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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9013</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -187,7 +187,7 @@
website update since they are based on randomly created values and the
page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R
Markdown</a>. However, the methodology remains unchanged. This page was
generated on 21 April 2023.</p>
generated on 08 May 2023.</p>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
@ -243,21 +243,21 @@ make the structure of your data generally look like this:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2023-04-21</td>
<td align="center">2023-05-08</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="even">
<td align="center">2023-04-21</td>
<td align="center">2023-05-08</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
</tr>
<tr class="odd">
<td align="center">2023-04-21</td>
<td align="center">2023-05-08</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>

4
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9013</small>
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9013</small>
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@ -385,19 +385,19 @@ names or codes, this would have worked exactly the same way:</p>
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span></span>
<span><span class="co">#&gt; rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
<span><span class="co">#&gt; 1 S I R I S S</span></span>
<span><span class="co">#&gt; 2 I I R I R R</span></span>
<span><span class="co">#&gt; 3 I S S I R R</span></span>
<span><span class="co">#&gt; 4 I R R I I I</span></span>
<span><span class="co">#&gt; 5 I S S R I R</span></span>
<span><span class="co">#&gt; 6 R R I R S I</span></span>
<span><span class="co">#&gt; 1 S R R S R R</span></span>
<span><span class="co">#&gt; 2 S R S I S R</span></span>
<span><span class="co">#&gt; 3 S R I I I S</span></span>
<span><span class="co">#&gt; 4 S I R I R R</span></span>
<span><span class="co">#&gt; 5 R S R R R I</span></span>
<span><span class="co">#&gt; 6 S S S R I R</span></span>
<span><span class="co">#&gt; kanamycin</span></span>
<span><span class="co">#&gt; 1 S</span></span>
<span><span class="co">#&gt; 2 S</span></span>
<span><span class="co">#&gt; 3 S</span></span>
<span><span class="co">#&gt; 4 R</span></span>
<span><span class="co">#&gt; 5 S</span></span>
<span><span class="co">#&gt; 6 S</span></span></code></pre></div>
<span><span class="co">#&gt; 1 I</span></span>
<span><span class="co">#&gt; 2 R</span></span>
<span><span class="co">#&gt; 3 I</span></span>
<span><span class="co">#&gt; 4 S</span></span>
<span><span class="co">#&gt; 5 R</span></span>
<span><span class="co">#&gt; 6 R</span></span></code></pre></div>
<p>We can now add the interpretation of MDR-TB to our data set. You can
use:</p>
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
@ -438,40 +438,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3159</td>
<td align="right">63.18%</td>
<td align="right">3159</td>
<td align="right">63.18%</td>
<td align="right">3189</td>
<td align="right">63.78%</td>
<td align="right">3189</td>
<td align="right">63.78%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">992</td>
<td align="right">19.84%</td>
<td align="right">4151</td>
<td align="right">83.02%</td>
<td align="right">996</td>
<td align="right">19.92%</td>
<td align="right">4185</td>
<td align="right">83.70%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">472</td>
<td align="right">9.44%</td>
<td align="right">4623</td>
<td align="right">92.46%</td>
<td align="right">465</td>
<td align="right">9.30%</td>
<td align="right">4650</td>
<td align="right">93.00%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">260</td>
<td align="right">5.20%</td>
<td align="right">4883</td>
<td align="right">97.66%</td>
<td align="right">239</td>
<td align="right">4.78%</td>
<td align="right">4889</td>
<td align="right">97.78%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">117</td>
<td align="right">2.34%</td>
<td align="right">111</td>
<td align="right">2.22%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>

4
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9013</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9013</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -178,7 +178,7 @@
<h4 data-toc-skip class="author">Dr. Matthijs
Berends</h4>
<h4 data-toc-skip class="date">21 April 2023</h4>
<h4 data-toc-skip class="date">08 May 2023</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/SPSS.Rmd" class="external-link"><code>vignettes/SPSS.Rmd</code></a></small>
<div class="d-none name"><code>SPSS.Rmd</code></div>
@ -257,7 +257,7 @@ data using a custom made website. The webdesign knowledge needed
<li>
<p><strong>R has a huge community.</strong></p>
<p>Many R users just ask questions on websites like <a href="https://stackoverflow.com" class="external-link">StackOverflow.com</a>, the largest
online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes" class="external-link">487 449
online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes" class="external-link">489 114
R-related questions</a> have already been asked on this platform (that
covers questions and answers for any programming language). In my own
experience, most questions are answered within a couple of

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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9013</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9013</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -176,7 +176,7 @@
<main id="main" class="col-md-9"><div class="page-header">
<img src="../logo.svg" class="logo" alt=""><h1>Data sets for download / own use</h1>
<h4 data-toc-skip class="date">21 April 2023</h4>
<h4 data-toc-skip class="date">08 May 2023</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
<div class="d-none name"><code>datasets.Rmd</code></div>

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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9013</small>
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4
articles/welcome_to_AMR.html
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@ -15,7 +15,7 @@
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@ -38,7 +38,7 @@
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9013</small>
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