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@ -10,7 +10,7 @@
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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="">1.8.2.9060</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9061</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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@ -183,43 +183,43 @@
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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] 0.0625 128 2 4 16 2 4 16 1 0.25 </span>
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<span class="r-out co"><span class="r-pr">#></span> [11] 8 0.01 0.002 16 8 32 128 0.5 4 128 </span>
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<span class="r-out co"><span class="r-pr">#></span> [21] >=256 >=256 2 0.005 0.001 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.001 0.0625 0.002 0.005 0.01 0.25 128 0.125 0.002 0.0625</span>
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<span class="r-out co"><span class="r-pr">#></span> [11] 0.025 0.25 >=256 64 0.002 0.0625 1 0.25 0.01 4 </span>
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<span class="r-out co"><span class="r-pr">#></span> [21] 4 1 0.5 0.002 0.025 </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] 22 40 45 27 37 43 39 32 34 49 43 14 41 11 29 13 27 8 16 45 7 11 23 39 50</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 43 6 16 49 45 14 26 43 40 22 38 32 15 38 8 47 17 22 50 50 37 32 36 18 14</span>
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<span class="r-in"><span><span class="fu">random_rsi</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 'rsi'</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] I S R S S I R R I R R R R R S S R S I I S I R S R</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] S R I S R S I S R R I I R S I S I R R I R S R S I</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] 16 0.01 0.025 16 0.0625 >=64 8 16 0.001 0.001 </span>
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<span class="r-out co"><span class="r-pr">#></span> [11] 1 4 0.025 0.125 0.005 >=64 0.005 0.25 >=64 4 </span>
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<span class="r-out co"><span class="r-pr">#></span> [21] 16 0.01 0.001 0.001 0.125 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.0625 0.01 0.01 1 64 1 64 64 2 </span>
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<span class="r-out co"><span class="r-pr">#></span> [10] 0.002 <=0.001 4 2 1 <=0.001 0.25 0.005 0.125 </span>
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<span class="r-out co"><span class="r-pr">#></span> [19] 0.025 2 16 0.5 0.5 64 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">"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 4 2 0.5 4 16 2 4 0.5 >=32 0.5 8 >=32 4 >=32</span>
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<span class="r-out co"><span class="r-pr">#></span> [16] 16 1 0.5 0.5 2 16 8 16 4 4 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 8 8 <=0.5 >=16 <=0.5 <=0.5 8 <=0.5 <=0.5 8 1 >=16 </span>
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<span class="r-out co"><span class="r-pr">#></span> [13] >=16 4 4 1 1 8 >=16 8 4 4 >=16 2 </span>
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<span class="r-out co"><span class="r-pr">#></span> [25] 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] 4 <=0.0625 <=0.0625 <=0.0625 >=16 4 2 0.5 </span>
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<span class="r-out co"><span class="r-pr">#></span> [9] 0.125 2 2 4 0.125 <=0.0625 0.125 0.5 </span>
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<span class="r-out co"><span class="r-pr">#></span> [17] 0.5 8 1 1 0.25 0.125 0.5 4 </span>
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<span class="r-out co"><span class="r-pr">#></span> [25] <=0.0625</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 1 0.25 1 2 2 1 1 1 8 </span>
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<span class="r-out co"><span class="r-pr">#></span> [10] 2 2 8 1 0.25 2 0.5 0.25 0.25 </span>
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<span class="r-out co"><span class="r-pr">#></span> [19] 2 0.25 0.25 0.0625 1 <=0.025 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] 20 11 47 15 29 47 48 15 19 13 21 46 38 48 14 39 49 34 41 39 49 42 10 44 44</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 13 40 38 28 44 48 11 44 45 45 24 49 41 50 8 42 40 47 41 50 45 40 31 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">"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] 16 11 12 12 14 14 15 15 13 17 14 17 16 12 12 15 13 13 13 17 17 14 17 14 17</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 15 17 15 13 12 13 12 14 12 17 17 17 13 12 15 12 17 11 11 15 14 14 14 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] 23 26 20 22 25 18 23 18 15 17 22 21 18 25 21 22 21 17 26 15 15 20 19 20 23</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 23 16 15 25 26 17 26 18 18 19 20 16 17 20 23 16 19 15 26 15 24 17 27 22 20</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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@ -228,11 +228,11 @@
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<footer><div class="pkgdown-footer-left">
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<p></p><p><code>AMR</code> (for R). Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> in collaboration with non-profit organisations<br><a target="_blank" href="https://www.certe.nl" class="external-link">Certe Medical Diagnostics and Advice Foundation</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>.</p>
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<p></p><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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</div>
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<div class="pkgdown-footer-right">
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<p></p><p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_rug.svg" style="max-width: 150px;"></a></p>
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<p></p><p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_rug.svg" style="max-width: 150px;"></a><a target="_blank" href="https://www.umcg.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_umcg.svg" style="max-width: 150px;"></a></p>
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</div>
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</footer></div>
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