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(v0.7.1.9091) percentage from clean pkg

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dr. M.S. (Matthijs) Berends
2019-09-30 16:45:36 +02:00
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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">0.7.1.9090</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9091</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">26 September 2019</h4>
<h4 class="date">30 September 2019</h4>
<div class="hidden name"><code>MDR.Rmd</code></div>
@ -230,19 +230,19 @@
<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 R R R S R</span></a>
<a class="sourceLine" id="cb3-4" data-line-number="4"><span class="co"># 2 R I R R R R</span></a>
<a class="sourceLine" id="cb3-5" data-line-number="5"><span class="co"># 3 S S R S R R</span></a>
<a class="sourceLine" id="cb3-6" data-line-number="6"><span class="co"># 4 S I S S R I</span></a>
<a class="sourceLine" id="cb3-7" data-line-number="7"><span class="co"># 5 I S R R R S</span></a>
<a class="sourceLine" id="cb3-8" data-line-number="8"><span class="co"># 6 R S S S R R</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="cb3-9" 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 R</span></a>
<a class="sourceLine" id="cb3-12" data-line-number="12"><span class="co"># 3 R</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 I</span></a>
<a class="sourceLine" id="cb3-15" data-line-number="15"><span class="co"># 6 I</span></a></code></pre></div>
<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="cb3-15" 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">$</span>mdr &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mdro.html">mdr_tb</a></span>(my_TB_data)</a>
<a class="sourceLine" id="cb4-2" data-line-number="2"><span class="co"># </span><span class="al">NOTE</span><span class="co">: No column found as input for `col_mo`, assuming all records contain Mycobacterium tuberculosis.</span></a>
@ -258,7 +258,7 @@
<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" data-line-number="1"><span class="kw"><a href="https://rdrr.io/pkg/clean/man/freq.html">freq</a></span>(my_TB_data<span class="op">$</span>mdr)</a></code></pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: factor &gt; ordered (numeric)<br>
Length: 5,000 (of which NA: 0 = 0.00%)<br>
Length: 5,000 (of which NA: 0 = 0%)<br>
Levels: 5: Negative &lt; Mono-resistant &lt; Poly-resistant &lt; Multi-drug-resistant &lt;…<br>
Unique: 5</p>
<table class="table">
@ -274,42 +274,42 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3255</td>
<td align="right">65.1%</td>
<td align="right">3255</td>
<td align="right">65.1%</td>
<td align="right">3250</td>
<td align="right">65.00%</td>
<td align="right">3250</td>
<td align="right">65.00%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">638</td>
<td align="right">12.8%</td>
<td align="right">3893</td>
<td align="right">77.9%</td>
<td align="right">634</td>
<td align="right">12.68%</td>
<td align="right">3884</td>
<td align="right">77.68%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">618</td>
<td align="right">12.4%</td>
<td align="right">4511</td>
<td align="right">90.2%</td>
<td align="right">623</td>
<td align="right">12.46%</td>
<td align="right">4507</td>
<td align="right">90.14%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">276</td>
<td align="right">5.5%</td>
<td align="right">4787</td>
<td align="right">95.7%</td>
<td align="right">282</td>
<td align="right">5.64%</td>
<td align="right">4789</td>
<td align="right">95.78%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensive drug-resistant</td>
<td align="right">213</td>
<td align="right">4.3%</td>
<td align="right">211</td>
<td align="right">4.22%</td>
<td align="right">5000</td>
<td align="right">100.0%</td>
<td align="right">100.00%</td>
</tr>
</tbody>
</table>