(v2.1.1.9198) support eucast expert rules 14 and 13.1

R/aa_globals.R

@@ -30,12 +30,18 @@
 # add new version numbers here, and add the rules themselves to "data-raw/eucast_rules.tsv" and clinical_breakpoints
 # (sourcing "data-raw/_pre_commit_checks.R" will process the TSV file)
 EUCAST_VERSION_BREAKPOINTS <- list(
-  # "13.0" = list(
-  #   version_txt = "v13.0",
-  #   year = 2023,
-  #   title = "'EUCAST Clinical Breakpoint Tables'",
-  #   url = "https://www.eucast.org/clinical_breakpoints/"
-  # ),
+  "14.0" = list(
+    version_txt = "v14.0",
+    year = 2024,
+    title = "'EUCAST Clinical Breakpoint Tables'",
+    url = "https://www.eucast.org/clinical_breakpoints/"
+  ),
+  "13.1" = list(
+    version_txt = "v13.1",
+    year = 2023,
+    title = "'EUCAST Clinical Breakpoint Tables'",
+    url = "https://www.eucast.org/clinical_breakpoints/"
+  ),
   "12.0" = list(
     version_txt = "v12.0",
     year = 2022,

R/ab.R

@@ -211,6 +211,12 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
       next
     }
 
+    # screening, but written without the hyphen, e.g., FOXS instead of FOX-S
+    if (substr(x[i], 4, 4) == "S" && paste0(substr(x[i], 1, 3), "-S") %in% AMR_env$AB_lookup$ab) {
+      x_new[i] <- paste0(substr(x[i], 1, 3), "-S")
+      next
+    }
+
     if (fast_mode == FALSE && flag_multiple_results == TRUE && x[i] %like% "[ ]") {
       from_text <- tryCatch(suppressWarnings(ab_from_text(x[i], translate_ab = FALSE)[[1]]),
         error = function(e) character(0)
@@ -306,7 +312,6 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
       next
     }
 
-
     # try if name ends with it
     found <- AMR_env$AB_lookup[which(AMR_env$AB_lookup$generalised_name %like% paste0(x_spelling, "$")), "ab", drop = TRUE]
     if (nchar(x[i]) >= 4 && length(found) > 0) {

R/amr_selectors.R

@@ -290,10 +290,10 @@ carbapenems <- function(only_sir_columns = FALSE, only_treatable = TRUE, return_
 
 #' @rdname antimicrobial_selectors
 #' @export
-cephalosporins <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
+cephalosporins <- function(only_sir_columns = FALSE, only_treatable = TRUE, return_all = TRUE, ...) {
   meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
   meet_criteria(return_all, allow_class = "logical", has_length = 1)
-  amr_select_exec("cephalosporins", only_sir_columns = only_sir_columns, return_all = return_all)
+  amr_select_exec("cephalosporins", only_sir_columns = only_sir_columns, only_treatable = only_treatable, return_all = return_all)
 }
 
 #' @rdname antimicrobial_selectors
@@ -314,10 +314,10 @@ cephalosporins_2nd <- function(only_sir_columns = FALSE, return_all = TRUE, ...)
 
 #' @rdname antimicrobial_selectors
 #' @export
-cephalosporins_3rd <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
+cephalosporins_3rd <- function(only_sir_columns = FALSE, only_treatable = TRUE, return_all = TRUE, ...) {
   meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
   meet_criteria(return_all, allow_class = "logical", has_length = 1)
-  amr_select_exec("cephalosporins_3rd", only_sir_columns = only_sir_columns, return_all = return_all)
+  amr_select_exec("cephalosporins_3rd", only_sir_columns = only_sir_columns, only_treatable = only_treatable, return_all = return_all)
 }
 
 #' @rdname antimicrobial_selectors

R/data.R

@@ -306,6 +306,8 @@
 #' ### Imported from WHONET
 #' Clinical breakpoints in this package were validated through and imported from [WHONET](https://whonet.org), a free desktop Windows application developed and supported by the WHO Collaborating Centre for Surveillance of Antimicrobial Resistance. More can be read on [their website](https://whonet.org). The developers of WHONET and this `AMR` package have been in contact about sharing their work. We highly appreciate their great development on the WHONET software.
 #'
+#' Our import and reproduction script can be found here: <https://github.com/msberends/AMR/blob/main/data-raw/reproduction_of_clinical_breakpoints.R>.
+#'
 #' ### Response from CLSI and EUCAST
 #' The CEO of CLSI and the chairman of EUCAST have endorsed the work and public use of this `AMR` package (and consequently the use of their breakpoints) in June 2023, when future development of distributing clinical breakpoints was discussed in a meeting between CLSI, EUCAST, WHO, developers of WHONET software, and developers of this `AMR` package.
 #'

