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WHONET/EARS-Net support
2019-01-29 00:06:50 +01:00
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(v0.6.1.9044) first_isolate fix for species
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WHONET/EARS-Net support
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2019-02-14 10:23:51 +01:00
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2019-01-29 00:06:50 +01:00
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2019-02-14 10:23:51 +01:00
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<h1>How to work with WHONET data</h1>
<h4 class="author">Matthijs S. Berends</h4>
(v0.6.1.9044) first_isolate fix for species
2019-05-31 14:25:11 +02:00
<h4 class="date">31 May 2019</h4>
WHONET/EARS-Net support
2019-01-29 00:06:50 +01:00
<div class="hidden name"><code>WHONET.Rmd</code></div>
</div>
freq update
2019-01-29 20:20:09 +01:00
<div id="import-of-data" class="section level1">
<h1 class="hasAnchor">
<a href="#import-of-data" class="anchor"></a>Import of data</h1>
<p>This tutorial assumes you already imported the WHONET data with e.g. the <a href="https://readxl.tidyverse.org/"><code>readxl</code> package</a>. In RStudio, this can be done using the menu button ‘Import Dataset’ in the tab ‘Environment’. Choose the option ‘From Excel’ and select your exported file. Make sure date fields are imported correctly.</p>
<p>An example syntax could look like this:</p>
benchmarks plots
2019-02-14 10:23:51 +01:00
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(readxl)</a>
<a class="sourceLine" id="cb1-2" title="2">data &lt;-<span class="st"> </span><span class="kw"><a href="https://readxl.tidyverse.org/reference/read_excel.html">read_excel</a></span>(<span class="dt">path =</span> <span class="st">"path/to/your/file.xlsx"</span>)</a></code></pre></div>
freq update
2019-01-29 20:20:09 +01:00
<p>This package comes with an <a href="./reference/WHONET.html">example data set <code>WHONET</code></a>. We will use it for this analysis.</p>
</div>
<div id="preparation" class="section level1">
<h1 class="hasAnchor">
<a href="#preparation" class="anchor"></a>Preparation</h1>
<p>First, load the relevant packages if you did not yet did this. I use the tidyverse for all of my analyses. All of them. If you don’t know it yet, I suggest you read about it on their website: <a href="https://www.tidyverse.org/" class="uri">https://www.tidyverse.org/</a>.</p>
benchmarks plots
2019-02-14 10:23:51 +01:00
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(dplyr) <span class="co"># part of tidyverse</span></a>
<a class="sourceLine" id="cb2-2" title="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(ggplot2) <span class="co"># part of tidyverse</span></a>
<a class="sourceLine" id="cb2-3" title="3"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(AMR) <span class="co"># this package</span></a></code></pre></div>
freq update
2019-01-29 20:20:09 +01:00
<p>We will have to transform some variables to simplify and automate the analysis:</p>
<ul>
mo codes for WHONET
2019-02-08 16:06:54 +01:00
<li>Microorganisms should be transformed to our own microorganism IDs (called an <code>mo</code>) using <a href="./reference/ITIS.html">the ITIS reference data set</a>, which contains all ~20,000 microorganisms from the taxonomic kingdoms Bacteria, Fungi and Protozoa. We do the tranformation with <code><a href="../reference/as.mo.html">as.mo()</a></code>. This function also recognises almost all WHONET abbreviations of microorganisms.</li>
freq update
2019-01-29 20:20:09 +01:00
<li>Antimicrobial results or interpretations have to be clean and valid. In other words, they should only contain values <code>"S"</code>, <code>"I"</code> or <code>"R"</code>. That is exactly where the <code><a href="../reference/as.rsi.html">as.rsi()</a></code> function is for.</li>
</ul>
benchmarks plots
2019-02-14 10:23:51 +01:00
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" title="1"><span class="co"># transform variables</span></a>
