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dr. M.S. (Matthijs) Berends
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@ -39,7 +39,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9002</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9005</span>
</span>
</div>
@ -75,6 +75,13 @@
Predict antimicrobial resistance
</a>
</li>
<li>
<a href="../articles/datasets.html">
<span class="fa fa-database"></span>
Download our reference data sets for own use
</a>
</li>
<li>
<a href="../articles/PCA.html">
<span class="fa fa-compress"></span>
@ -184,9 +191,7 @@
<div class="col-md-9 contents">
<div class="page-header toc-ignore">
<h1 data-toc-skip>How to determine multi-drug resistance (MDR)</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">14 August 2020</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/MDR.Rmd"><code>vignettes/MDR.Rmd</code></a></small>
<div class="hidden name"><code>MDR.Rmd</code></div>
@ -315,19 +320,19 @@ Unique: 2</p>
<div class="sourceCode" id="cb5"><pre class="downlit">
<span class="fu"><a href="https://rdrr.io/r/utils/head.html">head</a></span>(<span class="kw">my_TB_data</span>)
<span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span>
<span class="co"># 1 R R R R R S</span>
<span class="co"># 2 S R S I I S</span>
<span class="co"># 3 R R R S S S</span>
<span class="co"># 4 S I S R I S</span>
<span class="co"># 5 S R R R S R</span>
<span class="co"># 6 S S R S S R</span>
<span class="co"># 1 S S S S S R</span>
<span class="co"># 2 S R S R S S</span>
<span class="co"># 3 R S S S I R</span>
<span class="co"># 4 R S R S R R</span>
<span class="co"># 5 R S S R S R</span>
<span class="co"># 6 S R I S R S</span>
<span class="co"># kanamycin</span>
<span class="co"># 1 S</span>
<span class="co"># 2 I</span>
<span class="co"># 2 R</span>
<span class="co"># 3 R</span>
<span class="co"># 4 R</span>
<span class="co"># 5 S</span>
<span class="co"># 6 I</span>
<span class="co"># 4 S</span>
<span class="co"># 5 R</span>
<span class="co"># 6 R</span>
</pre></div>
<p>We can now add the interpretation of MDR-TB to our data set. You can use:</p>
<div class="sourceCode" id="cb6"><pre class="downlit">
@ -363,40 +368,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3241</td>
<td align="right">64.82%</td>
<td align="right">3241</td>
<td align="right">64.82%</td>
<td align="right">3203</td>
<td align="right">64.06%</td>
<td align="right">3203</td>
<td align="right">64.06%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">642</td>
<td align="right">12.84%</td>
<td align="right">3883</td>
<td align="right">77.66%</td>
<td align="right">682</td>
<td align="right">13.64%</td>
<td align="right">3885</td>
<td align="right">77.70%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">595</td>
<td align="right">11.90%</td>
<td align="right">4478</td>
<td align="right">89.56%</td>
<td align="right">627</td>
<td align="right">12.54%</td>
<td align="right">4512</td>
<td align="right">90.24%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">311</td>
<td align="right">6.22%</td>
<td align="right">4789</td>
<td align="right">95.78%</td>
<td align="right">268</td>
<td align="right">5.36%</td>
<td align="right">4780</td>
<td align="right">95.60%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">211</td>
<td align="right">4.22%</td>
<td align="right">220</td>
<td align="right">4.40%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>