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@ -39,7 +38,7 @@
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@ -75,6 +74,13 @@
Predict antimicrobial resistance
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Conduct principal component analysis for AMR
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@ -179,7 +185,7 @@
<h1>How to determine multi-drug resistance (MDR)</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">23 February 2020</h4>
<h4 class="date">17 March 2020</h4>
<div class="hidden name"><code>MDR.Rmd</code></div>
@ -274,7 +280,7 @@ Unique: 2</p>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb3-1"><a href="#cb3-1"></a><span class="co"># a helper function to get a random vector with values S, I and R</span></span>
<span id="cb3-2"><a href="#cb3-2"></a><span class="co"># with the probabilities 50% - 10% - 40%</span></span>
<span id="cb3-3"><a href="#cb3-3"></a>sample_rsi &lt;-<span class="st"> </span><span class="cf">function</span>() {</span>
<span id="cb3-4"><a href="#cb3-4"></a> <span class="kw"><a href="https://dplyr.tidyverse.org/reference/sample.html">sample</a></span>(<span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"S"</span>, <span class="st">"I"</span>, <span class="st">"R"</span>),</span>
<span id="cb3-4"><a href="#cb3-4"></a> <span class="kw"><a href="https://rdrr.io/r/base/sample.html">sample</a></span>(<span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"S"</span>, <span class="st">"I"</span>, <span class="st">"R"</span>),</span>
<span id="cb3-5"><a href="#cb3-5"></a> <span class="dt">size =</span> <span class="dv">5000</span>,</span>
<span id="cb3-6"><a href="#cb3-6"></a> <span class="dt">prob =</span> <span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="fl">0.5</span>, <span class="fl">0.1</span>, <span class="fl">0.4</span>),</span>
<span id="cb3-7"><a href="#cb3-7"></a> <span class="dt">replace =</span> <span class="ot">TRUE</span>)</span>
@ -298,19 +304,19 @@ Unique: 2</p>
<p>The data set now looks like this:</p>
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb5-1"><a href="#cb5-1"></a><span class="kw"><a href="https://rdrr.io/r/utils/head.html">head</a></span>(my_TB_data)</span>
<span id="cb5-2"><a href="#cb5-2"></a><span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
<span id="cb5-3"><a href="#cb5-3"></a><span class="co"># 1 S R S R R I</span></span>
<span id="cb5-4"><a href="#cb5-4"></a><span class="co"># 2 S R S S R S</span></span>
<span id="cb5-5"><a href="#cb5-5"></a><span class="co"># 3 I S R R S R</span></span>
<span id="cb5-6"><a href="#cb5-6"></a><span class="co"># 4 S S S S S R</span></span>
<span id="cb5-7"><a href="#cb5-7"></a><span class="co"># 5 S S S I R R</span></span>
<span id="cb5-8"><a href="#cb5-8"></a><span class="co"># 6 I I R R S S</span></span>
<span id="cb5-3"><a href="#cb5-3"></a><span class="co"># 1 S R R I R R</span></span>
<span id="cb5-4"><a href="#cb5-4"></a><span class="co"># 2 I R R R S R</span></span>
<span id="cb5-5"><a href="#cb5-5"></a><span class="co"># 3 R R R S R S</span></span>
<span id="cb5-6"><a href="#cb5-6"></a><span class="co"># 4 S S R R R S</span></span>
<span id="cb5-7"><a href="#cb5-7"></a><span class="co"># 5 S R S R S S</span></span>
<span id="cb5-8"><a href="#cb5-8"></a><span class="co"># 6 R S S S R S</span></span>
<span id="cb5-9"><a href="#cb5-9"></a><span class="co"># kanamycin</span></span>
<span id="cb5-10"><a href="#cb5-10"></a><span class="co"># 1 S</span></span>
<span id="cb5-11"><a href="#cb5-11"></a><span class="co"># 2 I</span></span>
<span id="cb5-11"><a href="#cb5-11"></a><span class="co"># 2 S</span></span>
<span id="cb5-12"><a href="#cb5-12"></a><span class="co"># 3 R</span></span>
<span id="cb5-13"><a href="#cb5-13"></a><span class="co"># 4 R</span></span>
<span id="cb5-14"><a href="#cb5-14"></a><span class="co"># 5 R</span></span>
<span id="cb5-15"><a href="#cb5-15"></a><span class="co"># 6 I</span></span></code></pre></div>
<span id="cb5-15"><a href="#cb5-15"></a><span class="co"># 6 R</span></span></code></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="sourceCode r"><code class="sourceCode r"><span id="cb6-1"><a href="#cb6-1"></a><span class="kw"><a href="../reference/mdro.html">mdro</a></span>(my_TB_data, <span class="dt">guideline =</span> <span class="st">"TB"</span>)</span></code></pre></div>
<p>or its shortcut <code><a href="../reference/mdro.html">mdr_tb()</a></code>:</p>
@ -339,40 +345,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3274</td>
<td align="right">65.48%</td>
<td align="right">3274</td>
<td align="right">65.48%</td>
<td align="right">3312</td>
<td align="right">66.24%</td>
<td align="right">3312</td>
<td align="right">66.24%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">651</td>
<td align="right">13.02%</td>
<td align="right">3925</td>
<td align="right">78.50%</td>
<td align="right">634</td>
<td align="right">12.68%</td>
<td align="right">3946</td>
<td align="right">78.92%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">612</td>
<td align="right">12.24%</td>
<td align="right">4537</td>
<td align="right">90.74%</td>
<td align="right">554</td>
<td align="right">11.08%</td>
<td align="right">4500</td>
<td align="right">90.00%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">288</td>
<td align="right">5.76%</td>
<td align="right">4825</td>
<td align="right">96.50%</td>
<td align="right">291</td>
<td align="right">5.82%</td>
<td align="right">4791</td>
<td align="right">95.82%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">175</td>
<td align="right">3.50%</td>
<td align="right">209</td>
<td align="right">4.18%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>
@ -381,7 +387,7 @@ Unique: 5</p>
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@ -394,7 +400,7 @@ Unique: 5</p>
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