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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="">1.8.2.9074</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9076</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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@ -75,17 +75,17 @@
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<a class="dropdown-item" href="../reference/mo_property.html">
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<span class="fa fa-bug"></span>
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Get properties of a microorganism
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Get taxonomy of a microorganism
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</a>
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<a class="dropdown-item" href="../reference/ab_property.html">
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<span class="fa fa-capsules"></span>
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Get properties of an antibiotic
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Get properties of an antibiotic drug
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</a>
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<a class="dropdown-item" href="../reference/av_property.html">
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<span class="fa fa-capsules"></span>
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Get properties of an antiviral agent
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Get properties of an antiviral drug
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</a>
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</div>
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</li>
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@ -183,42 +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] 2 64 0.025 0.5 0.001 0.001 >=128 >=128 4 0.5 0.002 0.01 </span>
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<span class="r-out co"><span class="r-pr">#></span> [13] 4 32 32 0.125 0.125 0.005 2 16 0.001 0.125 0.002 0.01 </span>
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<span class="r-out co"><span class="r-pr">#></span> [25] 0.01 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.005 1 0.001 0.025 64 1 16 8 8 64 0.002 4 </span>
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<span class="r-out co"><span class="r-pr">#></span> [13] 8 32 0.001 1 16 0.025 0.125 0.125 2 1 0.025 0.25 </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-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] 7 27 48 15 19 48 10 49 9 18 37 43 23 37 26 29 6 40 36 19 36 10 33 18 32</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 37 44 22 48 24 19 46 27 48 14 15 42 48 37 44 10 45 14 38 37 42 16 50 45 46</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 R R I S R I I I S S S R S S I S I I R S R I I S</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] I R I S R I I S I S R R S S S R R R I R I S S 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] 64 0.005 4 4 0.002 0.001 8 64 32 0.005 </span>
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<span class="r-out co"><span class="r-pr">#></span> [11] 1 0.025 0.01 2 0.01 0.5 64 4 8 0.002 </span>
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<span class="r-out co"><span class="r-pr">#></span> [21] 64 0.01 0.005 0.5 0.0625</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.5 0.01 32 0.125 <=0.001 64 0.025 0.125 8 </span>
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<span class="r-out co"><span class="r-pr">#></span> [10] 8 1 0.25 8 0.25 1 1 16 4 </span>
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<span class="r-out co"><span class="r-pr">#></span> [19] 0.25 0.0625 0.025 0.025 0.5 0.025 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] 16 16 1 2 2 16 16 8 2 2 >=32 4 1 4 16 </span>
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<span class="r-out co"><span class="r-pr">#></span> [16] 16 16 2 1 2 16 8 16 2 8 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 4 1 1 8 8 4 >=16 4 4 8 </span>
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<span class="r-out co"><span class="r-pr">#></span> [11] 8 <=0.25 2 4 >=16 <=0.25 0.5 2 1 8 </span>
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<span class="r-out co"><span class="r-pr">#></span> [21] 1 2 0.5 4 >=16 </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] 1 0.125 8 0.0625 0.025 0.025 0.5 8 0.125 0.5 </span>
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<span class="r-out co"><span class="r-pr">#></span> [11] 8 1 0.5 0.125 1 0.25 8 0.0625 2 2 </span>
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<span class="r-out co"><span class="r-pr">#></span> [21] 0.125 0.0625 1 4 0.125 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 1 0.25 2 0.125 2 2 2 4 0.25 2 1 0.5 </span>
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<span class="r-out co"><span class="r-pr">#></span> [13] 4 8 2 8 0.5 1 8 4 4 0.25 2 1 </span>
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<span class="r-out co"><span class="r-pr">#></span> [25] >=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] 42 27 16 43 29 46 49 22 27 8 36 28 40 44 41 8 12 45 44 42 38 49 24 40 10</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 46 29 42 21 45 46 44 26 15 19 40 14 38 48 19 49 46 13 21 44 21 36 13 41 42</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] 13 16 16 11 17 17 14 14 11 13 15 15 12 12 11 12 16 14 17 15 15 14 14 12 14</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 14 13 11 11 12 15 14 13 15 11 15 17 16 13 13 13 11 11 16 17 15 17 16 13 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] 27 17 19 26 24 23 23 25 17 27 15 15 26 20 19 26 22 19 18 26 21 20 17 24 23</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 25 23 16 16 27 17 27 17 23 22 26 19 21 17 18 20 17 18 21 19 23 23 27 18 23</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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