<a class="sourceLine" id="cb3-2" title="2">data &lt;-<span class="st"> </span>WHONET <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb3-3" title="3"><span class="st"> </span><span class="co"># get microbial ID based on given organism</span></a>
<a class="sourceLine" id="cb3-4" title="4"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(<span class="dt">mo =</span> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(Organism)) <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb3-5" title="5"><span class="st"> </span><span class="co"># transform everything from "AMP_ND10" to "CIP_EE" to the new `rsi` class</span></a>
memory for as.mo()
2019-03-15 13:57:25 +01:00
<a class="sourceLine" id="cb3-6" title="6"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_at</a></span>(<span class="kw"><a href="https://dplyr.tidyverse.org/reference/vars.html">vars</a></span>(AMP_ND10<span class="op">:</span>CIP_EE), as.rsi)</a></code></pre></div>
freq update
2019-01-29 20:20:09 +01:00
<p>No errors or warnings, so all values are transformed succesfully. Let’s check it though, with a couple of frequency tables:</p>
benchmarks plots
2019-02-14 10:23:51 +01:00
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" title="1"><span class="co"># our newly created `mo` variable</span></a>
<a class="sourceLine" id="cb4-2" title="2">data <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(mo, <span class="dt">nmax =</span> <span class="dv">10</span>)</a></code></pre></div>
<p><strong>Frequency table of <code>mo</code> from a <code>data.frame</code> (500 x 54)</strong></p>
fixes for microorganisms.codes
2019-05-28 16:50:40 +02:00
<p>Class: mo (character)<br>
freq fix
2019-01-30 16:00:55 +01:00
Length: 500 (of which NA: 0 = 0.00%)<br>
v0.6.0
2019-03-27 11:22:36 +01:00
Unique: 39</p>
memory for as.mo()
2019-03-15 13:57:25 +01:00
<p>Families: 10<br>
Genera: 17<br>
v0.6.0
2019-03-27 11:22:36 +01:00
Species: 38</p>
freq update
2019-01-29 20:20:09 +01:00
<table class="table">
<thead><tr class="header">
<th align="left"></th>
<th align="left">Item</th>
<th align="right">Count</th>
<th align="right">Percent</th>
<th align="right">Cum. Count</th>
<th align="right">Cum. Percent</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="left">B_ESCHR_COL</td>
as.rsi warning, site update
2019-02-09 22:16:24 +01:00
<td align="right">245</td>
<td align="right">49.0%</td>
<td align="right">245</td>
<td align="right">49.0%</td>
freq update
2019-01-29 20:20:09 +01:00
</tr>
<tr class="even">
<td align="left">2</td>
v0.6.0
2019-03-27 11:22:36 +01:00
<td align="left">B_STPHY_CNS</td>
as.rsi warning, site update
2019-02-09 22:16:24 +01:00
<td align="right">74</td>
<td align="right">14.8%</td>
<td align="right">319</td>
<td align="right">63.8%</td>
freq update
2019-01-29 20:20:09 +01:00
</tr>
<tr class="odd">
<td align="left">3</td>
as.rsi warning, site update
2019-02-09 22:16:24 +01:00
<td align="left">B_STPHY_EPI</td>
<td align="right">38</td>
<td align="right">7.6%</td>
<td align="right">357</td>
<td align="right">71.4%</td>
freq update
2019-01-29 20:20:09 +01:00
</tr>
<tr class="even">
<td align="left">4</td>
Catalogue of Life, replaces ITIS
2019-02-18 02:33:37 +01:00
<td align="left">B_STRPT_PNE</td>
freq update
2019-01-29 20:20:09 +01:00
<td align="right">31</td>
<td align="right">6.2%</td>
as.rsi warning, site update
2019-02-09 22:16:24 +01:00
<td align="right">388</td>
<td align="right">77.6%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">B_STPHY_HOM</td>
<td align="right">21</td>
<td align="right">4.2%</td>
<td align="right">409</td>
<td align="right">81.8%</td>
freq update
2019-01-29 20:20:09 +01:00
</tr>
<tr class="even">
<td align="left">6</td>
as.rsi warning, site update
2019-02-09 22:16:24 +01:00
<td align="left">B_PROTS_MIR</td>
<td align="right">9</td>
<td align="right">1.8%</td>
<td align="right">418</td>
<td align="right">83.6%</td>
freq update
2019-01-29 20:20:09 +01:00
</tr>
<tr class="odd">
<td align="left">7</td>
as.rsi warning, site update
2019-02-09 22:16:24 +01:00
