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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="">1.8.2.9032</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9033</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 S R I S S S</span></span>
<span><span class="co"># 2 I S R R R S</span></span>
<span><span class="co"># 3 S R S S I S</span></span>
<span><span class="co"># 4 I R S S R S</span></span>
<span><span class="co"># 5 I S I S S R</span></span>
<span><span class="co"># 6 R I I S S I</span></span>
<span><span class="co"># 1 I S S R S R</span></span>
<span><span class="co"># 2 I R R R S S</span></span>
<span><span class="co"># 3 I I S S R R</span></span>
<span><span class="co"># 4 R R I I R I</span></span>
<span><span class="co"># 5 R I R S S R</span></span>
<span><span class="co"># 6 I I I S I I</span></span>
<span><span class="co"># kanamycin</span></span>
<span><span class="co"># 1 I</span></span>
<span><span class="co"># 2 S</span></span>
<span><span class="co"># 1 S</span></span>
<span><span class="co"># 2 I</span></span>
<span><span class="co"># 3 I</span></span>
<span><span class="co"># 4 S</span></span>
<span><span class="co"># 5 S</span></span>
<span><span class="co"># 6 I</span></span></code></pre></div>
<span><span class="co"># 5 I</span></span>
<span><span class="co"># 6 S</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">3216</td>
<td align="right">64.32%</td>
<td align="right">3216</td>
<td align="right">64.32%</td>
<td align="right">3193</td>
<td align="right">63.86%</td>
<td align="right">3193</td>
<td align="right">63.86%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">1022</td>
<td align="right">20.44%</td>
<td align="right">4238</td>
<td align="right">84.76%</td>
<td align="right">988</td>
<td align="right">19.76%</td>
<td align="right">4181</td>
<td align="right">83.62%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">414</td>
<td align="right">8.28%</td>
<td align="right">4652</td>
<td align="right">93.04%</td>
<td align="right">429</td>
<td align="right">8.58%</td>
<td align="right">4610</td>
<td align="right">92.20%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">239</td>
<td align="right">4.78%</td>
<td align="right">4891</td>
<td align="right">97.82%</td>
<td align="right">282</td>
<td align="right">5.64%</td>
<td align="right">4892</td>
<td align="right">97.84%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">109</td>
<td align="right">2.18%</td>
<td align="right">108</td>
<td align="right">2.16%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>