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(v1.4.0.9034) MIC printing update

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dr. M.S. (Matthijs) Berends
2020-12-09 09:40:50 +01:00
parent 2145f1d1ba
commit c9fc7e8a45
31 changed files with 178 additions and 174 deletions
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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">1.4.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9034</span>
</span>
</div>
@ -318,19 +318,19 @@ Unique: 2</p>
<div class="sourceCode" id="cb5"><pre class="downlit">
<span class="fu"><a href="https://rdrr.io/r/utils/head.html">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 S S R R R R</span>
<span class="co"># 2 R S S R S S</span>
<span class="co"># 3 S R R R S S</span>
<span class="co"># 4 S S S S S S</span>
<span class="co"># 5 R S R S R S</span>
<span class="co"># 6 S S R S S S</span>
<span class="co"># 1 R I R S S S</span>
<span class="co"># 2 S R I R R S</span>
<span class="co"># 3 R S R R R R</span>
<span class="co"># 4 R S I R I S</span>
<span class="co"># 5 S R S R S R</span>
<span class="co"># 6 R R S R S S</span>
<span class="co"># kanamycin</span>
<span class="co"># 1 R</span>
<span class="co"># 2 R</span>
<span class="co"># 3 R</span>
<span class="co"># 2 S</span>
<span class="co"># 3 S</span>
<span class="co"># 4 S</span>
<span class="co"># 5 S</span>
<span class="co"># 6 S</span></pre></div>
<span class="co"># 5 R</span>
<span class="co"># 6 R</span></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="downlit">
<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></pre></div>
@ -361,40 +361,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3327</td>
<td align="right">66.54%</td>
<td align="right">3327</td>
<td align="right">66.54%</td>
<td align="right">3244</td>
<td align="right">64.88%</td>
<td align="right">3244</td>
<td align="right">64.88%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">632</td>
<td align="right">12.64%</td>
<td align="right">3959</td>
<td align="right">79.18%</td>
<td align="right">644</td>
<td align="right">12.88%</td>
<td align="right">3888</td>
<td align="right">77.76%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">536</td>
<td align="right">10.72%</td>
<td align="right">4495</td>
<td align="right">89.90%</td>
<td align="right">613</td>
<td align="right">12.26%</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">277</td>
<td align="right">5.54%</td>
<td align="right">4772</td>
<td align="right">95.44%</td>
<td align="right">304</td>
<td align="right">6.08%</td>
<td align="right">4805</td>
<td align="right">96.10%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">228</td>
<td align="right">4.56%</td>
<td align="right">195</td>
<td align="right">3.90%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>