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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="">1.8.2.9098</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9099</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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@ -32,60 +32,65 @@
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How to
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</a>
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<div class="dropdown-menu" aria-labelledby="dropdown--how-to">
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<a class="dropdown-item" href="../reference/AMR-options.html">
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<span class="fa fa-gear"></span>
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User- Or Team-specific Package Settings
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</a>
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<a class="dropdown-item" href="../articles/AMR.html">
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<span class="fa fa-directions"></span>
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Conduct AMR analysis
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Conduct AMR Analysis
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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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Predict antimicrobial resistance
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Predict Antimicrobial Resistance
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</a>
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<a class="dropdown-item" href="../articles/datasets.html">
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<span class="fa fa-database"></span>
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Data sets for download / own use
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Data Sets for Download / Own Use
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</a>
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<a class="dropdown-item" href="../articles/PCA.html">
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<span class="fa fa-compress"></span>
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Conduct principal component analysis for AMR
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Conduct Principal Component Analysis for AMR
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</a>
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<a class="dropdown-item" href="../articles/MDR.html">
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<span class="fa fa-skull-crossbones"></span>
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Determine multi-drug resistance (MDR)
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Determine Multi-Drug Resistance (MDR)
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</a>
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<a class="dropdown-item" href="../articles/WHONET.html">
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<span class="fa fa-globe-americas"></span>
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Work with WHONET data
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Work with WHONET Data
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</a>
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<a class="dropdown-item" href="../articles/SPSS.html">
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<span class="fa fa-file-upload"></span>
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Import data from SPSS/SAS/Stata
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Import Data From SPSS/SAS/Stata
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</a>
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<a class="dropdown-item" href="../articles/EUCAST.html">
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<span class="fa fa-exchange-alt"></span>
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Apply EUCAST rules
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Apply Eucast Rules
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</a>
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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 taxonomy 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 drug
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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 drug
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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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@ -183,41 +188,42 @@
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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] 4 >=128 0.0625 0.005 1 <=0.002 0.005 64 <=0.002</span>
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<span class="r-out co"><span class="r-pr">#></span> [10] 0.5 64 1 0.125 0.01 4 0.01 0.005 64 </span>
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<span class="r-out co"><span class="r-pr">#></span> [19] 64 64 64 16 64 0.125 2 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 64 0.01 64 0.005 0.125 <=0.001 0.25 128 0.025 </span>
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<span class="r-out co"><span class="r-pr">#></span> [10] 0.005 1 64 0.0625 1 0.005 8 >=256 128 </span>
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<span class="r-out co"><span class="r-pr">#></span> [19] 0.025 >=256 0.5 4 16 2 4 </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] 47 13 36 12 41 13 11 37 13 47 39 16 10 46 22 36 16 46 16 44 47 12 40 18 24</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 27 23 46 49 8 14 18 19 42 37 46 37 26 31 39 50 23 50 44 45 46 37 41 34 14</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 S I S S S S S R I R I I S R R S I S R R S I R I</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] R R R I R S S I S R I I I S S S R R R S I S S I 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] 2 0.025 1 2 64 0.25 16 4 128 </span>
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<span class="r-out co"><span class="r-pr">#></span> [10] 32 0.0625 4 0.0625 2 1 <=0.005 0.01 0.125 </span>
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<span class="r-out co"><span class="r-pr">#></span> [19] 16 4 0.025 4 4 32 16 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] <=0.001 0.25 4 1 >=128 0.0625 0.01 0.002 0.025 </span>
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<span class="r-out co"><span class="r-pr">#></span> [10] 0.0625 0.0625 0.25 0.125 0.25 0.01 0.025 0.125 0.0625 </span>
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<span class="r-out co"><span class="r-pr">#></span> [19] <=0.001 0.002 2 32 64 32 4 </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] 2 2 8 16 8 8 16 4 4 2 4 8 16 4 8 8 1 16 16 2 1 2 4 1 16</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 2 16 4 2 16 32 8 8 16 >=64 >=64 4 8 16 <=1 </span>
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<span class="r-out co"><span class="r-pr">#></span> [16] <=1 >=64 >=64 >=64 >=64 32 2 4 >=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">"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 1 2 <=0.125 0.5 2 1 0.5 0.25 </span>
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<span class="r-out co"><span class="r-pr">#></span> [10] <=0.125 2 0.25 <=0.125 <=0.125 2 2 <=0.125 >=4 </span>
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<span class="r-out co"><span class="r-pr">#></span> [19] 2 0.5 <=0.125 0.5 0.5 1 2 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 8 1 0.125 1 1 0.125 0.025 0.0625 0.125 8 </span>
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<span class="r-out co"><span class="r-pr">#></span> [11] 0.5 0.25 0.0625 0.0625 0.125 4 0.0625 8 0.25 0.0625</span>
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<span class="r-out co"><span class="r-pr">#></span> [21] 0.125 1 8 0.25 1 </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] 27 43 17 42 21 27 42 19 21 17 26 40 14 9 34 16 49 30 41 31 40 43 46 45 8</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 43 49 26 44 44 15 26 44 43 22 42 10 37 42 48 47 13 31 48 35 32 49 34 37 44</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] 15 11 13 11 11 12 17 11 12 12 17 17 16 14 14 16 14 15 12 17 15 15 16 12 15</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 16 17 16 12 17 14 13 11 15 15 12 13 16 14 11 11 15 17 16 17 17 14 13 11 11</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] 26 20 19 18 19 25 22 23 19 18 15 25 19 18 22 24 16 22 26 22 21 21 23 23 23</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 16 21 25 21 19 15 26 27 27 26 15 27 18 19 17 25 25 26 18 24 17 21 18 16 17</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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