P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-10 10:21:56 +02:00
Code Releases Activity

(v0.7.1.9055) algorithm improvements

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2019-08-13 16:15:08 +02:00
parent 6c4822164c
commit 7108454ba5
77 changed files with 644 additions and 582 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">0.7.1.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9055</span>
</span>
</div>
@ -185,7 +185,7 @@
<h1>How to determine multi-drug resistance (MDR)</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">08 August 2019</h4>
<h4 class="date">13 August 2019</h4>
<div class="hidden name"><code>MDR.Rmd</code></div>
@ -228,19 +228,19 @@
<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" data-line-number="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" data-line-number="2"><span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></a>
<a class="sourceLine" id="cb3-3" data-line-number="3"><span class="co"># 1 S S S S R S</span></a>
<a class="sourceLine" id="cb3-4" data-line-number="4"><span class="co"># 2 S R S R R S</span></a>
<a class="sourceLine" id="cb3-5" data-line-number="5"><span class="co"># 3 R R S S S S</span></a>
<a class="sourceLine" id="cb3-6" data-line-number="6"><span class="co"># 4 I R R S S S</span></a>
<a class="sourceLine" id="cb3-7" data-line-number="7"><span class="co"># 5 R I R S R R</span></a>
<a class="sourceLine" id="cb3-8" data-line-number="8"><span class="co"># 6 R S S S S R</span></a>
<a class="sourceLine" id="cb3-3" data-line-number="3"><span class="co"># 1 I R R R S R</span></a>
<a class="sourceLine" id="cb3-4" data-line-number="4"><span class="co"># 2 S R S S R R</span></a>
<a class="sourceLine" id="cb3-5" data-line-number="5"><span class="co"># 3 R R S R R S</span></a>
<a class="sourceLine" id="cb3-6" data-line-number="6"><span class="co"># 4 S S S S R R</span></a>
<a class="sourceLine" id="cb3-7" data-line-number="7"><span class="co"># 5 R S S S S R</span></a>
<a class="sourceLine" id="cb3-8" data-line-number="8"><span class="co"># 6 I S S R R S</span></a>
<a class="sourceLine" id="cb3-9" data-line-number="9"><span class="co"># kanamycin</span></a>
<a class="sourceLine" id="cb3-10" data-line-number="10"><span class="co"># 1 S</span></a>
<a class="sourceLine" id="cb3-11" data-line-number="11"><span class="co"># 2 R</span></a>
<a class="sourceLine" id="cb3-12" data-line-number="12"><span class="co"># 3 R</span></a>
<a class="sourceLine" id="cb3-13" data-line-number="13"><span class="co"># 4 I</span></a>
<a class="sourceLine" id="cb3-10" data-line-number="10"><span class="co"># 1 R</span></a>
<a class="sourceLine" id="cb3-11" data-line-number="11"><span class="co"># 2 I</span></a>
<a class="sourceLine" id="cb3-12" data-line-number="12"><span class="co"># 3 S</span></a>
<a class="sourceLine" id="cb3-13" data-line-number="13"><span class="co"># 4 R</span></a>
<a class="sourceLine" id="cb3-14" data-line-number="14"><span class="co"># 5 R</span></a>
<a class="sourceLine" id="cb3-15" data-line-number="15"><span class="co"># 6 R</span></a></code></pre></div>
<a class="sourceLine" id="cb3-15" data-line-number="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" data-line-number="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>
<a class="sourceLine" id="cb4-2" data-line-number="2"><span class="co"># </span><span class="al">NOTE</span><span class="co">: No column found as input for `col_mo`, assuming all records contain Mycobacterium tuberculosis.</span></a>
@ -272,39 +272,39 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistance</td>
<td align="right">3270</td>
<td align="right">65.4%</td>
<td align="right">3270</td>
<td align="right">65.4%</td>
<td align="right">3308</td>
<td align="right">66.2%</td>
<td align="right">3308</td>
<td align="right">66.2%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">645</td>
<td align="right">643</td>
<td align="right">12.9%</td>
<td align="right">3915</td>
<td align="right">78.3%</td>
<td align="right">3951</td>
<td align="right">79.0%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multidrug resistance</td>
<td align="right">593</td>
<td align="right">11.9%</td>
<td align="right">4508</td>
<td align="right">90.2%</td>
<td align="right">570</td>
<td align="right">11.4%</td>
<td align="right">4521</td>
<td align="right">90.4%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistance</td>
<td align="right">275</td>
<td align="right">5.5%</td>
<td align="right">4783</td>
<td align="right">263</td>
<td align="right">5.3%</td>
<td align="right">4784</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">217</td>
<td align="right">216</td>
<td align="right">4.3%</td>
<td align="right">5000</td>
<td align="right">100.0%</td>
@ -320,7 +320,7 @@ Unique: 5</p>
<footer><div class="copyright">
<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/">Alex W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a>.</p>
<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/">Alex W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a>.</p>
</div>
<div class="pkgdown">