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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="">1.8.2.9146</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9147</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">
@ -61,11 +61,6 @@
How to
</a>
<div class="dropdown-menu" aria-labelledby="dropdown--how-to">
<a class="dropdown-item" href="../reference/AMR-options.html">
<span class="fa fa-gear"></span>
User- Or Team-specific Package Settings
</a>
<a class="dropdown-item" href="../articles/AMR.html">
<span class="fa fa-directions"></span>
@ -84,7 +79,12 @@
<a class="dropdown-item" href="../articles/datasets.html">
<span class="fa fa-database"></span>
Data Sets for Download / Own Use
Download Data Sets for Own Use
</a>
<a class="dropdown-item" href="../reference/AMR-options.html">
<span class="fa fa-gear"></span>
Set User- Or Team-specific Package Settings
</a>
<a class="dropdown-item" href="../articles/PCA.html">
<span class="fa fa-compress"></span>

70
articles/MDR.html
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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="">1.8.2.9146</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9147</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">
@ -61,11 +61,6 @@
How to
</a>
<div class="dropdown-menu" aria-labelledby="dropdown--how-to">
<a class="dropdown-item" href="../reference/AMR-options.html">
<span class="fa fa-gear"></span>
User- Or Team-specific Package Settings
</a>
<a class="dropdown-item" href="../articles/AMR.html">
<span class="fa fa-directions"></span>
@ -84,7 +79,12 @@
<a class="dropdown-item" href="../articles/datasets.html">
<span class="fa fa-database"></span>
Data Sets for Download / Own Use
Download Data Sets for Own Use
</a>
<a class="dropdown-item" href="../reference/AMR-options.html">
<span class="fa fa-gear"></span>
Set User- Or Team-specific Package Settings
</a>
<a class="dropdown-item" href="../articles/PCA.html">
<span class="fa fa-compress"></span>
@ -385,18 +385,18 @@ 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 R R I S S R</span></span>
<span><span class="co">#&gt; 2 I R S R S R</span></span>
<span><span class="co">#&gt; 3 S R I S S R</span></span>
<span><span class="co">#&gt; 4 R R I S R S</span></span>
<span><span class="co">#&gt; 5 R R I I S I</span></span>
<span><span class="co">#&gt; 6 I R I R S R</span></span>
<span><span class="co">#&gt; 1 S S I S I S</span></span>
<span><span class="co">#&gt; 2 I S S I R I</span></span>
<span><span class="co">#&gt; 3 S S S S I S</span></span>
<span><span class="co">#&gt; 4 I I S R I I</span></span>
<span><span class="co">#&gt; 5 S I S R R S</span></span>
<span><span class="co">#&gt; 6 S S R R R R</span></span>
<span><span class="co">#&gt; kanamycin</span></span>
<span><span class="co">#&gt; 1 R</span></span>
<span><span class="co">#&gt; 2 R</span></span>
<span><span class="co">#&gt; 3 S</span></span>
<span><span class="co">#&gt; 1 S</span></span>
<span><span class="co">#&gt; 2 I</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 S</span></span>
<span><span class="co">#&gt; 5 R</span></span>
<span><span class="co">#&gt; 6 I</span></span></code></pre></div>
<p>We can now add the interpretation of MDR-TB to our data set. You can
use:</p>
@ -438,40 +438,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3270</td>
<td align="right">65.40%</td>
<td align="right">3270</td>
<td align="right">65.40%</td>
<td align="right">3246</td>
<td align="right">64.92%</td>
<td align="right">3246</td>
<td align="right">64.92%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">967</td>
<td align="right">19.34%</td>
<td align="right">4237</td>
<td align="right">84.74%</td>
<td align="right">939</td>
<td align="right">18.78%</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">437</td>
<td align="right">8.74%</td>
<td align="right">4674</td>
<td align="right">93.48%</td>
<td align="right">467</td>
<td align="right">9.34%</td>
<td align="right">4652</td>
<td align="right">93.04%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">227</td>
<td align="right">4.54%</td>
<td align="right">4901</td>
<td align="right">98.02%</td>
<td align="right">243</td>
<td align="right">4.86%</td>
<td align="right">4895</td>
<td align="right">97.90%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">99</td>
<td align="right">1.98%</td>
<td align="right">105</td>
<td align="right">2.10%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>

