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dr. M.S. (Matthijs) Berends
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DESCRIPTION
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Package: AMR Package: AMR
Version: 3.0.1.9081 Version: 3.0.1.9082
Date: 2026-06-27 Date: 2026-07-03
Title: Antimicrobial Resistance Data Analysis Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR) Description: Functions to simplify and standardise antimicrobial resistance (AMR)
data analysis and to work with microbial and antimicrobial properties by data analysis and to work with microbial and antimicrobial properties by

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NEWS.md
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# AMR 3.0.1.9081 # AMR 3.0.1.9082
Planned as v3.1.0, end of June 2026. Planned as v3.1.0, end of June 2026.

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README.Rmd
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@@ -22,7 +22,7 @@ Please visit our comprehensive package website <https://amr-for-r.org> to read m
Overview: Overview:
* Provides an **all-in-one solution** for antimicrobial resistance (AMR) data analysis in a One Health approach * Provides an **all-in-one solution** for antimicrobial resistance (AMR) data analysis in a One Health approach
* **Peer-reviewed**, used in over 175 countries, available in `r length(AMR:::LANGUAGES_SUPPORTED)` languages * **Peer-reviewed**, used in over 175 countries, cited over 100 times, available in `r length(AMR:::LANGUAGES_SUPPORTED)` languages
* Generates **antibiograms** - WISCA for empiric coverage estimates, or traditional/syndromic for AMR surveillance * Generates **antibiograms** - WISCA for empiric coverage estimates, or traditional/syndromic for AMR surveillance
* Provides the **full microbiological taxonomy** of `r AMR:::format_included_data_number(AMR::microorganisms)` distinct species and extensive info of `r AMR:::format_included_data_number(NROW(AMR::antimicrobials) + NROW(AMR::antivirals))` antimicrobial drugs * Provides the **full microbiological taxonomy** of `r AMR:::format_included_data_number(AMR::microorganisms)` distinct species and extensive info of `r AMR:::format_included_data_number(NROW(AMR::antimicrobials) + NROW(AMR::antivirals))` antimicrobial drugs
* Applies **CLSI `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, grepl("CLSI", guideline))$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, grepl("CLSI", guideline))$guideline)))`** and **EUCAST `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, grepl("EUCAST", guideline))$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, grepl("EUCAST", guideline))$guideline)))`** clinical and veterinary breakpoints, and ECOFFs, for MIC and disk zone interpretation * Applies **CLSI `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, grepl("CLSI", guideline))$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, grepl("CLSI", guideline))$guideline)))`** and **EUCAST `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, grepl("EUCAST", guideline))$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, grepl("EUCAST", guideline))$guideline)))`** clinical and veterinary breakpoints, and ECOFFs, for MIC and disk zone interpretation

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README.md
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@@ -10,8 +10,8 @@ Overview:
- Provides an **all-in-one solution** for antimicrobial resistance (AMR) - Provides an **all-in-one solution** for antimicrobial resistance (AMR)
data analysis in a One Health approach data analysis in a One Health approach
- **Peer-reviewed**, used in over 175 countries, available in 28 - **Peer-reviewed**, used in over 175 countries, cited over 100 times,
languages available in 28 languages
- Generates **antibiograms** - WISCA for empiric coverage estimates, or - Generates **antibiograms** - WISCA for empiric coverage estimates, or
traditional/syndromic for AMR surveillance traditional/syndromic for AMR surveillance
- Provides the **full microbiological taxonomy** of ~97 000 distinct - Provides the **full microbiological taxonomy** of ~97 000 distinct

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index.Rmd
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@@ -20,7 +20,7 @@ AMR:::reset_all_thrown_messages()
# The `AMR` Package for R <a href="https://amr-for-r.org/"><img src="./logo.svg" align="right" height="139" /></a> # The `AMR` Package for R <a href="https://amr-for-r.org/"><img src="./logo.svg" align="right" height="139" /></a>
* Provides an **all-in-one solution** for antimicrobial resistance (AMR) data analysis in a One Health approach * Provides an **all-in-one solution** for antimicrobial resistance (AMR) data analysis in a One Health approach
* **Peer-reviewed**, used in over 175 countries, available in `r length(AMR:::LANGUAGES_SUPPORTED)` languages * **Peer-reviewed**, used in over 175 countries, cites over 100 times, available in `r length(AMR:::LANGUAGES_SUPPORTED)` languages
* Generates **antibiograms** - WISCA for empiric coverage estimates, or traditional/syndromic for AMR surveillance * Generates **antibiograms** - WISCA for empiric coverage estimates, or traditional/syndromic for AMR surveillance
* Provides the **full microbiological taxonomy** of `r AMR:::format_included_data_number(AMR::microorganisms)` distinct species and extensive info of `r AMR:::format_included_data_number(NROW(AMR::antimicrobials) + NROW(AMR::antivirals))` antimicrobial drugs * Provides the **full microbiological taxonomy** of `r AMR:::format_included_data_number(AMR::microorganisms)` distinct species and extensive info of `r AMR:::format_included_data_number(NROW(AMR::antimicrobials) + NROW(AMR::antivirals))` antimicrobial drugs
* Applies **CLSI `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, grepl("CLSI", guideline))$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, grepl("CLSI", guideline))$guideline)))`** and **EUCAST `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, grepl("EUCAST", guideline))$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, grepl("EUCAST", guideline))$guideline)))`** clinical and veterinary breakpoints, and ECOFFs, for MIC and disk zone interpretation * Applies **CLSI `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, grepl("CLSI", guideline))$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, grepl("CLSI", guideline))$guideline)))`** and **EUCAST `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, grepl("EUCAST", guideline))$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, grepl("EUCAST", guideline))$guideline)))`** clinical and veterinary breakpoints, and ECOFFs, for MIC and disk zone interpretation
@@ -61,6 +61,8 @@ lang_txt <- AMR:::vector_and(paste(img, langs), sort = FALSE, quotes = FALSE)
With the help of contributors from all corners of the world, the `AMR` package is available in `r lang_txt`. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages. With the help of contributors from all corners of the world, the `AMR` package is available in `r lang_txt`. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.
The `AMR` package was cited [over 100 times](https://scholar.google.com/citations?view_op=view_citation&hl=en&citation_for_view=sAoHvIgAAAAJ:0EnyYjriUFMC) in scientific research.
## Practical examples ## Practical examples
### Filtering and selecting data ### Filtering and selecting data

