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(v0.7.1.9090) factor levels of mdr_tb

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dr. M.S. (Matthijs) Berends 2019-09-26 21:58:06 +02:00
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DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR
Version: 0.7.1.9089
Date: 2019-09-25
Version: 0.7.1.9090
Date: 2019-09-26
Title: Antimicrobial Resistance Analysis
Authors@R: c(
person(role = c("aut", "cre"),

5
NEWS.md
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@ -1,5 +1,5 @@
# AMR 0.7.1.9089
<small>Last updated: 25-Sep-2019</small>
# AMR 0.7.1.9090
<small>Last updated: 26-Sep-2019</small>
### Breaking
* Determination of first isolates now **excludes** all 'unknown' microorganisms at default, i.e. microbial code `"UNKNOWN"`. They can be included with the new parameter `include_unknown`:
@ -118,6 +118,7 @@
* Fix for determining the system's language
* Fix for `key_antibiotics()` on foreign systems
* Added 80 new LIS codes for microorganisms
* Relabeled the factor levels of `mdr_tb()`
#### Other
* Added Prof. Dr. Casper Albers as doctoral advisor and added Dr. Judith Fonville, Eric Hazenberg, Dr. Bart Meijer, Dr. Dennis Souverein and Annick Lenglet as contributors

2
R/mdro.R
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@ -484,7 +484,7 @@ mdro <- function(x,
if (guideline$code == "tb") {
factor(x = x$mdr_tb,
levels = 1:5,
labels = c("Negative", "Mono-resistance", "Poly-resistance", "Multidrug resistance", "Extensive drug resistance"),
labels = c("Negative", "Mono-resistant", "Poly-resistant", "Multi-drug-resistant", "Extensive drug-resistant"),
ordered = TRUE)
} else {
factor(x = x$MDRO,

