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

(v0.7.1.9015) Remove freq()

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2019-07-29 13:33:48 +02:00
parent 9ac5a34b36
commit 240f03a672
75 changed files with 668 additions and 2877 deletions
Download Patch File Download Diff File Expand all files Collapse all files

77
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">0.7.1.9012</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9015</span>
</span>
</div>
@ -118,13 +118,6 @@
Get properties of an antibiotic
</a>
</li>
<li>
<a href="../articles/freq.html">
<span class="fa fa-sort-amount-down"></span>
Create frequency tables
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
@ -192,7 +185,7 @@
<h1>How to determine multi-drug resistance (MDR)</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">10 July 2019</h4>
<h4 class="date">29 July 2019</h4>
<div class="hidden name"><code>MDR.Rmd</code></div>
@ -235,18 +228,18 @@
<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" 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 R S S R S R</span></a>
<a class="sourceLine" id="cb3-4" data-line-number="4"><span class="co"># 2 R S R S S S</span></a>
<a class="sourceLine" id="cb3-5" data-line-number="5"><span class="co"># 3 R R R R S R</span></a>
<a class="sourceLine" id="cb3-6" data-line-number="6"><span class="co"># 4 S S R S R S</span></a>
<a class="sourceLine" id="cb3-7" data-line-number="7"><span class="co"># 5 R R S I S S</span></a>
<a class="sourceLine" id="cb3-8" data-line-number="8"><span class="co"># 6 S S R R R S</span></a>
<a class="sourceLine" id="cb3-3" data-line-number="3"><span class="co"># 1 S S S R S S</span></a>
<a class="sourceLine" id="cb3-4" data-line-number="4"><span class="co"># 2 R S R R I R</span></a>
<a class="sourceLine" id="cb3-5" data-line-number="5"><span class="co"># 3 S R R R I R</span></a>
<a class="sourceLine" id="cb3-6" data-line-number="6"><span class="co"># 4 S S R I I R</span></a>
<a class="sourceLine" id="cb3-7" data-line-number="7"><span class="co"># 5 R S R S S R</span></a>
<a class="sourceLine" id="cb3-8" data-line-number="8"><span class="co"># 6 R S R R S R</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="cb3-10" data-line-number="10"><span class="co"># 1 I</span></a>
<a class="sourceLine" id="cb3-11" data-line-number="11"><span class="co"># 2 S</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="cb3-12" 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 S</span></a>
<a class="sourceLine" id="cb3-14" data-line-number="14"><span class="co"># 5 S</span></a>
<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">$</span>mdr &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mdro.html">mdr_tb</a></span>(my_TB_data)</a>
@ -257,9 +250,11 @@
<a class="sourceLine" id="cb4-6" data-line-number="6"><span class="co"># Author: WHO (World Health Organization)</span></a>
<a class="sourceLine" id="cb4-7" data-line-number="7"><span class="co"># Source: https://www.who.int/tb/publications/pmdt_companionhandbook/en/</span></a>
<a class="sourceLine" id="cb4-8" data-line-number="8"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Reliability might be improved if these antimicrobial results would be available too: CAP (capreomycin), RIB (rifabutin), RFP (rifapentine)</span></a></code></pre></div>
<p>And review the result with a frequency table:</p>
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" data-line-number="1"><span class="kw"><a href="../reference/freq.html">freq</a></span>(my_TB_data<span class="op">$</span>mdr)</a></code></pre></div>
<p><strong>Frequency table of <code>mdr</code> from <code>my_TB_data</code> (5,000 x 8)</strong></p>
<p>We also created a package dedicated to data cleaning and checking, called the <code>clean</code> package. It gets automatically installed with the <code>AMR</code> package, so we only have to load it:</p>
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(clean)</a></code></pre></div>
<p>It contains the <code><a href="https://www.rdocumentation.org/packages/clean/topics/freq">freq()</a></code> function, to create a frequency table:</p>
<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/clean/topics/freq">freq</a></span>(my_TB_data<span class="op">$</span>mdr)</a></code></pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: factor &gt; ordered (numeric)<br>
Length: 5,000 (of which NA: 0 = 0.00%)<br>
Levels: 5: Negative &lt; Mono-resistance &lt; Poly-resistance &lt; Multidrug resistance…<br>
@ -277,41 +272,41 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistance</td>
<td align="right">3,273</td>
<td align="right">65.5%</td>
<td align="right">3,273</td>
<td align="right">65.5%</td>
<td align="right">3225</td>
<td align="right">64.5%</td>
<td align="right">3225</td>
<td align="right">64.5%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">687</td>
<td align="right">13.7%</td>
<td align="right">3,960</td>
<td align="right">79.2%</td>
<td align="right">644</td>
<td align="right">12.9%</td>
<td align="right">3869</td>
<td align="right">77.4%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multidrug resistance</td>
<td align="right">569</td>
<td align="right">11.4%</td>
<td align="right">4,529</td>
<td align="right">90.6%</td>
<td align="right">626</td>
<td align="right">12.5%</td>
<td align="right">4495</td>
<td align="right">89.9%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistance</td>
<td align="right">277</td>
<td align="right">5.5%</td>
<td align="right">4,806</td>
<td align="right">96.1%</td>
<td align="right">288</td>
<td align="right">5.8%</td>
<td align="right">4783</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">194</td>
<td align="right">3.9%</td>
<td align="right">5,000</td>
<td align="right">217</td>
<td align="right">4.3%</td>
<td align="right">5000</td>
<td align="right">100.0%</td>
</tr>
</tbody>