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dr. M.S. (Matthijs) Berends
2019-05-29 00:36:48 +02:00
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@ -40,7 +40,7 @@
</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="Released version">0.6.1.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9040</span>
</span>
</div>
@ -242,17 +242,17 @@
<p>The data set looks like this now:</p>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/head">head</a></span>(my_TB_data)</a>
<a class="sourceLine" id="cb3-2" title="2"><span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></a>
<a class="sourceLine" id="cb3-3" title="3"><span class="co"># 1 S S R S R S</span></a>
<a class="sourceLine" id="cb3-4" title="4"><span class="co"># 2 R R R S S R</span></a>
<a class="sourceLine" id="cb3-5" title="5"><span class="co"># 3 S S S S S S</span></a>
<a class="sourceLine" id="cb3-6" title="6"><span class="co"># 4 S S S S S R</span></a>
<a class="sourceLine" id="cb3-7" title="7"><span class="co"># 5 R R S S R R</span></a>
<a class="sourceLine" id="cb3-8" title="8"><span class="co"># 6 R S S R S S</span></a>
<a class="sourceLine" id="cb3-3" title="3"><span class="co"># 1 S S R R S R</span></a>
<a class="sourceLine" id="cb3-4" title="4"><span class="co"># 2 R S S S S R</span></a>
<a class="sourceLine" id="cb3-5" title="5"><span class="co"># 3 S S S S I I</span></a>
<a class="sourceLine" id="cb3-6" title="6"><span class="co"># 4 S I R I I S</span></a>
<a class="sourceLine" id="cb3-7" title="7"><span class="co"># 5 S R S R R R</span></a>
<a class="sourceLine" id="cb3-8" title="8"><span class="co"># 6 R R R R S S</span></a>
<a class="sourceLine" id="cb3-9" title="9"><span class="co"># kanamycin</span></a>
<a class="sourceLine" id="cb3-10" title="10"><span class="co"># 1 S</span></a>
<a class="sourceLine" id="cb3-11" title="11"><span class="co"># 2 S</span></a>
<a class="sourceLine" id="cb3-12" title="12"><span class="co"># 3 S</span></a>
<a class="sourceLine" id="cb3-13" title="13"><span class="co"># 4 R</span></a>
<a class="sourceLine" id="cb3-11" title="11"><span class="co"># 2 R</span></a>
<a class="sourceLine" id="cb3-12" title="12"><span class="co"># 3 R</span></a>
<a class="sourceLine" id="cb3-13" title="13"><span class="co"># 4 S</span></a>
<a class="sourceLine" id="cb3-14" title="14"><span class="co"># 5 R</span></a>
<a class="sourceLine" id="cb3-15" title="15"><span class="co"># 6 I</span></a></code></pre></div>
<p>We can now add the interpretation of MDR-TB to our data set:</p>
@ -285,40 +285,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistance</td>
<td align="right">3,249</td>
<td align="right">65.0%</td>
<td align="right">3,249</td>
<td align="right">65.0%</td>
<td align="right">3,214</td>
<td align="right">64.3%</td>
<td align="right">3,214</td>
<td align="right">64.3%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">647</td>
<td align="right">12.9%</td>
<td align="right">3,896</td>
<td align="right">77.9%</td>
<td align="right">685</td>
<td align="right">13.7%</td>
<td align="right">3,899</td>
<td align="right">78.0%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multidrug resistance</td>
<td align="right">625</td>
<td align="right">12.5%</td>
<td align="right">4,521</td>
<td align="right">90.4%</td>
<td align="right">576</td>
<td align="right">11.5%</td>
<td align="right">4,475</td>
<td align="right">89.5%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistance</td>
<td align="right">281</td>
<td align="right">5.6%</td>
<td align="right">4,802</td>
<td align="right">96.0%</td>
<td align="right">294</td>
<td align="right">5.9%</td>
<td align="right">4,769</td>
<td align="right">95.4%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensive drug resistance</td>
<td align="right">198</td>
<td align="right">4.0%</td>
<td align="right">231</td>
<td align="right">4.6%</td>
<td align="right">5,000</td>
<td align="right">100.0%</td>
</tr>