2
docs/404.html
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9090</span>
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101
docs/articles/MDR.html
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@ -13,8 +13,9 @@
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@ -40,7 +41,7 @@
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@ -179,13 +180,14 @@
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<h1>How to determine multi-drug resistance (MDR)</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">13 August 2019</h4>
<h4 class="date">26 September 2019</h4>
<div class="hidden name"><code>MDR.Rmd</code></div>
@ -202,15 +204,15 @@
</ul>
<p>As an example, I will make a data set to determine multi-drug resistant TB:</p>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="co"># a helper function to get a random vector with values S, I and R</span></a>
<a class="sourceLine" id="cb1-2" data-line-number="2"><span class="co"># with the probabilities 50%-10%-40%</span></a>
<a class="sourceLine" id="cb1-2" data-line-number="2"><span class="co"># with the probabilities 50% - 10% - 40%</span></a>
<a class="sourceLine" id="cb1-3" data-line-number="3">sample_rsi &lt;-<span class="st"> </span><span class="cf">function</span>() {</a>
<a class="sourceLine" id="cb1-4" data-line-number="4"> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/sample">sample</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"S"</span>, <span class="st">"I"</span>, <span class="st">"R"</span>),</a>
<a class="sourceLine" id="cb1-4" data-line-number="4"> <span class="kw"><a href="https://rdrr.io/r/base/sample.html">sample</a></span>(<span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"S"</span>, <span class="st">"I"</span>, <span class="st">"R"</span>),</a>
<a class="sourceLine" id="cb1-5" data-line-number="5"> <span class="dt">size =</span> <span class="dv">5000</span>,</a>
<a class="sourceLine" id="cb1-6" data-line-number="6"> <span class="dt">prob =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="fl">0.5</span>, <span class="fl">0.1</span>, <span class="fl">0.4</span>),</a>
<a class="sourceLine" id="cb1-6" data-line-number="6"> <span class="dt">prob =</span> <span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="fl">0.5</span>, <span class="fl">0.1</span>, <span class="fl">0.4</span>),</a>
<a class="sourceLine" id="cb1-7" data-line-number="7"> <span class="dt">replace =</span> <span class="ot">TRUE</span>)</a>
<a class="sourceLine" id="cb1-8" data-line-number="8">}</a>
<a class="sourceLine" id="cb1-9" data-line-number="9"></a>
<a class="sourceLine" id="cb1-10" data-line-number="10">my_TB_data &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/data.frame">data.frame</a></span>(<span class="dt">rifampicin =</span> <span class="kw">sample_rsi</span>(),</a>
<a class="sourceLine" id="cb1-10" data-line-number="10">my_TB_data &lt;-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span>(<span class="dt">rifampicin =</span> <span class="kw">sample_rsi</span>(),</a>
<a class="sourceLine" id="cb1-11" data-line-number="11"> <span class="dt">isoniazid =</span> <span class="kw">sample_rsi</span>(),</a>
<a class="sourceLine" id="cb1-12" data-line-number="12"> <span class="dt">gatifloxacin =</span> <span class="kw">sample_rsi</span>(),</a>
<a class="sourceLine" id="cb1-13" data-line-number="13"> <span class="dt">ethambutol =</span> <span class="kw">sample_rsi</span>(),</a>
@ -218,7 +220,7 @@
<a class="sourceLine" id="cb1-15" data-line-number="15"> <span class="dt">moxifloxacin =</span> <span class="kw">sample_rsi</span>(),</a>
<a class="sourceLine" id="cb1-16" data-line-number="16"> <span class="dt">kanamycin =</span> <span class="kw">sample_rsi</span>())</a></code></pre></div>
<p>Because all column names are automatically verified for valid drug names or codes, this would have worked exactly the same:</p>
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" data-line-number="1">my_TB_data &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/data.frame">data.frame</a></span>(<span class="dt">RIF =</span> <span class="kw">sample_rsi</span>(),</a>
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" data-line-number="1">my_TB_data &lt;-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span>(<span class="dt">RIF =</span> <span class="kw">sample_rsi</span>(),</a>
<a class="sourceLine" id="cb2-2" data-line-number="2"> <span class="dt">INH =</span> <span class="kw">sample_rsi</span>(),</a>
<a class="sourceLine" id="cb2-3" data-line-number="3"> <span class="dt">GAT =</span> <span class="kw">sample_rsi</span>(),</a>
<a class="sourceLine" id="cb2-4" data-line-number="4"> <span class="dt">ETH =</span> <span class="kw">sample_rsi</span>(),</a>
@ -226,21 +228,21 @@
<a class="sourceLine" id="cb2-6" data-line-number="6"> <span class="dt">MFX =</span> <span class="kw">sample_rsi</span>(),</a>
<a class="sourceLine" id="cb2-7" data-line-number="7"> <span class="dt">KAN =</span> <span class="kw">sample_rsi</span>())</a></code></pre></div>
<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>
<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://rdrr.io/r/utils/head.html">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 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="cb3-3" data-line-number="3"><span class="co"># 1 R R R R S R</span></a>
<a class="sourceLine" id="cb3-4" data-line-number="4"><span class="co"># 2 R I R R R R</span></a>
<a class="sourceLine" id="cb3-5" data-line-number="5"><span class="co"># 3 S S R S R R</span></a>
<a class="sourceLine" id="cb3-6" data-line-number="6"><span class="co"># 4 S I S S R I</span></a>
<a class="sourceLine" id="cb3-7" data-line-number="7"><span class="co"># 5 I S R R R S</span></a>
<a class="sourceLine" id="cb3-8" data-line-number="8"><span class="co"># 6 R S S S R 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 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 S</span></a></code></pre></div>
<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 S</span></a>
<a class="sourceLine" id="cb3-14" data-line-number="14"><span class="co"># 5 I</span></a>
<a class="sourceLine" id="cb3-15" data-line-number="15"><span class="co"># 6 I</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">$</span>mdr &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mdro.html">mdr_tb</a></span>(my_TB_data)</a>
