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16
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="">3.0.1.9009</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9008</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 23 December 2025.</p>
generated on 06 January 2026.</p>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
@@ -125,7 +125,7 @@ including the requirements mentioned above.</p>
<p>The <code>AMR</code> package enables standardised and reproducible
AMR data analysis, with the application of evidence-based rules,
determination of first isolates, translation of various codes for
microorganisms and antimicrobial agents, determination of (multi-drug)
microorganisms and antimicrobial drugs, determination of (multi-drug)
resistant microorganisms, and calculation of antimicrobial resistance,
prevalence and future trends.</p>
</div>
@@ -147,21 +147,21 @@ make the structure of your data generally look like this:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2025-12-23</td>
<td align="center">2026-01-06</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">2025-12-23</td>
<td align="center">2026-01-06</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">2025-12-23</td>
<td align="center">2026-01-06</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@@ -847,14 +847,14 @@ language to be Spanish using the <code>language</code> argument:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">Gram negativo</td>
<td align="left">Gram-negative</td>
<td align="left">98% (96-99%,N=256)</td>
<td align="left">96% (95-98%,N=684)</td>
<td align="left">0% (0-10%,N=35)</td>
<td align="left">96% (94-97%,N=686)</td>
</tr>
<tr class="even">
<td align="left">Gram positivo</td>
<td align="left">Gram-positive</td>
<td align="left">0% (0-1%,N=436)</td>
<td align="left">63% (60-66%,N=1170)</td>
<td align="left">0% (0-1%,N=436)</td>

16
articles/AMR.md
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@@ -3,8 +3,8 @@
**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 23 December
2025.
methodology remains unchanged. This page was generated on 06 January
2026.
## Introduction
@@ -38,7 +38,7 @@ mentioned above.
The `AMR` package enables standardised and reproducible AMR data
analysis, with the application of evidence-based rules, determination of
first isolates, translation of various codes for microorganisms and
antimicrobial agents, determination of (multi-drug) resistant
antimicrobial drugs, determination of (multi-drug) resistant
microorganisms, and calculation of antimicrobial resistance, prevalence
and future trends.
@@ -52,9 +52,9 @@ structure of your data generally look like this:
| date | patient_id | mo | AMX | CIP |
|:----------:|:----------:|:----------------:|:---:|:---:|
| 2025-12-23 | abcd | Escherichia coli | S | S |
| 2025-12-23 | abcd | Escherichia coli | S | R |
| 2025-12-23 | efgh | Escherichia coli | R | S |
| 2026-01-06 | abcd | Escherichia coli | S | S |
| 2026-01-06 | abcd | Escherichia coli | S | R |
| 2026-01-06 | efgh | Escherichia coli | R | S |
### Needed R packages
@@ -672,8 +672,8 @@ antibiogram(example_isolates,
| Patógeno | Amikacina | Gentamicina | Kanamicina | Tobramicina |
|:--------------|:-------------------|:--------------------|:----------------|:-------------------|
| Gram negativo | 98% (96-99%,N=256) | 96% (95-98%,N=684) | 0% (0-10%,N=35) | 96% (94-97%,N=686) |
| Gram positivo | 0% (0-1%,N=436) | 63% (60-66%,N=1170) | 0% (0-1%,N=436) | 34% (31-38%,N=665) |
| Gram-negative | 98% (96-99%,N=256) | 96% (95-98%,N=684) | 0% (0-10%,N=35) | 96% (94-97%,N=686) |
| Gram-positive | 0% (0-1%,N=436) | 63% (60-66%,N=1170) | 0% (0-1%,N=436) | 34% (31-38%,N=665) |
