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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="">1.8.2.9074</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9076</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">
@ -104,17 +104,17 @@
<a class="dropdown-item" href="../reference/mo_property.html">
<span class="fa fa-bug"></span>
Get properties of a microorganism
Get taxonomy of a microorganism
</a>
<a class="dropdown-item" href="../reference/ab_property.html">
<span class="fa fa-capsules"></span>
Get properties of an antibiotic
Get properties of an antibiotic drug
</a>
<a class="dropdown-item" href="../reference/av_property.html">
<span class="fa fa-capsules"></span>
Get properties of an antiviral agent
Get properties of an antiviral drug
</a>
</div>
</li>
@ -375,19 +375,19 @@ 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"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
<span><span class="co"># 1 S R S S R R</span></span>
<span><span class="co"># 2 I S I S S R</span></span>
<span><span class="co"># 3 S I I R R S</span></span>
<span><span class="co"># 4 S R I R S R</span></span>
<span><span class="co"># 5 I R S S S I</span></span>
<span><span class="co"># 6 R R S I I I</span></span>
<span><span class="co"># 1 S S R S S S</span></span>
<span><span class="co"># 2 R I S S R I</span></span>
<span><span class="co"># 3 S S R S S R</span></span>
<span><span class="co"># 4 R R I S S I</span></span>
<span><span class="co"># 5 I S I I I S</span></span>
<span><span class="co"># 6 R R S R I I</span></span>
<span><span class="co"># kanamycin</span></span>
<span><span class="co"># 1 R</span></span>
<span><span class="co"># 1 I</span></span>
<span><span class="co"># 2 S</span></span>
<span><span class="co"># 3 I</span></span>
<span><span class="co"># 4 R</span></span>
<span><span class="co"># 5 S</span></span>
<span><span class="co"># 6 S</span></span></code></pre></div>
<span><span class="co"># 6 R</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">
@ -428,40 +428,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3249</td>
<td align="right">64.98%</td>
<td align="right">3249</td>
<td align="right">64.98%</td>
<td align="right">3144</td>
<td align="right">62.88%</td>
<td align="right">3144</td>
<td align="right">62.88%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">977</td>
<td align="right">19.54%</td>
<td align="right">4226</td>
<td align="right">84.52%</td>
<td align="right">1012</td>
<td align="right">20.24%</td>
<td align="right">4156</td>
<td align="right">83.12%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">420</td>
<td align="right">8.40%</td>
<td align="right">4646</td>
<td align="right">92.92%</td>
<td align="right">482</td>
<td align="right">9.64%</td>
<td align="right">4638</td>
<td align="right">92.76%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">249</td>
<td align="right">4.98%</td>
<td align="right">4895</td>
<td align="right">97.90%</td>
<td align="right">261</td>
<td align="right">5.22%</td>
<td align="right">4899</td>
<td align="right">97.98%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">105</td>
<td align="right">2.10%</td>
<td align="right">101</td>
<td align="right">2.02%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>