<td align="left">B_ENTRC_IUM</td>
<td align="right">8</td>
<td align="right">1.6%</td>
<td align="right">426</td>
<td align="right">85.2%</td>
freq update
2019-01-29 20:20:09 +01:00
</tr>
<tr class="even">
<td align="left">8</td>
as.rsi warning, site update
2019-02-09 22:16:24 +01:00
<td align="left">B_STPHY_CAP</td>
<td align="right">8</td>
<td align="right">1.6%</td>
<td align="right">434</td>
<td align="right">86.8%</td>
freq update
2019-01-29 20:20:09 +01:00
</tr>
<tr class="odd">
<td align="left">9</td>
memory for as.mo()
2019-03-15 13:57:25 +01:00
<td align="left">B_ENTRB_CLO</td>
<td align="right">5</td>
<td align="right">1.0%</td>
v0.6.0
2019-03-27 11:22:36 +01:00
<td align="right">439</td>
<td align="right">87.8%</td>
</tr>
<tr class="even">
<td align="left">10</td>
<td align="left">B_ENTRC_COL</td>
<td align="right">4</td>
<td align="right">0.8%</td>
<td align="right">443</td>
<td align="right">88.6%</td>
freq update
2019-01-29 20:20:09 +01:00
</tr>
</tbody>
</table>
v0.6.0
2019-03-27 11:22:36 +01:00
<p>(omitted 29 entries, n = 57 [11.4%])</p>
benchmarks plots
2019-02-14 10:23:51 +01:00
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" title="1"></a>
<a class="sourceLine" id="cb5-2" title="2"><span class="co"># our transformed antibiotic columns</span></a>
<a class="sourceLine" id="cb5-3" title="3"><span class="co"># amoxicillin/clavulanic acid (J01CR02) as an example</span></a>
<a class="sourceLine" id="cb5-4" title="4">data <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(AMC_ND2)</a></code></pre></div>
<p><strong>Frequency table of <code>AMC_ND2</code> from a <code>data.frame</code> (500 x 54)</strong></p>
fixes for microorganisms.codes
2019-05-28 16:50:40 +02:00
<p>Class: factor &gt; ordered &gt; rsi (numeric)<br>
as.rsi warning, site update
2019-02-09 22:16:24 +01:00
Length: 500 (of which NA: 19 = 3.80%)<br>
fixes for microorganisms.codes
2019-05-28 16:50:40 +02:00
Levels: 3: S &lt; I &lt; R<br>
freq fix
2019-01-30 16:00:55 +01:00
Unique: 3</p>
ab_info, other bug fixes
2019-05-16 21:20:00 +02:00
<p>Drug: Amoxicillin/clavulanic acid (AMC, J01CR02)<br>
Group: Beta-lactams/penicillins<br>
%SI: 78.59%</p>
freq update
2019-01-29 20:20:09 +01:00
<table class="table">
<thead><tr class="header">
<th align="left"></th>
<th align="left">Item</th>
<th align="right">Count</th>
<th align="right">Percent</th>
<th align="right">Cum. Count</th>
<th align="right">Cum. Percent</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="left">S</td>
as.rsi warning, site update
2019-02-09 22:16:24 +01:00
<td align="right">356</td>
<td align="right">74.0%</td>
<td align="right">356</td>
<td align="right">74.0%</td>
freq update
2019-01-29 20:20:09 +01:00
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">R</td>
as.rsi warning, site update
2019-02-09 22:16:24 +01:00
<td align="right">103</td>
<td align="right">21.4%</td>
<td align="right">459</td>
<td align="right">95.4%</td>
freq update
2019-01-29 20:20:09 +01:00
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">I</td>
<td align="right">22</td>
as.rsi warning, site update
2019-02-09 22:16:24 +01:00
<td align="right">4.6%</td>
<td align="right">481</td>
freq update
2019-01-29 20:20:09 +01:00
<td align="right">100.0%</td>
</tr>
</tbody>
</table>
</div>
<div id="analysis" class="section level1">
<h1 class="hasAnchor">
<a href="#analysis" class="anchor"></a>Analysis</h1>
<p><em>(more will be available soon)</em></p>
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WHONET/EARS-Net support
2019-01-29 00:06:50 +01:00
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freq update
2019-01-29 20:20:09 +01:00
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<h2 class="hasAnchor">
<a href="#tocnav" class="anchor"></a>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#import-of-data">Import of data</a></li>
<li><a href="#preparation">Preparation</a></li>
<li><a href="#analysis">Analysis</a></li>
</ul>
</div>
WHONET/EARS-Net support
2019-01-29 00:06:50 +01:00
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