#### Combined Antibiogram

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<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="">3.0.1.9009</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9008</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="">3.0.1.9009</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9008</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="">3.0.1.9009</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9008</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/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="">3.0.1.9009</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9008</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/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="">3.0.1.9009</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9008</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">
@@ -262,7 +262,7 @@ Levels: 5: S &lt; SDD &lt; I &lt; R &lt; NI<br>
Available: 481 (96.2%, NA: 19 = 3.8%)<br>
Unique: 3</p>
<p>Drug: Amoxicillin/clavulanic acid (AMC, J01CR02/QJ01CR02)<br>
Drug group: Beta-lactams/penicillins<br>
Drug group: Aminopenicillins<br>
%SI: 78.59%</p>
<table class="table">
<thead><tr class="header">

2
articles/WHONET.md
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@@ -112,7 +112,7 @@ Available: 481 (96.2%, NA: 19 = 3.8%)
Unique: 3
Drug: Amoxicillin/clavulanic acid (AMC, J01CR02/QJ01CR02)
Drug group: Beta-lactams/penicillins
Drug group: Aminopenicillins
%SI: 78.59%
| | Item | Count | Percent | Cum. Count | Cum. Percent |

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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="">3.0.1.9009</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9008</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">
@@ -363,14 +363,14 @@ all be used for the <code><a href="../reference/antibiogram.html">wisca()</a></c
<colgroup>
<col width="12%">
<col width="21%">
<col width="34%">
<col width="31%">
<col width="33%">
<col width="32%">
</colgroup>
<thead><tr class="header">
<th align="left">Grupo sindrómico</th>
<th align="left">Amoxicilina/ácido clavulánico</th>
<th align="left">Amoxicilina/ácido clavulánico + Ciprofloxacina</th>
<th align="left">Amoxicilina/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">

8
articles/WISCA.md
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@@ -207,10 +207,10 @@ wisca(data,
language = "Spanish")
```
| Grupo sindrómico | Amoxicilina/ácido clavulánico | Amoxicilina/ácido clavulánico + Ciprofloxacina | Amoxicilina/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%) |
| 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%) |
## Sensible defaults, which can be customised

32
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="">3.0.1.9009</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9008</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">23 December 2025</h4>
<h4 data-toc-skip class="date">06 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>
@@ -424,13 +424,13 @@ column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>a
<em>iv_ddd</em>, <em>iv_units</em>, and <em>loinc</em>.</p>
<p>This data set is in R available as <code>antimicrobials</code>, after
you load the <code>AMR</code> package.</p>
<p>It was last updated on 24 November 2025 10:24:02 UTC. Find more info
<p>It was last updated on 6 January 2026 22:08:50 UTC. Find more info
about the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/antimicrobials.html">data set
here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/antimicrobials.rds" class="external-link">original
R Data Structure (RDS) file</a> (45 kB)<br>
R Data Structure (RDS) file</a> (46 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/antimicrobials.txt" class="external-link">tab-separated
text file</a> (0.1 MB)<br>
@@ -454,22 +454,22 @@ DTA file</a> (10 kB)</li>
contain the ATC codes, common abbreviations, trade names and LOINC codes
as comma separated values.</p>
<p><strong>Example content</strong></p>
<table style="width:100%;" class="table">
<table class="table">
<colgroup>
<col width="1%">
<col width="2%">
<col width="7%">
<col width="7%">
<col width="9%">