14
articles/PCA.html
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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="">1.8.2.9146</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9147</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">
@ -61,11 +61,6 @@
How to
</a>
<div class="dropdown-menu" aria-labelledby="dropdown--how-to">
<a class="dropdown-item" href="../reference/AMR-options.html">
<span class="fa fa-gear"></span>
User- Or Team-specific Package Settings
</a>
<a class="dropdown-item" href="../articles/AMR.html">
<span class="fa fa-directions"></span>
@ -84,7 +79,12 @@
<a class="dropdown-item" href="../articles/datasets.html">
<span class="fa fa-database"></span>
Data Sets for Download / Own Use
Download Data Sets for Own Use
</a>
<a class="dropdown-item" href="../reference/AMR-options.html">
<span class="fa fa-gear"></span>
Set User- Or Team-specific Package Settings
</a>
<a class="dropdown-item" href="../articles/PCA.html">
<span class="fa fa-compress"></span>

18
articles/SPSS.html
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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="">1.8.2.9146</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9147</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">
@ -61,11 +61,6 @@
How to
</a>
<div class="dropdown-menu" aria-labelledby="dropdown--how-to">
<a class="dropdown-item" href="../reference/AMR-options.html">
<span class="fa fa-gear"></span>
User- Or Team-specific Package Settings
</a>
<a class="dropdown-item" href="../articles/AMR.html">
<span class="fa fa-directions"></span>
@ -84,7 +79,12 @@
<a class="dropdown-item" href="../articles/datasets.html">
<span class="fa fa-database"></span>
Data Sets for Download / Own Use
Download Data Sets for Own Use
</a>
<a class="dropdown-item" href="../reference/AMR-options.html">
<span class="fa fa-gear"></span>
Set User- Or Team-specific Package Settings
</a>
<a class="dropdown-item" href="../articles/PCA.html">
<span class="fa fa-compress"></span>
@ -178,7 +178,7 @@
<h4 data-toc-skip class="author">Dr. Matthijs
Berends</h4>
<h4 data-toc-skip class="date">24 February 2023</h4>
<h4 data-toc-skip class="date">26 February 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">481 631
online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes" class="external-link">482 447
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

14
articles/WHONET.html
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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="">1.8.2.9146</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9147</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">
@ -61,11 +61,6 @@
How to
</a>
<div class="dropdown-menu" aria-labelledby="dropdown--how-to">
<a class="dropdown-item" href="../reference/AMR-options.html">
<span class="fa fa-gear"></span>
User- Or Team-specific Package Settings
</a>
<a class="dropdown-item" href="../articles/AMR.html">
<span class="fa fa-directions"></span>
@ -84,7 +79,12 @@
<a class="dropdown-item" href="../articles/datasets.html">
<span class="fa fa-database"></span>
Data Sets for Download / Own Use
Download Data Sets for Own Use
</a>
<a class="dropdown-item" href="../reference/AMR-options.html">
<span class="fa fa-gear"></span>
Set User- Or Team-specific Package Settings
</a>
<a class="dropdown-item" href="../articles/PCA.html">
<span class="fa fa-compress"></span>

