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

Built site for AMR: 1.8.2.9147@4416394

Browse Source
This commit is contained in:
github-actions
2023-02-26 20:34:01 +00:00
parent 0be2d50036
commit 0484d7ab4d
101 changed files with 1551 additions and 1855 deletions
Download Patch File Download Diff File Expand all files Collapse all files

70
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="">1.8.2.9146</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9147</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">
@ -61,11 +61,6 @@
How to
</a>
<div class="dropdown-menu" aria-labelledby="dropdown--how-to">
<a class="dropdown-item" href="../reference/AMR-options.html">
<span class="fa fa-gear"></span>
User- Or Team-specific Package Settings
</a>
<a class="dropdown-item" href="../articles/AMR.html">
<span class="fa fa-directions"></span>
@ -84,7 +79,12 @@
<a class="dropdown-item" href="../articles/datasets.html">
<span class="fa fa-database"></span>
Data Sets for Download / Own Use
Download Data Sets for Own Use
</a>
<a class="dropdown-item" href="../reference/AMR-options.html">
<span class="fa fa-gear"></span>
Set User- Or Team-specific Package Settings
</a>
<a class="dropdown-item" href="../articles/PCA.html">
<span class="fa fa-compress"></span>
@ -385,18 +385,18 @@ 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">#&gt; rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
<span><span class="co">#&gt; 1 R R I S S R</span></span>
<span><span class="co">#&gt; 2 I R S R S R</span></span>
<span><span class="co">#&gt; 3 S R I S S R</span></span>
<span><span class="co">#&gt; 4 R R I S R S</span></span>
<span><span class="co">#&gt; 5 R R I I S I</span></span>
<span><span class="co">#&gt; 6 I R I R S R</span></span>
<span><span class="co">#&gt; 1 S S I S I S</span></span>
<span><span class="co">#&gt; 2 I S S I R I</span></span>
<span><span class="co">#&gt; 3 S S S S I S</span></span>
<span><span class="co">#&gt; 4 I I S R I I</span></span>
<span><span class="co">#&gt; 5 S I S R R S</span></span>
<span><span class="co">#&gt; 6 S S R R R R</span></span>
<span><span class="co">#&gt; kanamycin</span></span>
<span><span class="co">#&gt; 1 R</span></span>
<span><span class="co">#&gt; 2 R</span></span>
<span><span class="co">#&gt; 3 S</span></span>
<span><span class="co">#&gt; 1 S</span></span>
<span><span class="co">#&gt; 2 I</span></span>
<span><span class="co">#&gt; 3 I</span></span>
<span><span class="co">#&gt; 4 S</span></span>
<span><span class="co">#&gt; 5 S</span></span>
<span><span class="co">#&gt; 5 R</span></span>
<span><span class="co">#&gt; 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>
@ -438,40 +438,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3270</td>
<td align="right">65.40%</td>
<td align="right">3270</td>
<td align="right">65.40%</td>
<td align="right">3246</td>
<td align="right">64.92%</td>
<td align="right">3246</td>
<td align="right">64.92%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">967</td>
<td align="right">19.34%</td>
<td align="right">4237</td>
<td align="right">84.74%</td>
<td align="right">939</td>
<td align="right">18.78%</td>
<td align="right">4185</td>
<td align="right">83.70%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">437</td>
<td align="right">8.74%</td>
<td align="right">4674</td>
<td align="right">93.48%</td>
<td align="right">467</td>
<td align="right">9.34%</td>
<td align="right">4652</td>
<td align="right">93.04%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">227</td>
<td align="right">4.54%</td>
<td align="right">4901</td>
<td align="right">98.02%</td>
<td align="right">243</td>
<td align="right">4.86%</td>
<td align="right">4895</td>
<td align="right">97.90%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">99</td>
<td align="right">1.98%</td>
<td align="right">105</td>
<td align="right">2.10%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>