<col width="12%">
<col width="16%">
<col width="6%">
<col width="16%">
<col width="8%">
<col width="11%">
<col width="15%">
<col width="5%">
<col width="15%">
<col width="2%">
<col width="3%">
<col width="2%">
<col width="2%">
<col width="9%">
<col width="8%">
</colgroup>
<thead><tr class="header">
<th align="center">ab</th>
@@ -508,7 +508,7 @@ as comma separated values.</p>
<td align="center">AMX</td>
<td align="center">33613</td>
<td align="center">Amoxicillin</td>
<td align="center">Beta-lactams/penicillins</td>
<td align="center">Aminopenicillins, Penicillins, Beta-lactams</td>
<td align="center">J01CA04, QG51AA03, QJ01CA04</td>
<td align="center">Beta-lactam antibacterials, penicillins</td>
<td align="center">Penicillins with extended spectrum</td>
@@ -524,7 +524,7 @@ as comma separated values.</p>
<td align="center">AMC</td>
<td align="center">23665637</td>
<td align="center">Amoxicillin/clavulanic acid</td>
<td align="center">Beta-lactams/penicillins</td>
<td align="center">Aminopenicillins, Penicillins, Beta-lactams, …</td>
<td align="center">J01CR02, QJ01CR02</td>
<td align="center">Beta-lactam antibacterials, penicillins</td>
<td align="center">Combinations of penicillins, incl. beta-lactamase
@@ -541,7 +541,7 @@ inhibitors</td>
<td align="center">AMP</td>
<td align="center">6249</td>
<td align="center">Ampicillin</td>
<td align="center">Beta-lactams/penicillins</td>
<td align="center">Aminopenicillins, Penicillins, Beta-lactams</td>
<td align="center">J01CA01, QJ01CA01, QJ51CA01, …</td>
<td align="center">Beta-lactam antibacterials, penicillins</td>
<td align="center">Penicillins with extended spectrum</td>
@@ -557,7 +557,7 @@ inhibitors</td>
<td align="center">AZM</td>
<td align="center">447043</td>
<td align="center">Azithromycin</td>
<td align="center">Macrolides/lincosamides</td>
<td align="center">Macrolides</td>
<td align="center">J01FA10, QJ01FA10, QS01AA26, …</td>
<td align="center">Macrolides, lincosamides and streptogramins</td>
<td align="center">Macrolides</td>
@@ -573,7 +573,7 @@ inhibitors</td>
<td align="center">PEN</td>
<td align="center">5904</td>
<td align="center">Benzylpenicillin</td>
<td align="center">Beta-lactams/penicillins</td>
<td align="center">Penicillins, Beta-lactams</td>
<td align="center">J01CE01, QJ01CE01, QJ51CE01, …</td>
<td align="center">Combinations of antibacterials</td>
<td align="center">Combinations of antibacterials</td>

22
articles/datasets.md
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@@ -100,15 +100,15 @@ names:
This data set is in R available as `antimicrobials`, after you load the
`AMR` package.
It was last updated on 24 November 2025 10:24:02 UTC. Find more info
about the contents, (scientific) source, and structure of this [data set
It was last updated on 6 January 2026 22:08:50 UTC. Find more info about
the contents, (scientific) source, and structure of this [data set
here](https://amr-for-r.org/reference/antimicrobials.html).
**Direct download links:**
- Download as [original R Data Structure (RDS)
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/antimicrobials.rds)
(45 kB)
(46 kB)
- Download as [tab-separated text
file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/antimicrobials.txt)
(0.1 MB)
@@ -134,14 +134,14 @@ as comma separated values.
**Example content**
| ab | cid | name | group | atc | atc_group1 | atc_group2 | abbreviations | synonyms | oral_ddd | oral_units | iv_ddd | iv_units | loinc |
|:---:|:--------:|:---------------------------:|:------------------------:|:------------------------------:|:-------------------------------------------:|:------------------------------------------------------------:|:-------------------:|:-------------------------------------------------------:|:--------:|:----------:|:------:|:--------:|:------------------------------:|