18
articles/datasets.html
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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="">1.8.2.9146</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9147</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">
@ -61,11 +61,6 @@
How to
</a>
<div class="dropdown-menu" aria-labelledby="dropdown--how-to">
<a class="dropdown-item" href="../reference/AMR-options.html">
<span class="fa fa-gear"></span>
User- Or Team-specific Package Settings
</a>
<a class="dropdown-item" href="../articles/AMR.html">
<span class="fa fa-directions"></span>
@ -84,7 +79,12 @@
<a class="dropdown-item" href="../articles/datasets.html">
<span class="fa fa-database"></span>
Data Sets for Download / Own Use
Download Data Sets for Own Use
</a>
<a class="dropdown-item" href="../reference/AMR-options.html">
<span class="fa fa-gear"></span>
Set User- Or Team-specific Package Settings
</a>
<a class="dropdown-item" href="../articles/PCA.html">
<span class="fa fa-compress"></span>
@ -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">24 February 2023</h4>
<h4 data-toc-skip class="date">26 February 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>
@ -206,7 +206,7 @@ column names:<br><em>mo</em>, <em>fullname</em>, <em>status</em>, <em>kingdom</e
<em>gbif_renamed_to</em>, <em>prevalence</em>, and <em>snomed</em>.</p>
<p>This data set is in R available as <code>microorganisms</code>, after
you load the <code>AMR</code> package.</p>
<p>It was last updated on 6 February 2023 10:57:22 UTC. Find more info
<p>It was last updated on 26 February 2023 20:26:58 UTC. Find more info
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>

14
articles/index.html
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@ -10,7 +10,7 @@
<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="">1.8.2.9146</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9147</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">
@ -32,11 +32,6 @@
How to
</a>
<div class="dropdown-menu" aria-labelledby="dropdown--how-to">
<a class="dropdown-item" href="../reference/AMR-options.html">
<span class="fa fa-gear"></span>
User- Or Team-specific Package Settings
</a>
<a class="dropdown-item" href="../articles/AMR.html">
<span class="fa fa-directions"></span>
@ -55,7 +50,12 @@
<a class="dropdown-item" href="../articles/datasets.html">
<span class="fa fa-database"></span>
Data Sets for Download / Own Use
Download Data Sets for Own Use
</a>
<a class="dropdown-item" href="../reference/AMR-options.html">
<span class="fa fa-gear"></span>
Set User- Or Team-specific Package Settings
</a>
<a class="dropdown-item" href="../articles/PCA.html">
<span class="fa fa-compress"></span>

14
articles/resistance_predict.html
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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="">1.8.2.9146</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9147</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">
@ -61,11 +61,6 @@
How to
</a>
<div class="dropdown-menu" aria-labelledby="dropdown--how-to">
<a class="dropdown-item" href="../reference/AMR-options.html">
<span class="fa fa-gear"></span>
User- Or Team-specific Package Settings
</a>
<a class="dropdown-item" href="../articles/AMR.html">
<span class="fa fa-directions"></span>
@ -84,7 +79,12 @@
<a class="dropdown-item" href="../articles/datasets.html">
<span class="fa fa-database"></span>
Data Sets for Download / Own Use
Download Data Sets for Own Use
</a>
<a class="dropdown-item" href="../reference/AMR-options.html">
<span class="fa fa-gear"></span>
Set User- Or Team-specific Package Settings
</a>
<a class="dropdown-item" href="../articles/PCA.html">
<span class="fa fa-compress"></span>

14
articles/welcome_to_AMR.html
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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="">1.8.2.9146</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9147</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">
@ -61,11 +61,6 @@
How to
</a>
<div class="dropdown-menu" aria-labelledby="dropdown--how-to">
<a class="dropdown-item" href="../reference/AMR-options.html">
<span class="fa fa-gear"></span>
User- Or Team-specific Package Settings
</a>
<a class="dropdown-item" href="../articles/AMR.html">
<span class="fa fa-directions"></span>
@ -84,7 +79,12 @@
<a class="dropdown-item" href="../articles/datasets.html">
<span class="fa fa-database"></span>
Data Sets for Download / Own Use
Download Data Sets for Own Use
</a>
<a class="dropdown-item" href="../reference/AMR-options.html">
<span class="fa fa-gear"></span>
Set User- Or Team-specific Package Settings
</a>
<a class="dropdown-item" href="../articles/PCA.html">
<span class="fa fa-compress"></span>