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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="">3.0.1.9047</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9048</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 21 April 2026.</p>
generated on 22 April 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">2026-04-21</td>
<td align="center">2026-04-22</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">2026-04-21</td>
<td align="center">2026-04-22</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">2026-04-21</td>
<td align="center">2026-04-22</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>

8
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 21 April 2026.
methodology remains unchanged. This page was generated on 22 April 2026.
## Introduction
@@ -51,9 +51,9 @@ structure of your data generally look like this:
| date | patient_id | mo | AMX | CIP |
|:----------:|:----------:|:----------------:|:---:|:---:|
| 2026-04-21 | abcd | Escherichia coli | S | S |
| 2026-04-21 | abcd | Escherichia coli | S | R |
| 2026-04-21 | efgh | Escherichia coli | R | S |
| 2026-04-22 | abcd | Escherichia coli | S | S |
| 2026-04-22 | abcd | Escherichia coli | S | R |
| 2026-04-22 | 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="">3.0.1.9047</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9048</small>
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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="">3.0.1.9047</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9048</small>
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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="">3.0.1.9047</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9048</small>
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2
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="">3.0.1.9047</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9048</small>
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2
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="">3.0.1.9047</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9048</small>
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2
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="">3.0.1.9047</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9048</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">

34
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="">3.0.1.9047</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9048</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">21 April 2026</h4>
<h4 data-toc-skip class="date">22 April 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>
@@ -876,11 +876,11 @@ DTA file</a> (83 kB)</li>
<code>intrinsic_resistant</code>: Intrinsic Bacterial
Resistance<a class="anchor" aria-label="anchor" href="#intrinsic_resistant-intrinsic-bacterial-resistance"></a>
</h2>
<p>A data set with 271 905 rows and 2 columns, containing the following
<p>A data set with 285 928 rows and 2 columns, containing the following
column names:<br><em>mo</em> and <em>ab</em>.</p>
<p>This data set is in R available as <code>intrinsic_resistant</code>,
after you load the <code>AMR</code> package.</p>
<p>It was last updated on 28 March 2025 10:17:49 UTC. Find more info
<p>It was last updated on 22 April 2026 06:16:44 UTC. Find more info
about the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/intrinsic_resistant.html">data set
here</a>.</p>
<p><strong>Direct download links:</strong></p>
@@ -889,22 +889,22 @@ here</a>.</p>
R Data Structure (RDS) file</a> (0.1 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/intrinsic_resistant.txt" class="external-link">tab-separated
text file</a> (10.1 MB)<br>
text file</a> (10.6 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/intrinsic_resistant.xlsx" class="external-link">Microsoft
Excel workbook</a> (2.9 MB)<br>
Excel workbook</a> (3.3 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/intrinsic_resistant.feather" class="external-link">Apache
Feather file</a> (2.3 MB)<br>
Feather file</a> (2.5 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/intrinsic_resistant.parquet" class="external-link">Apache
Parquet file</a> (0.3 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/intrinsic_resistant.sav" class="external-link">IBM
SPSS Statistics data file</a> (14.8 MB)<br>
SPSS Statistics data file</a> (15.5 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/intrinsic_resistant.dta" class="external-link">Stata
DTA file</a> (22.6 MB)</li>
DTA file</a> (27.5 MB)</li>
</ul>
<p><strong>Example content</strong></p>
<p>Example rows when filtering on <em>Enterobacter cloacae</em>:</p>
@@ -1060,8 +1060,16 @@ DTA file</a> (22.6 MB)</li>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Ostreogrycin</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Pirlimycin</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Primycin</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Pristinamycin</td>
@@ -1142,6 +1150,14 @@ DTA file</a> (22.6 MB)</li>
<td align="center">Enterobacter cloacae</td>
<td align="center">Vancomycin</td>
</tr>
<tr class="even">
<td align="center">Enterobacter cloacae</td>
<td align="center">Virginiamycine</td>
</tr>
<tr class="odd">
<td align="center">Enterobacter cloacae</td>
<td align="center">Zorbamycin</td>
</tr>
</tbody>
</table>
<hr>

18
articles/datasets.md
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@@ -249,14 +249,14 @@ here](https://amr-for-r.org/reference/microorganisms.groups.html).
## `intrinsic_resistant`: Intrinsic Bacterial Resistance
A data set with 271 905 rows and 2 columns, containing the following
A data set with 285 928 rows and 2 columns, containing the following
column names:
*mo* and *ab*.
This data set is in R available as `intrinsic_resistant`, after you load
the `AMR` package.
It was last updated on 28 March 2025 10:17:49 UTC. Find more info about
It was last updated on 22 April 2026 06:16:44 UTC. Find more info about
the contents, (scientific) source, and structure of this [data set
here](https://amr-for-r.org/reference/intrinsic_resistant.html).
@@ -267,22 +267,22 @@ here](https://amr-for-r.org/reference/intrinsic_resistant.html).
(0.1 MB)
- Download as [tab-separated text
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/intrinsic_resistant.txt)
(10.1 MB)
(10.6 MB)
- Download as [Microsoft Excel
workbook](https://github.com/msberends/AMR/raw/main/data-raw/datasets/intrinsic_resistant.xlsx)
(2.9 MB)
(3.3 MB)
- Download as [Apache Feather
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/intrinsic_resistant.feather)
(2.3 MB)
(2.5 MB)
- Download as [Apache Parquet
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/intrinsic_resistant.parquet)
(0.3 MB)
- Download as [IBM SPSS Statistics data
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/intrinsic_resistant.sav)
(14.8 MB)
(15.5 MB)
- Download as [Stata DTA
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/intrinsic_resistant.dta)
(22.6 MB)
(27.5 MB)
**Example content**
@@ -326,7 +326,9 @@ Example rows when filtering on *Enterobacter cloacae*:
| Enterobacter cloacae | Norvancomycin |
| Enterobacter cloacae | Oleandomycin |
| Enterobacter cloacae | Oritavancin |
| Enterobacter cloacae | Ostreogrycin |
| Enterobacter cloacae | Pirlimycin |
| Enterobacter cloacae | Primycin |
| Enterobacter cloacae | Pristinamycin |
| Enterobacter cloacae | Quinupristin/dalfopristin |
| Enterobacter cloacae | Ramoplanin |
@@ -347,6 +349,8 @@ Example rows when filtering on *Enterobacter cloacae*:
| Enterobacter cloacae | Tylosin |
| Enterobacter cloacae | Tylvalosin |
| Enterobacter cloacae | Vancomycin |
| Enterobacter cloacae | Virginiamycine |
| Enterobacter cloacae | Zorbamycin |
------------------------------------------------------------------------

2
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="">3.0.1.9047</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9048</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">