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dr. M.S. (Matthijs) Berends
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@ -41,7 +41,7 @@
</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">0.7.1.9091</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0</span>
</span>
</div>
@ -187,7 +187,7 @@
<h1>How to determine multi-drug resistance (MDR)</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">30 September 2019</h4>
<h4 class="date">13 October 2019</h4>
<div class="hidden name"><code>MDR.Rmd</code></div>
@ -230,18 +230,18 @@
<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" data-line-number="1"><span class="kw"><a href="https://rdrr.io/r/utils/head.html">head</a></span>(my_TB_data)</a>
<a class="sourceLine" id="cb3-2" data-line-number="2"><span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></a>
<a class="sourceLine" id="cb3-3" data-line-number="3"><span class="co"># 1 R S R R S R</span></a>
<a class="sourceLine" id="cb3-4" data-line-number="4"><span class="co"># 2 I R S R R R</span></a>
<a class="sourceLine" id="cb3-5" data-line-number="5"><span class="co"># 3 R R R S R R</span></a>
<a class="sourceLine" id="cb3-6" data-line-number="6"><span class="co"># 4 R S I I R S</span></a>
<a class="sourceLine" id="cb3-7" data-line-number="7"><span class="co"># 5 S S I I R S</span></a>
<a class="sourceLine" id="cb3-8" data-line-number="8"><span class="co"># 6 S S S R S S</span></a>
<a class="sourceLine" id="cb3-3" data-line-number="3"><span class="co"># 1 R S S I S S</span></a>
<a class="sourceLine" id="cb3-4" data-line-number="4"><span class="co"># 2 I R S R S R</span></a>
<a class="sourceLine" id="cb3-5" data-line-number="5"><span class="co"># 3 S S R R R R</span></a>
<a class="sourceLine" id="cb3-6" data-line-number="6"><span class="co"># 4 S R R S S S</span></a>
<a class="sourceLine" id="cb3-7" data-line-number="7"><span class="co"># 5 S R R S R R</span></a>
<a class="sourceLine" id="cb3-8" data-line-number="8"><span class="co"># 6 R S S R R S</span></a>
<a class="sourceLine" id="cb3-9" data-line-number="9"><span class="co"># kanamycin</span></a>
<a class="sourceLine" id="cb3-10" data-line-number="10"><span class="co"># 1 R</span></a>
<a class="sourceLine" id="cb3-11" data-line-number="11"><span class="co"># 2 S</span></a>
<a class="sourceLine" id="cb3-12" data-line-number="12"><span class="co"># 3 S</span></a>
<a class="sourceLine" id="cb3-13" data-line-number="13"><span class="co"># 4 R</span></a>
<a class="sourceLine" id="cb3-14" data-line-number="14"><span class="co"># 5 R</span></a>
<a class="sourceLine" id="cb3-11" data-line-number="11"><span class="co"># 2 R</span></a>
<a class="sourceLine" id="cb3-12" data-line-number="12"><span class="co"># 3 I</span></a>
<a class="sourceLine" id="cb3-13" data-line-number="13"><span class="co"># 4 S</span></a>
<a class="sourceLine" id="cb3-14" data-line-number="14"><span class="co"># 5 S</span></a>
<a class="sourceLine" id="cb3-15" data-line-number="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" data-line-number="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>
@ -251,7 +251,8 @@
<a class="sourceLine" id="cb4-5" data-line-number="5"><span class="co"># Version: WHO/HTM/TB/2014.11</span></a>
<a class="sourceLine" id="cb4-6" data-line-number="6"><span class="co"># Author: WHO (World Health Organization)</span></a>
<a class="sourceLine" id="cb4-7" data-line-number="7"><span class="co"># Source: https://www.who.int/tb/publications/pmdt_companionhandbook/en/</span></a>
<a class="sourceLine" id="cb4-8" data-line-number="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>
<a class="sourceLine" id="cb4-8" data-line-number="8"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Auto-guessing columns suitable for analysis...</span></a>
<a class="sourceLine" id="cb4-9" data-line-number="9"><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>We also created a package dedicated to data cleaning and checking, called the <code>clean</code> package. It gets automatically installed with the <code>AMR</code> package, so we only have to load it:</p>
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" data-line-number="1"><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span>(clean)</a></code></pre></div>
<p>It contains the <code><a href="https://rdrr.io/pkg/clean/man/freq.html">freq()</a></code> function, to create a frequency table:</p>
@ -274,40 +275,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3250</td>
<td align="right">65.00%</td>
<td align="right">3250</td>
<td align="right">65.00%</td>
<td align="right">3246</td>
<td align="right">64.92%</td>
<td align="right">3246</td>
<td align="right">64.92%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">634</td>
<td align="right">12.68%</td>
<td align="right">3884</td>
<td align="right">77.68%</td>
<td align="right">681</td>
<td align="right">13.62%</td>
<td align="right">3927</td>
<td align="right">78.54%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">623</td>
<td align="right">12.46%</td>
<td align="right">4507</td>
<td align="right">90.14%</td>
<td align="right">593</td>
<td align="right">11.86%</td>
<td align="right">4520</td>
<td align="right">90.40%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">282</td>
<td align="right">5.64%</td>
<td align="right">4789</td>
<td align="right">95.78%</td>
<td align="right">276</td>
<td align="right">5.52%</td>
<td align="right">4796</td>
<td align="right">95.92%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensive drug-resistant</td>
<td align="right">211</td>
<td align="right">4.22%</td>
<td align="right">204</td>
<td align="right">4.08%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>