R/eucast_rules.R

@@ -72,7 +72,7 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
 #' @param administration route of administration, either `r vector_or(dosage$administration)`
 #' @param only_sir_columns a [logical] to indicate whether only antimicrobial columns must be detected that were transformed to class `sir` (see [as.sir()]) on beforehand (default is `FALSE`)
 #' @param custom_rules custom rules to apply, created with [custom_eucast_rules()]
-#' @param overwrite a [logical] to indicate whether non-`NA` values must be overwritten (defaults to `TRUE`). With `FALSE`, only `NA` values are changed.
+#' @param overwrite A [logical] indicating whether to overwrite non-`NA` values (default: `FALSE`). When `FALSE`, only `NA` values are modified. To ensure compliance with EUCAST guidelines, **this should remain** `FALSE`, as EUCAST notes often state that an organism "should be tested for susceptibility to individual agents or be reported resistant."
 #' @inheritParams first_isolate
 #' @details
 #' **Note:** This function does not translate MIC values to SIR values. Use [as.sir()] for that. \cr
@@ -167,13 +167,13 @@ eucast_rules <- function(x,
                          info = interactive(),
                          rules = getOption("AMR_eucastrules", default = c("breakpoints", "expert")),
                          verbose = FALSE,
-                         version_breakpoints = 12.0,
+                         version_breakpoints = 14.0,
                          version_expertrules = 3.3,
                          # TODO version_resistant_phenotypes = 1.2,
                          ampc_cephalosporin_resistance = NA,
                          only_sir_columns = FALSE,
                          custom_rules = NULL,
-                         overwrite = TRUE,
+                         overwrite = FALSE,
                          ...) {
   meet_criteria(x, allow_class = "data.frame")
   meet_criteria(col_mo, allow_class = "character", has_length = 1, is_in = colnames(x), allow_NULL = TRUE)
@@ -630,10 +630,10 @@ eucast_rules <- function(x,
 
   # sometimes, the screenings are missing but the names are actually available
   # we only hints on remaining rows in `eucast_rules_df`
-  screening_abx <- c("FOX", "BTL", "CLI", "NAL", "NOR", "OXA", "PEF", "PEN", "TCY")
+  screening_abx <- as.character(AMR::antimicrobials$ab[which(AMR::antimicrobials$ab %like% "-S$")])
   screening_abx <- screening_abx[screening_abx %in% unique(unlist(strsplit(EUCAST_RULES_DF$and_these_antibiotics[!is.na(EUCAST_RULES_DF$and_these_antibiotics)], ", *")))]
-  for (ab in screening_abx) {
-    ab_s <- paste0(ab, "-S")
+  for (ab_s in screening_abx) {
+    ab <- gsub("-S$", "", ab_s)
     if (ab %in% names(cols_ab) && !ab_s %in% names(cols_ab)) {
       if (isTRUE(info)) {
         message_("Using column '", cols_ab[names(cols_ab) == ab],
@@ -1130,7 +1130,7 @@ edit_sir <- function(x,
     if (any(!vapply(FUN.VALUE = logical(1), x[, cols, drop = FALSE], is.sir), na.rm = TRUE)) {
       track_changes$sir_warn <- cols[!vapply(FUN.VALUE = logical(1), x[, cols, drop = FALSE], is.sir)]
     }
-    non_SIR <- !(new_edits[rows, cols] == "S" | new_edits[rows, cols] == "I" | new_edits[rows, cols] == "R" | new_edits[rows, cols] == "SDD" | new_edits[rows, cols] == "NI")
+    non_SIR <- is.na(new_edits[rows, cols]) | !(new_edits[rows, cols] == "S" | new_edits[rows, cols] == "I" | new_edits[rows, cols] == "R" | new_edits[rows, cols] == "SDD" | new_edits[rows, cols] == "NI")
     tryCatch(
       # insert into original table
       if (isTRUE(overwrite)) {