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@@ -35,11 +35,11 @@
<a href="#main" class="visually-hidden-focusable">Skip to contents</a>
<nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary"><div class="container">
<nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-primary" data-bs-theme="dark"><div class="container">
<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="">2.1.1.9018</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9021</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">
@@ -402,19 +402,19 @@ names or codes, this would have worked exactly the same way:</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">#&gt; rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
<span><span class="co">#&gt; 1 I I I S I I</span></span>
<span><span class="co">#&gt; 2 S I S R S R</span></span>
<span><span class="co">#&gt; 3 I I I I I I</span></span>
<span><span class="co">#&gt; 4 S R R R R I</span></span>
<span><span class="co">#&gt; 5 I S I S S R</span></span>
<span><span class="co">#&gt; 6 R I S I R S</span></span>
<span><span class="co">#&gt; 1 I R S S S S</span></span>
<span><span class="co">#&gt; 2 S S I R R S</span></span>
<span><span class="co">#&gt; 3 R I I I R I</span></span>
<span><span class="co">#&gt; 4 I S S S S S</span></span>
<span><span class="co">#&gt; 5 I I I S I S</span></span>
<span><span class="co">#&gt; 6 R S R S I I</span></span>
<span><span class="co">#&gt; kanamycin</span></span>
<span><span class="co">#&gt; 1 I</span></span>
<span><span class="co">#&gt; 2 R</span></span>
<span><span class="co">#&gt; 1 R</span></span>
<span><span class="co">#&gt; 2 I</span></span>
<span><span class="co">#&gt; 3 S</span></span>
<span><span class="co">#&gt; 4 R</span></span>
<span><span class="co">#&gt; 4 I</span></span>
<span><span class="co">#&gt; 5 I</span></span>
<span><span class="co">#&gt; 6 R</span></span></code></pre></div>
<span><span class="co">#&gt; 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">
@@ -455,40 +455,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3224</td>
<td align="right">64.48%</td>
<td align="right">3224</td>
<td align="right">64.48%</td>
<td align="right">3223</td>
<td align="right">64.46%</td>
<td align="right">3223</td>
<td align="right">64.46%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">988</td>
<td align="right">19.76%</td>
<td align="right">4212</td>
<td align="right">84.24%</td>
<td align="right">967</td>
<td align="right">19.34%</td>
<td align="right">4190</td>
<td align="right">83.80%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">460</td>
<td align="right">9.20%</td>
<td align="right">4672</td>
<td align="right">93.44%</td>
<td align="right">454</td>
<td align="right">9.08%</td>
<td align="right">4644</td>
<td align="right">92.88%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">234</td>
<td align="right">4.68%</td>
<td align="right">4906</td>
<td align="right">98.12%</td>
<td align="right">245</td>
<td align="right">4.90%</td>
<td align="right">4889</td>
<td align="right">97.78%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">94</td>
<td align="right">1.88%</td>
<td align="right">111</td>
<td align="right">2.22%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>