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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="">2.1.0.9001</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.0.9002</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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@ -328,7 +328,6 @@ on this data set, we get:</p>
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<span> <span class="fu"><a href="https://msberends.github.io/cleaner/reference/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="op">)</span> <span class="co"># show frequency table of the result</span></span>
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<span><span class="co">#> Warning: in mdro(): NA introduced for isolates where the available percentage of</span></span>
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<span><span class="co">#> antimicrobial classes was below 50% (set with pct_required_classes)</span></span></code></pre></div>
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<p>(16 isolates had no test results)</p>
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<p><strong>Frequency table</strong></p>
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<p>Class: factor > ordered (numeric)<br>
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Length: 2,000<br>
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@ -402,19 +401,19 @@ names or codes, this would have worked exactly the same way:</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 R S R S I</span></span>
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<span><span class="co">#> 2 I I S R I R</span></span>
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<span><span class="co">#> 3 R R R R S I</span></span>
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<span><span class="co">#> 4 S S I R R R</span></span>
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<span><span class="co">#> 5 I R R R I I</span></span>
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<span><span class="co">#> 6 I R I R R R</span></span>
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<span><span class="co">#> 1 R R S R I I</span></span>
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<span><span class="co">#> 2 I R R I R R</span></span>
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<span><span class="co">#> 3 S R S R R I</span></span>
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<span><span class="co">#> 4 S I I I S R</span></span>
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<span><span class="co">#> 5 S I R R R S</span></span>
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<span><span class="co">#> 6 R R I I R R</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 R</span></span>
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<span><span class="co">#> 1 S</span></span>
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<span><span class="co">#> 2 I</span></span>
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<span><span class="co">#> 3 R</span></span>
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<span><span class="co">#> 4 S</span></span>
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<span><span class="co">#> 5 S</span></span>
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<span><span class="co">#> 6 S</span></span></code></pre></div>
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<span><span class="co">#> 5 I</span></span>
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<span><span class="co">#> 6 R</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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@ -455,40 +454,40 @@ 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">3234</td>
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<td align="right">64.68%</td>
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<td align="right">3234</td>
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<td align="right">64.68%</td>
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<td align="right">3179</td>
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<td align="right">63.58%</td>
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<td align="right">3179</td>
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<td align="right">63.58%</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">943</td>
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<td align="right">18.86%</td>
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<td align="right">4177</td>
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<td align="right">83.54%</td>
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<td align="right">988</td>
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<td align="right">19.76%</td>
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<td align="right">4167</td>
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<td align="right">83.34%</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">475</td>
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<td align="right">9.50%</td>
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<td align="right">4652</td>
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<td align="right">93.04%</td>
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<td align="right">449</td>
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<td align="right">8.98%</td>
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<td align="right">4616</td>
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<td align="right">92.32%</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">262</td>
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<td align="right">5.24%</td>
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<td align="right">4914</td>
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<td align="right">98.28%</td>
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<td align="right">268</td>
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<td align="right">5.36%</td>
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<td align="right">4884</td>
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<td align="right">97.68%</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">86</td>
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<td align="right">1.72%</td>
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<td align="right">116</td>
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<td align="right">2.32%</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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