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(v1.1.0.9021) 1st isolates update

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dr. M.S. (Matthijs) Berends
2020-05-28 10:51:56 +02:00
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@ -39,7 +39,7 @@
</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">1.1.0.9019</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9021</span>
</span>
</div>
@ -186,7 +186,7 @@
<h1 data-toc-skip>How to determine multi-drug resistance (MDR)</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">25 May 2020</h4>
<h4 class="date">28 May 2020</h4>
<small class="dont-index">Source: <a href="https://gitlab.com/msberends/AMR/blob/master/vignettes/MDR.Rmd"><code>vignettes/MDR.Rmd</code></a></small>
<div class="hidden name"><code>MDR.Rmd</code></div>
@ -259,16 +259,16 @@ Unique: 2</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Negative</td>
<td align="right">1596</td>
<td align="right">93.28%</td>
<td align="right">1596</td>
<td align="right">93.28%</td>
<td align="right">1595</td>
<td align="right">93.22%</td>
<td align="right">1595</td>
<td align="right">93.22%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Multi-drug-resistant (MDR)</td>
<td align="right">115</td>
<td align="right">6.72%</td>
<td align="right">116</td>
<td align="right">6.78%</td>
<td align="right">1711</td>
<td align="right">100.00%</td>
</tr>
@ -302,19 +302,19 @@ Unique: 2</p>
<p>The data set now looks like this:</p>
<div class="sourceCode" id="cb5"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/utils/head.html">head</a></span>(<span class="no">my_TB_data</span>)
<span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span>
<span class="co"># 1 S S R R S S</span>
<span class="co"># 2 R R S R S R</span>
<span class="co"># 3 R S S R S S</span>
<span class="co"># 4 R S S S S R</span>
<span class="co"># 5 S R R S R R</span>
<span class="co"># 6 R R R R R R</span>
<span class="co"># 1 R S R I I S</span>
<span class="co"># 2 S R S I R I</span>
<span class="co"># 3 S S I S R R</span>
<span class="co"># 4 I R S S I S</span>
<span class="co"># 5 S S R R R S</span>
<span class="co"># 6 I R R R R S</span>
<span class="co"># kanamycin</span>
<span class="co"># 1 R</span>
<span class="co"># 2 S</span>
<span class="co"># 3 S</span>
<span class="co"># 3 I</span>
<span class="co"># 4 S</span>
<span class="co"># 5 R</span>
<span class="co"># 6 R</span></pre></body></html></div>
<span class="co"># 6 I</span></pre></body></html></div>
<p>We can now add the interpretation of MDR-TB to our data set. You can use:</p>
<div class="sourceCode" id="cb6"><html><body><pre class="r"><span class="fu"><a href="../reference/mdro.html">mdro</a></span>(<span class="no">my_TB_data</span>, <span class="kw">guideline</span> <span class="kw">=</span> <span class="st">"TB"</span>)</pre></body></html></div>
<p>or its shortcut <code><a href="../reference/mdro.html">mdr_tb()</a></code>:</p>
@ -343,40 +343,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3239</td>
<td align="right">64.78%</td>
<td align="right">3239</td>
<td align="right">64.78%</td>
<td align="right">3192</td>
<td align="right">63.84%</td>
<td align="right">3192</td>
<td align="right">63.84%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">655</td>
<td align="right">13.10%</td>
<td align="right">3894</td>
<td align="right">77.88%</td>
<td align="right">667</td>
<td align="right">13.34%</td>
<td align="right">3859</td>
<td align="right">77.18%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">593</td>
<td align="right">11.86%</td>
<td align="right">4487</td>
<td align="right">89.74%</td>
<td align="right">637</td>
<td align="right">12.74%</td>
<td align="right">4496</td>
<td align="right">89.92%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">304</td>
<td align="right">6.08%</td>
<td align="right">4791</td>
<td align="right">95.82%</td>
<td align="right">287</td>
<td align="right">5.74%</td>
<td align="right">4783</td>
<td align="right">95.66%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">209</td>
<td align="right">4.18%</td>
<td align="right">217</td>
<td align="right">4.34%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>