P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-08 20:02:04 +02:00
Code Releases Activity

(v1.4.0.9046) get_episode

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2020-12-27 00:07:00 +01:00
parent 291f802be3
commit acbd0cf7ca
99 changed files with 1143 additions and 683 deletions
Download Patch File Download Diff File Expand all files Collapse all files

58
docs/articles/MDR.html
View File

@ -12,7 +12,7 @@
<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous">
<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css">
<script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
@ -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">1.4.0.9044</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
</span>
</div>
@ -311,17 +311,17 @@ Unique: 2</p>
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
<code class="sourceCode R"><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 I R S</span>
<span class="co"># 2 I S R I I R</span>
<span class="co"># 3 R R R S I R</span>
<span class="co"># 4 I I R R S S</span>
<span class="co"># 5 I R I S S R</span>
<span class="co"># 6 I R I I S I</span>
<span class="co"># 1 R I R S I S</span>
<span class="co"># 2 I S I S S R</span>
<span class="co"># 3 I I I R I R</span>
<span class="co"># 4 S S I S R I</span>
<span class="co"># 5 I R S R S R</span>
<span class="co"># 6 I I I R S I</span>
<span class="co"># kanamycin</span>
<span class="co"># 1 R</span>
<span class="co"># 2 S</span>
<span class="co"># 1 S</span>
<span class="co"># 2 I</span>
<span class="co"># 3 I</span>
<span class="co"># 4 I</span>
<span class="co"># 4 S</span>
<span class="co"># 5 I</span>
<span class="co"># 6 R</span></code></pre></div>
<p>We can now add the interpretation of MDR-TB to our data set. You can use:</p>
@ -354,40 +354,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3214</td>
<td align="right">64.28%</td>
<td align="right">3214</td>
<td align="right">64.28%</td>
<td align="right">3219</td>
<td align="right">64.38%</td>
<td align="right">3219</td>
<td align="right">64.38%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">997</td>
<td align="right">19.94%</td>
<td align="right">4211</td>
<td align="right">84.22%</td>
<td align="right">982</td>
<td align="right">19.64%</td>
<td align="right">4201</td>
<td align="right">84.02%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">442</td>
<td align="right">8.84%</td>
<td align="right">4653</td>
<td align="right">93.06%</td>
<td align="right">434</td>
<td align="right">8.68%</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">239</td>
<td align="right">4.78%</td>
<td align="right">4892</td>
<td align="right">97.84%</td>
<td align="right">251</td>
<td align="right">5.02%</td>
<td align="right">4886</td>
<td align="right">97.72%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">108</td>
<td align="right">2.16%</td>
<td align="right">114</td>
<td align="right">2.28%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>