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@ -38,7 +38,7 @@
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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="">1.8.2.9095</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9096</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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@ -348,46 +348,46 @@ Unique: 2</p>
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<p>For another example, I will create a data set to determine multi-drug
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resistant TB:</p>
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<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
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<code class="sourceCode R"><span><span class="co"># random_rsi() is a helper function to generate</span></span>
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<code class="sourceCode R"><span><span class="co"># random_sir() is a helper function to generate</span></span>
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<span><span class="co"># a random vector with values S, I and R</span></span>
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<span><span class="va">my_TB_data</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span>
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<span> rifampicin <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
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<span> isoniazid <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
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<span> gatifloxacin <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
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<span> ethambutol <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
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<span> pyrazinamide <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
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<span> moxifloxacin <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
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<span> kanamycin <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span></span>
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<span> rifampicin <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_sir</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
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<span> isoniazid <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_sir</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
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<span> gatifloxacin <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_sir</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
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<span> ethambutol <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_sir</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
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<span> pyrazinamide <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_sir</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
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<span> moxifloxacin <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_sir</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
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<span> kanamycin <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_sir</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span></span>
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<span><span class="op">)</span></span></code></pre></div>
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<p>Because all column names are automatically verified for valid drug
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names or codes, this would have worked exactly the same way:</p>
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<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
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<code class="sourceCode R"><span><span class="va">my_TB_data</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span>
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<span> RIF <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
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<span> INH <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
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<span> GAT <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
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<span> ETH <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
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<span> PZA <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
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<span> MFX <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
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<span> KAN <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span></span>
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<span> RIF <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_sir</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
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<span> INH <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_sir</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
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<span> GAT <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_sir</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
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<span> ETH <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_sir</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
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<span> PZA <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_sir</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
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<span> MFX <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_sir</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,</span>
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<span> KAN <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_sir</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span></span>
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<span><span class="op">)</span></span></code></pre></div>
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<p>The data set now looks like this:</p>
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<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
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<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span></span>
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<span><span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
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<span><span class="co"># 1 R I I I R I</span></span>
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<span><span class="co"># 2 I R I I R S</span></span>
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<span><span class="co"># 3 R S I S S I</span></span>
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<span><span class="co"># 4 S R S R I I</span></span>
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<span><span class="co"># 5 S R R R I I</span></span>
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<span><span class="co"># 6 R I S S S R</span></span>
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<span><span class="co"># 1 I S S I S I</span></span>
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<span><span class="co"># 2 R R R R I S</span></span>
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<span><span class="co"># 3 R I R R I R</span></span>
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<span><span class="co"># 4 R S I S S I</span></span>
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<span><span class="co"># 5 I I S S S I</span></span>
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<span><span class="co"># 6 I I I R R I</span></span>
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<span><span class="co"># kanamycin</span></span>
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<span><span class="co"># 1 I</span></span>
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<span><span class="co"># 2 I</span></span>
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<span><span class="co"># 3 S</span></span>
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<span><span class="co"># 4 I</span></span>
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<span><span class="co"># 1 S</span></span>
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<span><span class="co"># 2 S</span></span>
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<span><span class="co"># 3 I</span></span>
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<span><span class="co"># 4 R</span></span>
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<span><span class="co"># 5 I</span></span>
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<span><span class="co"># 6 I</span></span></code></pre></div>
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<span><span class="co"># 6 S</span></span></code></pre></div>
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<p>We can now add the interpretation of MDR-TB to our data set. You can
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use:</p>
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<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
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@ -428,40 +428,40 @@ Unique: 5</p>
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<tr class="odd">
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<td align="left">1</td>
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<td align="left">Mono-resistant</td>
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<td align="right">3201</td>
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<td align="right">64.02%</td>
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<td align="right">3201</td>
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<td align="right">64.02%</td>
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<td align="right">3238</td>
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<td align="right">64.76%</td>
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<td align="right">3238</td>
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<td align="right">64.76%</td>
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</tr>
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<tr class="even">
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<td align="left">2</td>
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<td align="left">Negative</td>
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<td align="right">981</td>
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<td align="right">19.62%</td>
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<td align="right">4182</td>
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<td align="right">83.64%</td>
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<td align="right">994</td>
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<td align="right">19.88%</td>
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<td align="right">4232</td>
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<td align="right">84.64%</td>
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</tr>
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<tr class="odd">
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<td align="left">3</td>
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<td align="left">Multi-drug-resistant</td>
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<td align="right">441</td>
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<td align="right">8.82%</td>
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<td align="right">4623</td>
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<td align="right">92.46%</td>
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<td align="right">425</td>
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<td align="right">8.50%</td>
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<td align="right">4657</td>
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<td align="right">93.14%</td>
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</tr>
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<tr class="even">
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<td align="left">4</td>
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<td align="left">Poly-resistant</td>
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<td align="right">258</td>
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<td align="right">5.16%</td>
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<td align="right">4881</td>
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<td align="right">97.62%</td>
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<td align="right">247</td>
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<td align="right">4.94%</td>
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<td align="right">4904</td>
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<td align="right">98.08%</td>
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</tr>
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<tr class="odd">
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<td align="left">5</td>
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<td align="left">Extensively drug-resistant</td>
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<td align="right">119</td>
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<td align="right">2.38%</td>
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<td align="right">96</td>
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<td align="right">1.92%</td>
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<td align="right">5000</td>
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<td align="right">100.00%</td>
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</tr>
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