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(v1.1.0.9015) new default eucast_rules

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dr. M.S. (Matthijs) Berends
2020-05-20 12:00:17 +02:00
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docs/articles/MDR.html
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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">1.1.0.9014</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9015</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">19 May 2020</h4>
<h4 class="date">20 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>
@ -302,18 +302,18 @@ 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 R R R R S R</span>
<span class="co"># 2 I S R R S R</span>
<span class="co"># 3 S R R R I S</span>
<span class="co"># 4 R R R R R R</span>
<span class="co"># 5 S R I R R R</span>
<span class="co"># 6 S R R S R S</span>
<span class="co"># 1 R R R R S S</span>
<span class="co"># 2 S S S I R S</span>
<span class="co"># 3 S R S I S I</span>
<span class="co"># 4 S R S S S R</span>
<span class="co"># 5 R S R S S R</span>
<span class="co"># 6 I S R R R R</span>
<span class="co"># kanamycin</span>
<span class="co"># 1 S</span>
<span class="co"># 1 I</span>
<span class="co"># 2 S</span>
<span class="co"># 3 S</span>
<span class="co"># 4 S</span>
<span class="co"># 5 R</span>
<span class="co"># 3 R</span>
<span class="co"># 4 I</span>
<span class="co"># 5 I</span>
<span class="co"># 6 S</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>
@ -343,40 +343,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3294</td>
<td align="right">65.88%</td>
<td align="right">3294</td>
<td align="right">65.88%</td>
<td align="right">3288</td>
<td align="right">65.76%</td>
<td align="right">3288</td>
<td align="right">65.76%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">613</td>
<td align="right">12.26%</td>
<td align="right">3907</td>
<td align="right">78.14%</td>
<td align="right">631</td>
<td align="right">12.62%</td>
<td align="right">3919</td>
<td align="right">78.38%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">572</td>
<td align="right">11.44%</td>
<td align="right">4479</td>
<td align="right">89.58%</td>
<td align="right">582</td>
<td align="right">11.64%</td>
<td align="right">4501</td>
<td align="right">90.02%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">312</td>
<td align="right">6.24%</td>
<td align="right">4791</td>
<td align="right">95.82%</td>
<td align="right">298</td>
<td align="right">5.96%</td>
<td align="right">4799</td>
<td align="right">95.98%</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">201</td>
<td align="right">4.02%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>