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10
articles/AMR.html
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@@ -30,7 +30,7 @@
<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="">3.0.1.9008</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9012</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">
@@ -91,7 +91,7 @@
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 06 January 2026.</p>
generated on 07 January 2026.</p>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
@@ -147,21 +147,21 @@ make the structure of your data generally look like this:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2026-01-06</td>
<td align="center">2026-01-07</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">2026-01-06</td>
<td align="center">2026-01-07</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">2026-01-06</td>
<td align="center">2026-01-07</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>

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articles/AMR.md
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@@ -3,7 +3,7 @@
**Note:** values on this page will change with every website update
since they are based on randomly created values and the page was written
in [R Markdown](https://rmarkdown.rstudio.com/). However, the
methodology remains unchanged. This page was generated on 06 January
methodology remains unchanged. This page was generated on 07 January
2026.
## Introduction
@@ -52,9 +52,9 @@ structure of your data generally look like this:
| date | patient_id | mo | AMX | CIP |
|:----------:|:----------:|:----------------:|:---:|:---:|
| 2026-01-06 | abcd | Escherichia coli | S | S |
| 2026-01-06 | abcd | Escherichia coli | S | R |
| 2026-01-06 | efgh | Escherichia coli | R | S |
| 2026-01-07 | abcd | Escherichia coli | S | S |
| 2026-01-07 | abcd | Escherichia coli | S | R |
| 2026-01-07 | efgh | Escherichia coli | R | S |
### Needed R packages

2
articles/AMR_for_Python.html
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@@ -30,7 +30,7 @@
<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="">3.0.1.9008</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9012</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">

2
articles/AMR_with_tidymodels.html
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@@ -30,7 +30,7 @@
<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="">3.0.1.9008</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9012</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">

2
articles/EUCAST.html
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@@ -30,7 +30,7 @@
<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="">3.0.1.9008</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9012</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">

4
articles/PCA.html
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@@ -30,7 +30,7 @@
<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="">3.0.1.9008</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9012</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">
@@ -194,7 +194,7 @@ function:</p>
<span><span class="co">#&gt; [1] "Caryophanales" "Enterobacterales" "Lactobacillales" "Pseudomonadales"</span></span>
<span><span class="co">#&gt; Importance of components:</span></span>
<span><span class="co">#&gt; PC1 PC2 PC3 PC4 PC5 PC6 PC7</span></span>
<span><span class="co">#&gt; Standard deviation 2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 1.232e-16</span></span>
<span><span class="co">#&gt; Standard deviation 2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 9.577e-17</span></span>
<span><span class="co">#&gt; Proportion of Variance 0.5799 0.3531 0.0471 0.01435 0.00541 0.00012 0.000e+00</span></span>
<span><span class="co">#&gt; Cumulative Proportion 0.5799 0.9330 0.9801 0.99446 0.99988 1.00000 1.000e+00</span></span></code></pre></div>
<pre><code><span><span class="co">#&gt; Groups (n=4, named as 'order'):</span></span>

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articles/PCA.md
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@@ -113,7 +113,7 @@ summary(pca_result)
#> [1] "Caryophanales" "Enterobacterales" "Lactobacillales" "Pseudomonadales"
#> Importance of components:
#> PC1 PC2 PC3 PC4 PC5 PC6 PC7
#> Standard deviation 2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 1.232e-16
#> Standard deviation 2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 9.577e-17
#> Proportion of Variance 0.5799 0.3531 0.0471 0.01435 0.00541 0.00012 0.000e+00
#> Cumulative Proportion 0.5799 0.9330 0.9801 0.99446 0.99988 1.00000 1.000e+00
```

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articles/WHONET.html
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@@ -30,7 +30,7 @@
<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="">3.0.1.9008</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9012</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">

8
articles/WISCA.html
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@@ -30,7 +30,7 @@
<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="">3.0.1.9008</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9012</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">
@@ -368,9 +368,9 @@ all be used for the <code><a href="../reference/antibiogram.html">wisca()</a></c
</colgroup>
<thead><tr class="header">
<th align="left">Grupo sindrómico</th>
<th align="left">Amoxicillin ácido clavulánico</th>
<th align="left">Amoxicillin ácido clavulánico + Ciprofloxacin</th>
<th align="left">Amoxicillin ácido clavulánico + Gentamicina</th>
<th align="left">Amoxicillin/ácido clavulánico</th>
<th align="left">Amoxicillin/ácido clavulánico + Ciprofloxacin</th>
<th align="left">Amoxicillin/ácido clavulánico + Gentamicina</th>
</tr></thead>
<tbody>
<tr class="odd">

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articles/WISCA.md
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@@ -207,7 +207,7 @@ wisca(data,
language = "Spanish")
```
| Grupo sindrómico | Amoxicillin ácido clavulánico | Amoxicillin ácido clavulánico + Ciprofloxacin | Amoxicillin ácido clavulánico + Gentamicina |
| Grupo sindrómico | Amoxicillin/ácido clavulánico | Amoxicillin/ácido clavulánico + Ciprofloxacin | Amoxicillin/ácido clavulánico + Gentamicina |
|:-----------------|:------------------------------|:----------------------------------------------|:--------------------------------------------|
| No UCI | 70% (67.8-72.4%) | 85.3% (83.3-87.2%) | 87% (85.3-88.8%) |
| UCI | 80.9% (77.7-83.9%) | 88.2% (85.5-90.6%) | 90.9% (88.7-93%) |

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articles/datasets.html
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@@ -30,7 +30,7 @@
<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="">3.0.1.9008</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9012</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">
@@ -80,7 +80,7 @@
<main id="main" class="col-md-9"><div class="page-header">
<img src="../logo.svg" class="logo" alt=""><h1>Download data sets for download / own use</h1>
<h4 data-toc-skip class="date">06 January 2026</h4>
<h4 data-toc-skip class="date">07 January 2026</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/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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articles/index.html
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@@ -7,7 +7,7 @@
<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="">3.0.1.9008</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9012</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">