0.008 0.125 0.001 0.032 8 >=128 0.032 0.008 8 >=128 </span>
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<span class="r-out co"><span class="r-pr">#></span> [21] 0.125 0.0001 0.5 64 1 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.25 0.064 0.5 0.004 0.0001 0.032 0.008 16 0.016 0.125 </span>
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<span class="r-out co"><span class="r-pr">#></span> [11] 0.0002 0.001 0.008 0.004 0.064 256 0.5 32 512 0.0002</span>
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<span class="r-out co"><span class="r-pr">#></span> [21] 0.004 1 0.002 0.0005 0.064 </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 <span style="color: #0000BB;"><disk></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 49 39 29 30 16 23 44 50 25 28 29 14 44 34 8 33 33 34 38 42 10 42 43 11 46</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 49 44 31 11 27 33 39 24 19 43 30 44 33 31 22 13 37 19 26 29 44 12 46 18 27</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 <span style="color: #0000BB;"><sir></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] I S S S R R S R I I I I S R S I S S S R R I R S I</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] I R I S R S R R I R R I S S S I R R S I R S 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"># 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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@@ -144,30 +144,28 @@
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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 <span style="color: #0000BB;"><mic></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 256 <=0.0001 <=0.0001 0.016 1 0.016 2 8 </span>
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<span class="r-out co"><span class="r-pr">#></span> [9] 0.5 0.004 0.032 0.004 0.001 0.001 0.064 0.002 </span>
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<span class="r-out co"><span class="r-pr">#></span> [17] 0.032 0.004 0.008 16 0.125 <=0.0001 0.001 0.008 </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] 0.004 0.0002 0.008 0.25 0.0005 0.0002 8 0.032 0.0005 0.016 </span>
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<span class="r-out co"><span class="r-pr">#></span> [11] 0.032 32 1 0.0005 0.016 0.002 0.016 0.0005 0.004 0.25 </span>
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<span class="r-out co"><span class="r-pr">#></span> [21] 0.0005 0.016 0.001 0.25 0.032 </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 <span style="color: #0000BB;"><mic></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.5 <=0.25 0.5 4 1 1 0.5 0.5 0.5 <=0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> [11] 0.5 0.5 2 1 <=0.25 <=0.25 8 <=0.25 1 1 </span>
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<span class="r-out co"><span class="r-pr">#></span> [21] <=0.25 0.5 16 2 0.5 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.5 >=1 0.5 0.5 0.5 0.5 >=1 0.5 0.5 0.5 0.5 0.5 0.5 0.5 >=1 0.5 >=1 0.5 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> [20] 0.5 0.5 >=1 >=1 >=1 >=1</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 <span style="color: #0000BB;"><mic></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.125 0.125 0.125 0.125 0.125 >=0.25 0.125 0.125 0.125 0.125 </span>
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<span class="r-out co"><span class="r-pr">#></span> [11] >=0.25 0.125 >=0.25 0.125 0.125 0.125 >=0.25 0.125 >=0.25 >=0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> [21] >=0.25 0.125 0.125 0.125 >=0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.25 <=0.125 <=0.125 0.25 0.25 <=0.125 0.25 0.25 0.25 </span>
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<span class="r-out co"><span class="r-pr">#></span> [10] 0.25 <=0.125 <=0.125 0.25 0.25 <=0.125 <=0.125 <=0.125 0.25 </span>
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<span class="r-out co"><span class="r-pr">#></span> [19] <=0.125 <=0.125 <=0.125 <=0.125 0.25 0.25 0.25 </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 <span style="color: #0000BB;"><disk></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 18 32 21 19 23 10 30 18 22 34 19 32 28 18 25 7 27 23 28 17 29 18 22 28 23</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 10 32 34 18 17 31 31 21 18 19 27 18 20 11 34 30 28 20 29 9 21 33 34 25 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">"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 <span style="color: #0000BB;"><disk></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 22 18 13 22 17 12 20 20 16 20 22 22 18 20 20 22 22 16 13 17 15 17 16 22 15</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 17 17 20 22 13 21 21 14 11 18 18 18 21 18 14 22 19 20 18 16 17 12 22 21 19</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 <span style="color: #0000BB;"><disk></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 31 30 30 28 24 35 28 34 28 29 27 29 24 21 13 16 34 19 26 20 27 32 32 24 26</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 24 31 26 26 33 16 29 17 28 27 27 35 33 33 29 32 18 33 33 29 28 32 25 17 31</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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@@ -176,7 +174,7 @@
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<footer><div class="pkgdown-footer-left">
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<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p>
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<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
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</div>
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<div class="pkgdown-footer-right">
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