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index.md
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- Provides an **all-in-one solution** for antimicrobial resistance (AMR) - Provides an **all-in-one solution** for antimicrobial resistance (AMR)
data analysis in a One Health approach data analysis in a One Health approach
- **Peer-reviewed**, used in over 175 countries, available in 28 - **Peer-reviewed**, used in over 175 countries, cites over 100 times,
languages available in 28 languages
- Generates **antibiograms** - WISCA for empiric coverage estimates, or - Generates **antibiograms** - WISCA for empiric coverage estimates, or
traditional/syndromic for AMR surveillance traditional/syndromic for AMR surveillance
- Provides the **full microbiological taxonomy** of ~97 000 distinct - Provides the **full microbiological taxonomy** of ~97 000 distinct
@@ -144,6 +144,10 @@ Urdu, and
Vietnamese. Antimicrobial drug (group) names and colloquial Vietnamese. Antimicrobial drug (group) names and colloquial
microorganism names are provided in these languages. microorganism names are provided in these languages.
The `AMR` package was cited [over 100
times](https://scholar.google.com/citations?view_op=view_citation&hl=en&citation_for_view=sAoHvIgAAAAJ:0EnyYjriUFMC)
in scientific research.
## Practical examples ## Practical examples
### Filtering and selecting data ### Filtering and selecting data
@@ -229,7 +233,7 @@ wisca(example_isolates,
| Piperacillin/tazobactam | Piperacillin/tazobactam + Gentamicin | Piperacillin/tazobactam + Tobramycin | | Piperacillin/tazobactam | Piperacillin/tazobactam + Gentamicin | Piperacillin/tazobactam + Tobramycin |
|:------------------------|:-------------------------------------|:-------------------------------------| |:------------------------|:-------------------------------------|:-------------------------------------|
| 70% (64.7-75.2%) | 93.6% (92.2-95.1%) | 89.8% (87-92.5%) | | 69.9% (64.9-75.3%) | 93.6% (92.1-95%) | 89.9% (87-92.4%) |
WISCA supports stratification by any clinical variable, so you can WISCA supports stratification by any clinical variable, so you can
generate syndrome-specific or ward-specific coverage estimates: generate syndrome-specific or ward-specific coverage estimates:
@@ -244,9 +248,9 @@ wisca(example_isolates,
| Syndromic Group | Piperacillin/tazobactam | Piperacillin/tazobactam + Gentamicin | Piperacillin/tazobactam + Tobramycin | | Syndromic Group | Piperacillin/tazobactam | Piperacillin/tazobactam + Gentamicin | Piperacillin/tazobactam + Tobramycin |
|:----------------|:------------------------|:-------------------------------------|:-------------------------------------| |:----------------|:------------------------|:-------------------------------------|:-------------------------------------|
| Clinical | 74.6% (68.6-80.6%) | 93.7% (92.1-95.1%) | 90.4% (87-93.1%) | | Clinical | 74.5% (68.6-80.5%) | 93.7% (91.7-95.1%) | 90.4% (87.1-93.1%) |
| ICU | 57% (48.6-65.7%) | 86.8% (83.6-89.8%) | 82.9% (78.1-87.3%) | | ICU | 57% (48.6-65.6%) | 86.7% (83.3-89.9%) | 83% (78.1-87.5%) |
| Outpatient | 56.9% (45.9-68.2%) | 76.7% (70.6-82.3%) | 68% (57.6-77.2%) | | Outpatient | 57.4% (46-69.1%) | 76.7% (70.5-82.7%) | 67.7% (57.3-77.4%) |
**For AMR surveillance**, traditional antibiograms remain the right tool **For AMR surveillance**, traditional antibiograms remain the right tool
for tracking resistance per species over time: for tracking resistance per species over time:
@@ -349,11 +353,6 @@ example_isolates %>%
summarise(across(c(GEN, TOB), summarise(across(c(GEN, TOB),
list(total_R = resistance, list(total_R = resistance,
conf_int = function(x) sir_confidence_interval(x, collapse = "-")))) conf_int = function(x) sir_confidence_interval(x, collapse = "-"))))
#> ℹ `resistance()` assumes the EUCAST guideline and thus
#> considers the 'I' category susceptible. Set the `guideline`
#> argument or the `AMR_guideline` option to either "CLSI" or
#> "EUCAST", see `?AMR-options`.
#> ℹ This message will be shown once per session.
#> # A tibble: 3 × 5 #> # A tibble: 3 × 5
#> ward GEN_total_R GEN_conf_int TOB_total_R TOB_conf_int #> ward GEN_total_R GEN_conf_int TOB_total_R TOB_conf_int
#> <chr> <dbl> <chr> <dbl> <chr> #> <chr> <dbl> <chr> <dbl> <chr>