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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9006</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -314,19 +314,19 @@ Unique: 2</p>
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<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>
<span><span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
<span><span class="co"># 1 I I I I I S</span></span>
<span><span class="co"># 2 R R S R R S</span></span>
<span><span class="co"># 3 I S I S R I</span></span>
<span><span class="co"># 4 S I S I S R</span></span>
<span><span class="co"># 5 R S R S S R</span></span>
<span><span class="co"># 6 I I R R R S</span></span>
<span><span class="co"># 1 I R S R I S</span></span>
<span><span class="co"># 2 I S S S S S</span></span>
<span><span class="co"># 3 R I R I S I</span></span>
<span><span class="co"># 4 R I R R S R</span></span>
<span><span class="co"># 5 S S S I R I</span></span>
<span><span class="co"># 6 I S I I S R</span></span>
<span><span class="co"># kanamycin</span></span>
<span><span class="co"># 1 R</span></span>
<span><span class="co"># 2 I</span></span>
<span><span class="co"># 3 R</span></span>
<span><span class="co"># 4 S</span></span>
<span><span class="co"># 5 R</span></span>
<span><span class="co"># 6 R</span></span></code></pre></div>
<span><span class="co"># 2 S</span></span>
<span><span class="co"># 3 S</span></span>
<span><span class="co"># 4 R</span></span>
<span><span class="co"># 5 S</span></span>
<span><span class="co"># 6 I</span></span></code></pre></div>
<p>We can now add the interpretation of MDR-TB to our data set. You can use:</p>
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/mdro.html">mdro</a></span><span class="op">(</span><span class="va">my_TB_data</span>, guideline <span class="op">=</span> <span class="st">"TB"</span><span class="op">)</span></span></code></pre></div>
@ -357,40 +357,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3139</td>
<td align="right">62.78%</td>
<td align="right">3139</td>
<td align="right">62.78%</td>
<td align="right">3309</td>
<td align="right">66.18%</td>
<td align="right">3309</td>
<td align="right">66.18%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">1034</td>
<td align="right">20.68%</td>
<td align="right">4173</td>
<td align="right">83.46%</td>
<td align="right">923</td>
<td align="right">18.46%</td>
<td align="right">4232</td>
<td align="right">84.64%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">469</td>
<td align="right">9.38%</td>
<td align="right">4642</td>
<td align="right">92.84%</td>
<td align="right">452</td>
<td align="right">9.04%</td>
<td align="right">4684</td>
<td align="right">93.68%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">250</td>
<td align="right">5.00%</td>
<td align="right">4892</td>
<td align="right">97.84%</td>
<td align="right">221</td>
<td align="right">4.42%</td>
<td align="right">4905</td>
<td align="right">98.10%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">108</td>
<td align="right">2.16%</td>
<td align="right">95</td>
<td align="right">1.90%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>