From 65445bcfbe472d6036d3b210a956f6ab62680322 Mon Sep 17 00:00:00 2001 From: Matthijs Berends Date: Fri, 3 Jul 2026 19:11:40 +0200 Subject: [PATCH] (v3.0.1.9082) website --- DESCRIPTION | 4 ++-- NEWS.md | 2 +- README.Rmd | 2 +- README.md | 4 ++-- index.Rmd | 4 +++- index.md | 21 ++++++++++----------- 6 files changed, 19 insertions(+), 18 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index f37cea002..553fe09f5 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: AMR -Version: 3.0.1.9081 -Date: 2026-06-27 +Version: 3.0.1.9082 +Date: 2026-07-03 Title: Antimicrobial Resistance Data Analysis Description: Functions to simplify and standardise antimicrobial resistance (AMR) data analysis and to work with microbial and antimicrobial properties by diff --git a/NEWS.md b/NEWS.md index 1b3fa465e..320a02f2d 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 3.0.1.9081 +# AMR 3.0.1.9082 Planned as v3.1.0, end of June 2026. diff --git a/README.Rmd b/README.Rmd index 0c04b17d9..d73f5e9a5 100644 --- a/README.Rmd +++ b/README.Rmd @@ -22,7 +22,7 @@ Please visit our comprehensive package website to read m Overview: * 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 * 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 diff --git a/README.md b/README.md index a8fc69fa4..c29d19476 100755 --- a/README.md +++ b/README.md @@ -10,8 +10,8 @@ Overview: - 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 28 - languages +- **Peer-reviewed**, used in over 175 countries, cited over 100 times, + available in 28 languages - Generates **antibiograms** - WISCA for empiric coverage estimates, or traditional/syndromic for AMR surveillance - Provides the **full microbiological taxonomy** of ~97 000 distinct diff --git a/index.Rmd b/index.Rmd index e3814f985..6ab49161a 100644 --- a/index.Rmd +++ b/index.Rmd @@ -20,7 +20,7 @@ AMR:::reset_all_thrown_messages() # The `AMR` Package for R * 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 * 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 @@ -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. +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 ### Filtering and selecting data diff --git a/index.md b/index.md index 31f49bfda..8414a2df4 100644 --- a/index.md +++ b/index.md @@ -5,8 +5,8 @@ - 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 28 - languages +- **Peer-reviewed**, used in over 175 countries, cites over 100 times, + available in 28 languages - Generates **antibiograms** - WISCA for empiric coverage estimates, or traditional/syndromic for AMR surveillance - Provides the **full microbiological taxonomy** of ~97 000 distinct @@ -144,6 +144,10 @@ Urdu, and Vietnamese. 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 ### Filtering and selecting data @@ -229,7 +233,7 @@ wisca(example_isolates, | 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 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 | |:----------------|:------------------------|:-------------------------------------|:-------------------------------------| -| Clinical | 74.6% (68.6-80.6%) | 93.7% (92.1-95.1%) | 90.4% (87-93.1%) | -| ICU | 57% (48.6-65.7%) | 86.8% (83.6-89.8%) | 82.9% (78.1-87.3%) | -| Outpatient | 56.9% (45.9-68.2%) | 76.7% (70.6-82.3%) | 68% (57.6-77.2%) | +| Clinical | 74.5% (68.6-80.5%) | 93.7% (91.7-95.1%) | 90.4% (87.1-93.1%) | +| ICU | 57% (48.6-65.6%) | 86.7% (83.3-89.9%) | 83% (78.1-87.5%) | +| 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 tracking resistance per species over time: @@ -349,11 +353,6 @@ example_isolates %>% summarise(across(c(GEN, TOB), list(total_R = resistance, 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 #> ward GEN_total_R GEN_conf_int TOB_total_R TOB_conf_int #>