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(v0.7.0.9001) new pathovars, small fixes

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dr. M.S. (Matthijs) Berends
2019-06-07 22:47:37 +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">0.7.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0.9000</span>
</span>
</div>
@ -199,7 +199,7 @@
<h1>How to determine multi-drug resistance (MDR)</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">03 June 2019</h4>
<h4 class="date">07 June 2019</h4>
<div class="hidden name"><code>MDR.Rmd</code></div>
@ -242,18 +242,18 @@
<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 S R I S</span></a>
<a class="sourceLine" id="cb3-4" title="4"><span class="co"># 2 R R R I R S</span></a>
<a class="sourceLine" id="cb3-5" title="5"><span class="co"># 3 R S S S S I</span></a>
<a class="sourceLine" id="cb3-6" title="6"><span class="co"># 4 S R S R S S</span></a>
<a class="sourceLine" id="cb3-7" title="7"><span class="co"># 5 R S S S S R</span></a>
<a class="sourceLine" id="cb3-8" title="8"><span class="co"># 6 R S S S R R</span></a>
<a class="sourceLine" id="cb3-3" title="3"><span class="co"># 1 R S R R I R</span></a>
<a class="sourceLine" id="cb3-4" title="4"><span class="co"># 2 I S S I S R</span></a>
<a class="sourceLine" id="cb3-5" title="5"><span class="co"># 3 S R S R I R</span></a>
<a class="sourceLine" id="cb3-6" title="6"><span class="co"># 4 R R R R R R</span></a>
<a class="sourceLine" id="cb3-7" title="7"><span class="co"># 5 S S S S R S</span></a>
<a class="sourceLine" id="cb3-8" title="8"><span class="co"># 6 S I S R R I</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 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 S</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="cb3-10" 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 R</span></a>
<a class="sourceLine" id="cb3-13" title="13"><span class="co"># 4 I</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 S</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">$</span>mdr &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mdro.html">mdr_tb</a></span>(my_TB_data)</a>
@ -263,8 +263,7 @@
<a class="sourceLine" id="cb4-5" title="5"><span class="co"># Version: WHO/HTM/TB/2014.11</span></a>
<a class="sourceLine" id="cb4-6" title="6"><span class="co"># Author: WHO (World Health Organization)</span></a>
<a class="sourceLine" id="cb4-7" title="7"><span class="co"># Source: https://www.who.int/tb/publications/pmdt_companionhandbook/en/</span></a>
<a class="sourceLine" id="cb4-8" title="8"><span class="co"># Warning: Reliability might be improved if these antimicrobial results would</span></a>
<a class="sourceLine" id="cb4-9" title="9"><span class="co"># be available too: CAP (capreomycin), RIB (rifabutin), RFP (rifapentine)</span></a></code></pre></div>
<a class="sourceLine" id="cb4-8" title="8"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Reliability might be improved if these antimicrobial results would be available too: CAP (capreomycin), RIB (rifabutin), RFP (rifapentine)</span></a></code></pre></div>
<p>And review the result with a frequency table:</p>
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" title="1"><span class="kw"><a href="../reference/freq.html">freq</a></span>(my_TB_data<span class="op">$</span>mdr)</a></code></pre></div>
<p><strong>Frequency table of <code>mdr</code> from <code>my_TB_data</code> (5,000 x 8)</strong></p>
@ -285,40 +284,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistance</td>
<td align="right">3,238</td>
<td align="right">64.8%</td>
<td align="right">3,238</td>
<td align="right">64.8%</td>
<td align="right">3,283</td>
<td align="right">65.7%</td>
<td align="right">3,283</td>
<td align="right">65.7%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">662</td>
<td align="right">13.2%</td>
<td align="right">3,900</td>
<td align="right">78.0%</td>
<td align="right">650</td>
<td align="right">13.0%</td>
<td align="right">3,933</td>
<td align="right">78.7%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multidrug resistance</td>
<td align="right">613</td>
<td align="right">12.3%</td>
<td align="right">4,513</td>
<td align="right">90.3%</td>
<td align="right">593</td>
<td align="right">11.9%</td>
<td align="right">4,526</td>
<td align="right">90.5%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistance</td>
<td align="right">279</td>
<td align="right">5.6%</td>
<td align="right">4,792</td>
<td align="right">95.8%</td>
<td align="right">259</td>
<td align="right">5.2%</td>
<td align="right">4,785</td>
<td align="right">95.7%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensive drug resistance</td>
<td align="right">208</td>
<td align="right">4.2%</td>
<td align="right">215</td>
<td align="right">4.3%</td>
<td align="right">5,000</td>
<td align="right">100.0%</td>
</tr>