| AMK | 37768 | Amikacin | Aminoglycosides | D06AX12, J01GB06, QD06AX12, … | Aminoglycoside antibacterials | Other aminoglycosides | ak, ami, amik, … | amikacillin, amikacina, amikacine, … | | | 1.0 | g | 101493-5, 11-7, 12-5, … |
| AMX | 33613 | Amoxicillin | Beta-lactams/penicillins | J01CA04, QG51AA03, QJ01CA04 | Beta-lactam antibacterials, penicillins | Penicillins with extended spectrum | ac, amox, amoxic, … | acuotricina, alfamox, alfida, … | 1.5 | g | 3.0 | g | 101498-4, 15-8, 16-6, … |
| AMC | 23665637 | Amoxicillin/clavulanic acid | Beta-lactams/penicillins | J01CR02, QJ01CR02 | Beta-lactam antibacterials, penicillins | Combinations of penicillins, incl. beta-lactamase inhibitors | a/c, amcl, aml, … | amocla, amoclan, amoclav, … | 1.5 | g | 3.0 | g | |
| AMP | 6249 | Ampicillin | Beta-lactams/penicillins | J01CA01, QJ01CA01, QJ51CA01, … | Beta-lactam antibacterials, penicillins | Penicillins with extended spectrum | am, amp, amp100, … | adobacillin, alpen, amblosin, … | 2.0 | g | 6.0 | g | 101477-8, 101478-6, 18864-9, … |
| AZM | 447043 | Azithromycin | Macrolides/lincosamides | J01FA10, QJ01FA10, QS01AA26, … | Macrolides, lincosamides and streptogramins | Macrolides | az, azi, azit, … | aritromicina, aruzilina, azasite, … | 0.3 | g | 0.5 | g | 100043-9, 16420-2, 16421-0, … |
| PEN | 5904 | Benzylpenicillin | Beta-lactams/penicillins | J01CE01, QJ01CE01, QJ51CE01, … | Combinations of antibacterials | Combinations of antibacterials | bepe, pen, peni, … | bencilpenicilina, benzopenicillin, benzylpenicilline, … | | | 3.6 | g | |
| ab | cid | name | group | atc | atc_group1 | atc_group2 | abbreviations | synonyms | oral_ddd | oral_units | iv_ddd | iv_units | loinc |
|:---:|:--------:|:---------------------------:|:----------------------------------------------:|:------------------------------:|:-------------------------------------------:|:------------------------------------------------------------:|:-------------------:|:-------------------------------------------------------:|:--------:|:----------:|:------:|:--------:|:------------------------------:|
| AMK | 37768 | Amikacin | Aminoglycosides | D06AX12, J01GB06, QD06AX12, … | Aminoglycoside antibacterials | Other aminoglycosides | ak, ami, amik, … | amikacillin, amikacina, amikacine, … | | | 1.0 | g | 101493-5, 11-7, 12-5, … |
| AMX | 33613 | Amoxicillin | Aminopenicillins, Penicillins, Beta-lactams | J01CA04, QG51AA03, QJ01CA04 | Beta-lactam antibacterials, penicillins | Penicillins with extended spectrum | ac, amox, amoxic, … | acuotricina, alfamox, alfida, … | 1.5 | g | 3.0 | g | 101498-4, 15-8, 16-6, … |
| AMC | 23665637 | Amoxicillin/clavulanic acid | Aminopenicillins, Penicillins, Beta-lactams, … | J01CR02, QJ01CR02 | Beta-lactam antibacterials, penicillins | Combinations of penicillins, incl. beta-lactamase inhibitors | a/c, amcl, aml, … | amocla, amoclan, amoclav, … | 1.5 | g | 3.0 | g | |
| AMP | 6249 | Ampicillin | Aminopenicillins, Penicillins, Beta-lactams | J01CA01, QJ01CA01, QJ51CA01, … | Beta-lactam antibacterials, penicillins | Penicillins with extended spectrum | am, amp, amp100, … | adobacillin, alpen, amblosin, … | 2.0 | g | 6.0 | g | 101477-8, 101478-6, 18864-9, … |
| AZM | 447043 | Azithromycin | Macrolides | J01FA10, QJ01FA10, QS01AA26, … | Macrolides, lincosamides and streptogramins | Macrolides | az, azi, azit, … | aritromicina, aruzilina, azasite, … | 0.3 | g | 0.5 | g | 100043-9, 16420-2, 16421-0, … |
| PEN | 5904 | Benzylpenicillin | Penicillins, Beta-lactams | J01CE01, QJ01CE01, QJ51CE01, … | Combinations of antibacterials | Combinations of antibacterials | bepe, pen, peni, … | bencilpenicilina, benzopenicillin, benzylpenicilline, … | | | 3.6 | g | |
------------------------------------------------------------------------

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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="">3.0.1.9009</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9008</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">