P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-08 20:41:58 +02:00
Code Releases Activity

(v0.7.1.9005) new rsi calculations, atc class removal

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2019-07-01 14:03:15 +02:00
parent 65c6702b21
commit 156d550895
78 changed files with 1169 additions and 911 deletions
Download Patch File Download Diff File Expand all files Collapse all files

58
docs/articles/MDR.html
View File

@ -40,7 +40,7 @@
</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">0.7.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9005</span>
</span>
</div>
@ -192,7 +192,7 @@
<h1>How to determine multi-drug resistance (MDR)</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">23 June 2019</h4>
<h4 class="date">01 July 2019</h4>
<div class="hidden name"><code>MDR.Rmd</code></div>
@ -235,18 +235,18 @@
<p>The data set looks like this now:</p>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/head">head</a></span>(my_TB_data)</a>
<a class="sourceLine" id="cb3-2" title="2"><span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></a>
<a class="sourceLine" id="cb3-3" title="3"><span class="co"># 1 R S R S S S</span></a>
<a class="sourceLine" id="cb3-4" title="4"><span class="co"># 2 I R S S I S</span></a>
<a class="sourceLine" id="cb3-5" title="5"><span class="co"># 3 S R R R S R</span></a>
<a class="sourceLine" id="cb3-6" title="6"><span class="co"># 4 R S R R I S</span></a>
<a class="sourceLine" id="cb3-7" title="7"><span class="co"># 5 I R R S R S</span></a>
<a class="sourceLine" id="cb3-8" title="8"><span class="co"># 6 S S S S R R</span></a>
<a class="sourceLine" id="cb3-3" title="3"><span class="co"># 1 R R S S R I</span></a>
<a class="sourceLine" id="cb3-4" title="4"><span class="co"># 2 R R S R S R</span></a>
<a class="sourceLine" id="cb3-5" title="5"><span class="co"># 3 R S S R R R</span></a>
<a class="sourceLine" id="cb3-6" title="6"><span class="co"># 4 R R S S S I</span></a>
<a class="sourceLine" id="cb3-7" title="7"><span class="co"># 5 R R S S R I</span></a>
<a class="sourceLine" id="cb3-8" title="8"><span class="co"># 6 R S R R S S</span></a>
<a class="sourceLine" id="cb3-9" title="9"><span class="co"># kanamycin</span></a>
<a class="sourceLine" id="cb3-10" title="10"><span class="co"># 1 S</span></a>
<a class="sourceLine" id="cb3-11" title="11"><span class="co"># 2 I</span></a>
<a class="sourceLine" id="cb3-11" title="11"><span class="co"># 2 S</span></a>
<a class="sourceLine" id="cb3-12" title="12"><span class="co"># 3 S</span></a>
<a class="sourceLine" id="cb3-13" title="13"><span class="co"># 4 S</span></a>
<a class="sourceLine" id="cb3-14" title="14"><span class="co"># 5 S</span></a>
<a class="sourceLine" id="cb3-13" title="13"><span class="co"># 4 R</span></a>
<a class="sourceLine" id="cb3-14" title="14"><span class="co"># 5 R</span></a>
<a class="sourceLine" id="cb3-15" title="15"><span class="co"># 6 S</span></a></code></pre></div>
<p>We can now add the interpretation of MDR-TB to our data set:</p>
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" title="1">my_TB_data<span class="op">$</span>mdr &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mdro.html">mdr_tb</a></span>(my_TB_data)</a>
@ -277,40 +277,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistance</td>
<td align="right">3,206</td>
<td align="right">64.1%</td>
<td align="right">3,206</td>
<td align="right">64.1%</td>
<td align="right">3,222</td>
<td align="right">64.4%</td>
<td align="right">3,222</td>
<td align="right">64.4%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">689</td>
<td align="right">13.8%</td>
<td align="right">3,895</td>
<td align="right">77.9%</td>
<td align="right">659</td>
<td align="right">13.2%</td>
<td align="right">3,881</td>
<td align="right">77.6%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multidrug resistance</td>
<td align="right">578</td>
<td align="right">11.6%</td>
<td align="right">4,473</td>
<td align="right">89.5%</td>
<td align="right">589</td>
<td align="right">11.8%</td>
<td align="right">4,470</td>
<td align="right">89.4%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistance</td>
<td align="right">299</td>
<td align="right">6.0%</td>
<td align="right">4,772</td>
<td align="right">95.4%</td>
<td align="right">313</td>
<td align="right">6.3%</td>
<td align="right">4,783</td>
<td align="right">95.7%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensive drug resistance</td>
<td align="right">228</td>
<td align="right">4.6%</td>
<td align="right">217</td>
<td align="right">4.3%</td>
<td align="right">5,000</td>
<td align="right">100.0%</td>
</tr>