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(v1.4.0) matching score update

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dr. M.S. (Matthijs) Berends
2020-10-08 11:16:03 +02:00
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commit 28e77680c5
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docs/articles/MDR.html
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@ -187,7 +187,7 @@
</header><script src="MDR_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
</header><script src="MDR_files/header-attrs-2.3/header-attrs.js"></script><script src="MDR_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
<div class="col-md-9 contents">
<div class="page-header toc-ignore">
<h1 data-toc-skip>How to determine multi-drug resistance (MDR)</h1>
@ -218,7 +218,7 @@
</li>
<li>
<p><code>guideline = "EUCAST"</code></p>
<p>The European international guideline - EUCAST Expert Rules Version 3.1 “Intrinsic Resistance and Exceptional Phenotypes Tables” (<a href="http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf">link</a>)</p>
<p>The European international guideline - EUCAST Expert Rules Version 3.1 “Intrinsic Resistance and Exceptional Phenotypes Tables” (<a href="https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf">link</a>)</p>
</li>
<li>
<p><code>guideline = "TB"</code></p>
@ -317,19 +317,19 @@ 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 I R S R R S</span>
<span class="co"># 2 R R S S S R</span>
<span class="co"># 3 S S R S S S</span>
<span class="co"># 4 R R R S R R</span>
<span class="co"># 5 S R S R R S</span>
<span class="co"># 6 S S R R R S</span>
<span class="co"># 1 R S S R S I</span>
<span class="co"># 2 I S S S I R</span>
<span class="co"># 3 R R R R R R</span>
<span class="co"># 4 R I S R S S</span>
<span class="co"># 5 S S I S S R</span>
<span class="co"># 6 S S S R S S</span>
<span class="co"># kanamycin</span>
<span class="co"># 1 I</span>
<span class="co"># 2 R</span>
<span class="co"># 1 R</span>
<span class="co"># 2 S</span>
<span class="co"># 3 R</span>
<span class="co"># 4 R</span>
<span class="co"># 5 R</span>
<span class="co"># 6 S</span>
<span class="co"># 5 S</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 +363,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3235</td>
<td align="right">64.70%</td>
<td align="right">3235</td>
<td align="right">64.70%</td>
<td align="right">3225</td>
<td align="right">64.50%</td>
<td align="right">3225</td>
<td align="right">64.50%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">657</td>
<td align="right">13.14%</td>
<td align="right">3892</td>
<td align="right">77.84%</td>
<td align="right">698</td>
<td align="right">13.96%</td>
<td align="right">3923</td>
<td align="right">78.46%</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">4487</td>
<td align="right">89.74%</td>
<td align="right">581</td>
<td align="right">11.62%</td>
<td align="right">4504</td>
<td align="right">90.08%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">306</td>
<td align="right">6.12%</td>
<td align="right">4793</td>
<td align="right">95.86%</td>
<td align="right">298</td>
<td align="right">5.96%</td>
<td align="right">4802</td>
<td align="right">96.04%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">207</td>
<td align="right">4.14%</td>
<td align="right">198</td>
<td align="right">3.96%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>