(v3.0.1.9082) website

DESCRIPTION

@@ -1,6 +1,6 @@
 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
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)
   data analysis and to work with microbial and antimicrobial properties by

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.
 

README.Rmd

@@ -22,7 +22,7 @@ Please visit our comprehensive package website <https://amr-for-r.org> 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

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
+- **Peer-reviewed**, used in over 175 countries, cited over 100 times,
-  languages
+  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

index.Rmd

@@ -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>
 
 * 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

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
+- **Peer-reviewed**, used in over 175 countries, cites over 100 times,
-  languages
+  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%)                     |
+| 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 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
 #>   <chr>            <dbl> <chr>              <dbl> <chr>