mirror of
https://github.com/msberends/AMR.git
synced 2025-07-08 16:02:02 +02:00
fixes for microorganisms.codes
This commit is contained in:
@ -199,7 +199,7 @@
|
||||
<h1>How to determine multi-drug resistance (MDR)</h1>
|
||||
<h4 class="author">Matthijs S. Berends</h4>
|
||||
|
||||
<h4 class="date">23 May 2019</h4>
|
||||
<h4 class="date">28 May 2019</h4>
|
||||
|
||||
|
||||
<div class="hidden name"><code>MDR.Rmd</code></div>
|
||||
@ -243,18 +243,18 @@
|
||||
<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 S S R S</span></a>
|
||||
<a class="sourceLine" id="cb3-5" title="5"><span class="co"># 3 R S R R S S</span></a>
|
||||
<a class="sourceLine" id="cb3-6" title="6"><span class="co"># 4 S I R S R R</span></a>
|
||||
<a class="sourceLine" id="cb3-7" title="7"><span class="co"># 5 R S R R S S</span></a>
|
||||
<a class="sourceLine" id="cb3-8" title="8"><span class="co"># 6 I I S 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="cb3-9" 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 R</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="cb3-14" title="14"><span class="co"># 5 S</span></a>
|
||||
<a class="sourceLine" id="cb3-15" title="15"><span class="co"># 6 R</span></a></code></pre></div>
|
||||
<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>
|
||||
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" title="1">my_TB_data<span class="op">$</span>mdr <-<span class="st"> </span><span class="kw"><a href="../reference/mdro.html">mdr_tb</a></span>(my_TB_data)</a>
|
||||
<a class="sourceLine" id="cb4-2" title="2"><span class="co"># </span><span class="al">NOTE</span><span class="co">: No column found as input for `col_mo`, assuming all records contain Mycobacterium tuberculosis.</span></a>
|
||||
@ -285,39 +285,39 @@ Unique: 5</p>
|
||||
<tr class="odd">
|
||||
<td align="left">1</td>
|
||||
<td align="left">Mono-resistance</td>
|
||||
<td align="right">3,240</td>
|
||||
<td align="right">64.8%</td>
|
||||
<td align="right">3,240</td>
|
||||
<td align="right">64.8%</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>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">2</td>
|
||||
<td align="left">Negative</td>
|
||||
<td align="right">641</td>
|
||||
<td align="right">12.8%</td>
|
||||
<td align="right">3,881</td>
|
||||
<td align="right">77.6%</td>
|
||||
<td align="right">647</td>
|
||||
<td align="right">12.9%</td>
|
||||
<td align="right">3,896</td>
|
||||
<td align="right">77.9%</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">3</td>
|
||||
<td align="left">Multidrug resistance</td>
|
||||
<td align="right">638</td>
|
||||
<td align="right">12.8%</td>
|
||||
<td align="right">4,519</td>
|
||||
<td align="right">625</td>
|
||||
<td align="right">12.5%</td>
|
||||
<td align="right">4,521</td>
|
||||
<td align="right">90.4%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">4</td>
|
||||
<td align="left">Poly-resistance</td>
|
||||
<td align="right">279</td>
|
||||
<td align="right">281</td>
|
||||
<td align="right">5.6%</td>
|
||||
<td align="right">4,798</td>
|
||||
<td align="right">4,802</td>
|
||||
<td align="right">96.0%</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">5</td>
|
||||
<td align="left">Extensive drug resistance</td>
|
||||
<td align="right">202</td>
|
||||
<td align="right">198</td>
|
||||
<td align="right">4.0%</td>
|
||||
<td align="right">5,000</td>
|
||||
<td align="right">100.0%</td>
|
||||
|
Reference in New Issue
Block a user