<a class="sourceLine" id="cb4-2" data-line-number="2"><span class="co"># </span><span class="al">NOTE</span><span class="co">: No column found as input for `col_mo`, assuming all records contain Mycobacterium tuberculosis.</span></a>
@ -251,13 +253,13 @@
<a class="sourceLine" id="cb4-7" data-line-number="7"><span class="co"># Source: https://www.who.int/tb/publications/pmdt_companionhandbook/en/</span></a>
<a class="sourceLine" id="cb4-8" data-line-number="8"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Reliability might be improved if these antimicrobial results would be available too: CAP (capreomycin), RIB (rifabutin), RFP (rifapentine)</span></a></code></pre></div>
<p>We also created a package dedicated to data cleaning and checking, called the <code>clean</code> package. It gets automatically installed with the <code>AMR</code> package, so we only have to load it:</p>
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(clean)</a></code></pre></div>
<p>It contains the <code><a href="https://www.rdocumentation.org/packages/clean/topics/freq">freq()</a></code> function, to create a frequency table:</p>
<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/clean/topics/freq">freq</a></span>(my_TB_data<span class="op">$</span>mdr)</a></code></pre></div>
<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://rdrr.io/r/base/library.html">library</a></span>(clean)</a></code></pre></div>
<p>It contains the <code><a href="https://rdrr.io/pkg/clean/man/freq.html">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://rdrr.io/pkg/clean/man/freq.html">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>
Levels: 5: Negative &lt; Mono-resistant &lt; Poly-resistant &lt; Multi-drug-resistant &lt;…<br>
Unique: 5</p>
<table class="table">
<thead><tr class="header">
@ -271,40 +273,40 @@ Unique: 5</p>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistance</td>
<td align="right">3308</td>
<td align="right">66.2%</td>
<td align="right">3308</td>
<td align="right">66.2%</td>
<td align="left">Mono-resistant</td>
<td align="right">3255</td>
<td align="right">65.1%</td>
<td align="right">3255</td>
<td align="right">65.1%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">643</td>
<td align="right">12.9%</td>
<td align="right">3951</td>
<td align="right">79.0%</td>
<td align="right">638</td>
<td align="right">12.8%</td>
<td align="right">3893</td>
<td align="right">77.9%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multidrug resistance</td>
<td align="right">570</td>
<td align="right">11.4%</td>
<td align="right">4521</td>
<td align="right">90.4%</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">618</td>
<td align="right">12.4%</td>
<td align="right">4511</td>
<td align="right">90.2%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistance</td>
<td align="right">263</td>
<td align="right">5.3%</td>
<td align="right">4784</td>
<td align="left">Poly-resistant</td>
<td align="right">276</td>
<td align="right">5.5%</td>
<td align="right">4787</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">216</td>
<td align="left">Extensive drug-resistant</td>
<td align="right">213</td>
<td align="right">4.3%</td>
<td align="right">5000</td>
<td align="right">100.0%</td>
@ -314,18 +316,21 @@ Unique: 5</p>
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<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>
<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.j.albers/">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a>.</p>
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@ -84,7 +84,7 @@
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<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">0.7.1.9089</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9090</span>
</span>
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@ -84,7 +84,7 @@
</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">0.7.1.9089</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9090</span>
</span>
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2
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@ -43,7 +43,7 @@
</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">0.7.1.9089</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9090</span>
</span>
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docs/news/index.html
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@ -84,7 +84,7 @@
</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">0.7.1.9089</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9090</span>
</span>
</div>
@ -231,11 +231,11 @@
</div>
<div id="amr-0-7-1-9089" class="section level1">
<div id="amr-0-7-1-9090" class="section level1">
<h1 class="page-header">
<a href="#amr-0-7-1-9089" class="anchor"></a>AMR 0.7.1.9089<small> Unreleased </small>
<a href="#amr-0-7-1-9090" class="anchor"></a>AMR 0.7.1.9090<small> Unreleased </small>
</h1>
<p><small>Last updated: 25-Sep-2019</small></p>
<p><small>Last updated: 26-Sep-2019</small></p>
<div id="breaking" class="section level3">
<h3 class="hasAnchor">
<a href="#breaking" class="anchor"></a>Breaking</h3>
@ -367,6 +367,8 @@ Since this is a major change, usage of the old <code>also_single_tested</code> w
<li>Fix for determining the system’s language</li>
<li>Fix for <code><a href="../reference/key_antibiotics.html">key_antibiotics()</a></code> on foreign systems</li>
<li>Added 80 new LIS codes for microorganisms</li>
<li>Relabeled the factor levels of <code><a href="../reference/mdro.html">mdr_tb()</a></code>
</li>
</ul>
<div id="other" class="section level4">
<h4 class="hasAnchor">
@ -1286,7 +1288,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<div id="tocnav">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#amr-0-7-1-9089">0.7.1.9089</a></li>
<li><a href="#amr-0-7-1-9090">0.7.1.9090</a></li>
<li><a href="#amr-0-7-1">0.7.1</a></li>
<li><a href="#amr-0-7-0">0.7.0</a></li>
<li><a href="#amr-0-6-1">0.6.1</a></li>

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docs/reference/index.html
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@ -84,7 +84,7 @@
</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">0.7.1.9089</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9090</span>
</span>
</div>

2
vignettes/MDR.Rmd
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@ -31,7 +31,7 @@ As an example, I will make a data set to determine multi-drug resistant TB:
```{r}
# a helper function to get a random vector with values S, I and R
# with the probabilities 50%-10%-40%
# with the probabilities 50% - 10% - 40%
sample_rsi <- function() {
sample(c("S", "I", "R"),
size = 5000,