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(v1.7.1.9030) unit test

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dr. M.S. (Matthijs) Berends
2021-08-29 23:50:45 +02:00
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@ -44,7 +44,7 @@
</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">1.7.1.9024</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
</span>
</div>
@ -174,13 +174,6 @@
Source Code
</a>
</li>
<li>
<a href="../survey.html">
<span class="fa fa-clipboard-list"></span>
Survey
</a>
</li>
</ul>
</div>
@ -364,19 +357,19 @@ Unique: 2</p>
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span>
<span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span>
<span class="co"># 1 I I I S R R</span>
<span class="co"># 2 I R R R I R</span>
<span class="co"># 3 S I R S I I</span>
<span class="co"># 4 S S S S I R</span>
<span class="co"># 5 R S R I I S</span>
<span class="co"># 6 I R S R R I</span>
<span class="co"># 1 S I I R I I</span>
<span class="co"># 2 S S I I R R</span>
<span class="co"># 3 I S S I I R</span>
<span class="co"># 4 S R S R S R</span>
<span class="co"># 5 R S R S R R</span>
<span class="co"># 6 I S S R I S</span>
<span class="co"># kanamycin</span>
<span class="co"># 1 I</span>
<span class="co"># 2 R</span>
<span class="co"># 3 I</span>
<span class="co"># 4 R</span>
<span class="co"># 5 R</span>
<span class="co"># 6 S</span></code></pre></div>
<span class="co"># 6 I</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="cb9"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="../reference/mdro.html">mdro</a></span><span class="op">(</span><span class="va">my_TB_data</span>, guideline <span class="op">=</span> <span class="st">"TB"</span><span class="op">)</span></code></pre></div>
@ -419,40 +412,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3227</td>
<td align="right">64.54%</td>
<td align="right">3227</td>
<td align="right">64.54%</td>
<td align="right">3144</td>
<td align="right">62.88%</td>
<td align="right">3144</td>
<td align="right">62.88%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">990</td>
<td align="right">19.80%</td>
<td align="right">4217</td>
<td align="right">84.34%</td>
<td align="right">1027</td>
<td align="right">20.54%</td>
<td align="right">4171</td>
<td align="right">83.42%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">464</td>
<td align="right">9.28%</td>
<td align="right">4681</td>
<td align="right">93.62%</td>
<td align="right">4635</td>
<td align="right">92.70%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">223</td>
<td align="right">4.46%</td>
<td align="right">4904</td>
<td align="right">98.08%</td>
<td align="right">257</td>
<td align="right">5.14%</td>
<td align="right">4892</td>
<td align="right">97.84%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">96</td>
<td align="right">1.92%</td>
<td align="right">108</td>
<td align="right">2.16%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>