P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-27 17:47:54 +02:00
Code Releases Activity

Built site for AMR: 1.8.2.9111@aa48c6b

Browse Source
This commit is contained in:
github-actions
2023-02-08 16:01:47 +00:00
parent c43e91eaee
commit 769ace0b66
112 changed files with 1836 additions and 1173 deletions
Download Patch File Download Diff File Expand all files Collapse all files

63
articles/MDR.html
View File

@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9103</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -71,6 +71,11 @@
Conduct AMR Analysis
</a>
<a class="dropdown-item" href="../reference/antibiogram.html">
<span class="fa fa-file-prescription"></span>
Generate Antibiogram (Trad./Syndromic/WISCA)
</a>
<a class="dropdown-item" href="../articles/resistance_predict.html">
<span class="fa fa-dice"></span>
@ -380,19 +385,19 @@ names or codes, this would have worked exactly the same way:</p>
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><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>
<span><span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
<span><span class="co"># 1 S S R I I R</span></span>
<span><span class="co"># 2 R R S S I I</span></span>
<span><span class="co"># 3 S R S S I S</span></span>
<span><span class="co"># 4 R I R S S R</span></span>
<span><span class="co"># 5 R I R I S S</span></span>
<span><span class="co"># 6 I I I R S I</span></span>
<span><span class="co"># 1 I S I I S I</span></span>
<span><span class="co"># 2 S S S S I S</span></span>
<span><span class="co"># 3 R R I S I R</span></span>
<span><span class="co"># 4 I I R S S R</span></span>
<span><span class="co"># 5 R I S S I S</span></span>
<span><span class="co"># 6 R S R I R I</span></span>
<span><span class="co"># kanamycin</span></span>
<span><span class="co"># 1 I</span></span>
<span><span class="co"># 2 R</span></span>
<span><span class="co"># 3 R</span></span>
<span><span class="co"># 4 I</span></span>
<span><span class="co"># 2 S</span></span>
<span><span class="co"># 3 S</span></span>
<span><span class="co"># 4 S</span></span>
<span><span class="co"># 5 R</span></span>
<span><span class="co"># 6 R</span></span></code></pre></div>
<span><span class="co"># 6 I</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="cb9"><pre class="downlit sourceCode r">
@ -433,40 +438,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3174</td>
<td align="right">63.48%</td>
<td align="right">3174</td>
<td align="right">63.48%</td>
<td align="right">3141</td>
<td align="right">62.82%</td>
<td align="right">3141</td>
<td align="right">62.82%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">1008</td>
<td align="right">20.16%</td>
<td align="right">4182</td>
<td align="right">83.64%</td>
<td align="right">1012</td>
<td align="right">20.24%</td>
<td align="right">4153</td>
<td align="right">83.06%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">451</td>
<td align="right">9.02%</td>
<td align="right">4633</td>
<td align="right">92.66%</td>
<td align="right">477</td>
<td align="right">9.54%</td>
<td align="right">4630</td>
<td align="right">92.60%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">255</td>
<td align="right">5.10%</td>
<td align="right">4888</td>
<td align="right">97.76%</td>
<td align="right">257</td>
<td align="right">5.14%</td>
<td align="right">4887</td>
<td align="right">97.74%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">112</td>
<td align="right">2.24%</td>
<td align="right">113</td>
<td align="right">2.26%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>