diff --git a/DESCRIPTION b/DESCRIPTION index 223b63bb1..8fdd71251 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 3.0.1.9045 +Version: 3.0.1.9047 Date: 2026-04-21 Title: Antimicrobial Resistance Data Analysis Description: Functions to simplify and standardise antimicrobial resistance (AMR) diff --git a/NEWS.md b/NEWS.md index bbfe873e4..0ea9981fb 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 3.0.1.9045 +# AMR 3.0.1.9047 ### New * Support for clinical breakpoints of 2026 of both CLSI and EUCAST, by adding all of their over 5,700 new clinical breakpoints to the `clinical_breakpoints` data set for usage in `as.sir()`. EUCAST 2026 is now the new default guideline for all MIC and disk diffusion interpretations. @@ -32,6 +32,7 @@ * Fixed a bug to disregard `NI` for susceptibility proportion functions * Fixed Italian translation of CoNS to Stafilococco coagulasi-negativo and CoPS to Stafilococco coagulasi-positivo (#256) * Fixed SIR and MIC coercion of combined values, e.g. `as.sir("<= 0.002; S") ` or `as.mic("S; 0.002")` (#252) +* Fixed translation of foreign languages in `sir_df()` (#272) ### Updates * Extensive `cli` integration for better message handling and clickable links in messages and warnings (#191, #265) diff --git a/R/ab_property.R b/R/ab_property.R index ce0098c05..84adad5e2 100755 --- a/R/ab_property.R +++ b/R/ab_property.R @@ -361,7 +361,7 @@ ab_property <- function(x, property = "name", language = get_AMR_locale(), ...) meet_criteria(x, allow_NA = TRUE) meet_criteria(property, is_in = colnames(AMR::antimicrobials), has_length = 1) language <- validate_language(language) - translate_into_language(ab_validate(x = x, property = property, ...), language = language) + translate_into_language(ab_validate(x = x, property = property, ...), language = language, only_affect_ab_names = TRUE) } #' @rdname ab_property diff --git a/R/interpretive_rules.R b/R/interpretive_rules.R index 8f3562724..0e333d415 100755 --- a/R/interpretive_rules.R +++ b/R/interpretive_rules.R @@ -1140,7 +1140,7 @@ edit_sir <- function(x, add_if_missing) { cols <- unique(cols[!is.na(cols) & !is.null(cols)]) rows <- unique(rows) - + # for Verbose Mode, keep track of all changes and return them track_changes <- list( added = 0, diff --git a/man/amr-tidymodels.Rd b/man/amr-tidymodels.Rd index 7103b651c..2352636ed 100644 --- a/man/amr-tidymodels.Rd +++ b/man/amr-tidymodels.Rd @@ -73,7 +73,6 @@ These steps integrate with \code{recipes::recipe()} and work like standard prepr } \examples{ if (require("tidymodels")) { - # The below approach formed the basis for this paper: DOI 10.3389/fmicb.2025.1582703 # Presence of ESBL genes was predicted based on raw MIC values. @@ -92,13 +91,10 @@ if (require("tidymodels")) { # Create and prep a recipe with MIC log2 transformation mic_recipe <- recipe(esbl ~ ., data = training_data) \%>\% - # Optionally remove non-predictive variables remove_role(genus, old_role = "predictor") \%>\% - # Apply the log2 transformation to all MIC predictors step_mic_log2(all_mic_predictors()) \%>\% - # And apply the preparation steps prep() @@ -119,13 +115,15 @@ if (require("tidymodels")) { bind_cols(out_testing) # Evaluate predictions using standard classification metrics - our_metrics <- metric_set(accuracy, - recall, - precision, - sensitivity, - specificity, - ppv, - npv) + our_metrics <- metric_set( + accuracy, + recall, + precision, + sensitivity, + specificity, + ppv, + npv + ) metrics <- our_metrics(predictions, truth = esbl, estimate = .pred_class) # Show performance diff --git a/man/pca.Rd b/man/pca.Rd index c6fd50dc6..5e88c1efc 100644 --- a/man/pca.Rd +++ b/man/pca.Rd @@ -79,12 +79,12 @@ if (require("dplyr")) { # new ggplot2 plotting method using this package: if (require("dplyr") && require("ggplot2")) { - ggplot_pca(pca_result) + ggplot_pca(pca_result) } if (require("dplyr") && require("ggplot2")) { - ggplot_pca(pca_result) + - scale_colour_viridis_d() + - labs(title = "Title here") + ggplot_pca(pca_result) + + scale_colour_viridis_d() + + labs(title = "Title here") } } } diff --git a/man/plot.Rd b/man/plot.Rd index ae6c61d0d..7bfefc681 100644 --- a/man/plot.Rd +++ b/man/plot.Rd @@ -321,7 +321,7 @@ if (require("ggplot2")) { theme_minimal() + geom_boxplot(fill = NA, colour = "grey30") + geom_jitter(width = 0.25) - labs(title = "scale_y_mic()/scale_colour_sir() automatically applied") + labs(title = "scale_y_mic()/scale_colour_sir() automatically applied") mic_sir_plot }