(v3.0.1.9042) add EUCAST breakpoint table v16 to interpretive_rules()

R/aa_globals.R

@@ -30,6 +30,12 @@
 # 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(
+  "16.0" = list(
+    version_txt = "v16.0",
+    year = 2026,
+    title = "'EUCAST Clinical Breakpoint Tables'",
+    url = "https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/"
+  ),
   "15.0" = list(
     version_txt = "v15.0",
     year = 2025,

R/aa_helper_functions.R

@@ -359,9 +359,9 @@ stop_ifnot_installed <- function(package) {
   if (any(!installed) && any(package == "rstudioapi")) {
     stop("This function only works in RStudio when using R >= 3.2.", call. = FALSE)
   } else if (any(!installed)) {
-    stop("This requires the ", vector_and(package[!installed]), " package.",
-      "\nTry to install with install.packages().",
-      call. = FALSE
+    stop_(
+      "This requires the ", vector_and(paste0("{.pkg ", package[!installed], "}"), quotes = FALSE), " package.",
+      "\nTry to install with {.fun install.packages}."
     )
   } else {
     return(invisible())
@@ -747,7 +747,7 @@ format_included_data_number <- function(data) {
   paste0(ifelse(rounder == 0, "", "~"), format(round(n, rounder), decimal.mark = ".", big.mark = " "))
 }
 
-vector_or <- function(v, quotes = TRUE, reverse = FALSE, sort = TRUE, initial_captital = FALSE, last_sep = " or ") {
+vector_or <- function(v, quotes = TRUE, reverse = FALSE, sort = TRUE, initial_captital = FALSE, last_sep = " or ", documentation = FALSE) {
   # makes unique and sorts, and this also removed NAs
   v <- unique(v)
   has_na <- anyNA(v)
@@ -761,17 +761,25 @@ vector_or <- function(v, quotes = TRUE, reverse = FALSE, sort = TRUE, initial_ca
     v <- rev(v)
   }
   if (isTRUE(quotes)) {
-    quotes <- '"'
+    if (isTRUE(documentation)) {
+      quotes <- '"'
+    } else {
+      # use cli to format as values
+      quotes <- c("{.val ", "}")
+    }
   } else if (isFALSE(quotes)) {
     quotes <- ""
   } else {
     quotes <- quotes[1L]
   }
+  if (length(quotes) == 1) {
+    quotes <- c(quotes, quotes)
+  }
   if (isTRUE(initial_captital)) {
     v[1] <- gsub("^([a-z])", "\\U\\1", v[1], perl = TRUE)
   }
   if (length(v) <= 1) {
-    return(paste0(quotes, v, quotes))
+    return(paste0(quotes[1], v, quotes[2]))
   }
   if (identical(v, c("I", "R", "S"))) {
     # class 'sir' should be sorted like this
@@ -790,7 +798,7 @@ vector_or <- function(v, quotes = TRUE, reverse = FALSE, sort = TRUE, initial_ca
   if (is.numeric(v)) {
     v <- trimws(vapply(FUN.VALUE = character(1), v, format, scientific = FALSE))
   }
-  quoted <- paste0(quotes, v, quotes)
+  quoted <- paste0(quotes[1], v, quotes[2])
   quoted[NAs] <- "NA"
   # all commas except for last item, so will become '"val1", "val2", "val3" or "val4"'
   paste0(
@@ -799,10 +807,11 @@ vector_or <- function(v, quotes = TRUE, reverse = FALSE, sort = TRUE, initial_ca
   )
 }
 
-vector_and <- function(v, quotes = TRUE, reverse = FALSE, sort = TRUE, initial_captital = FALSE) {
+vector_and <- function(v, quotes = TRUE, reverse = FALSE, sort = TRUE, initial_captital = FALSE, documentation = FALSE) {
   vector_or(
     v = v, quotes = quotes, reverse = reverse, sort = sort,
-    initial_captital = initial_captital, last_sep = " and "
+    initial_captital = initial_captital, documentation = documentation,
+    last_sep = " and "
   )
 }
 

R/amr_selectors.R

@@ -857,7 +857,7 @@ all_any_amr_selector <- function(type, ..., na.rm = TRUE) {
   cols_ab <- c(...)
   result <- cols_ab[toupper(cols_ab) %in% VALID_SIR_LEVELS]
   if (length(result) == 0) {
-    message_("Filtering ", type, " of columns ", vector_and(font_bold(cols_ab, collapse = NULL), quotes = "'"), ' to contain value "S", "I" or "R"')
+    message_("Filtering ", type, " of columns ", vector_and(paste0("{.field ", font_bold(cols_ab, collapse = NULL), "}"), quotes = FALSE), " to only contain values ", vector_or(VALID_SIR_LEVELS))
     result <- VALID_SIR_LEVELS
   }
   cols_ab <- cols_ab[!cols_ab %in% result]

R/custom_eucast_rules.R

@@ -80,7 +80,7 @@
 #'
 #' ### Using taxonomic properties in rules
 #'
-#' There is one exception in columns used for the rules: all column names of the [microorganisms] data set can also be used, but do not have to exist in the data set. These column names are: `r vector_and(colnames(microorganisms), sort = FALSE)`. Thus, this next example will work as well, despite the fact that the `df` data set does not contain a column `genus`:
+#' There is one exception in columns used for the rules: all column names of the [microorganisms] data set can also be used, but do not have to exist in the data set. These column names are: `r vector_and(colnames(microorganisms), sort = FALSE, documentation = TRUE)`. Thus, this next example will work as well, despite the fact that the `df` data set does not contain a column `genus`:
 #'
 #' ```r
 #' y <- custom_eucast_rules(

R/interpretive_rules.R

@@ -76,7 +76,7 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
 #' @param overwrite A [logical] indicating whether to overwrite existing SIR values (default: `FALSE`). When `FALSE`, only non-SIR values are modified (i.e., any value that is not already S, I or R). 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
+#' **Note:** This function does not translate MIC or disk values to SIR values. Use [as.sir()] for that. \cr
 #' **Note:** When ampicillin (AMP, J01CA01) is not available but amoxicillin (AMX, J01CA04) is, the latter will be used for all rules where there is a dependency on ampicillin. These drugs are interchangeable when it comes to expression of antimicrobial resistance. \cr
 #'
 #' The file containing all EUCAST rules is located here: <https://github.com/msberends/AMR/blob/main/data-raw/eucast_rules.tsv>.  **Note:** Old taxonomic names are replaced with the current taxonomy where applicable. For example, *Ochrobactrum anthropi* was renamed to *Brucella anthropi* in 2020; the original EUCAST rules v3.1 and v3.2 did not yet contain this new taxonomic name. The `AMR` package contains the full microbial taxonomy updated until `r documentation_date(max(TAXONOMY_VERSION$GBIF$accessed_date, TAXONOMY_VERSION$LPSN$accessed_date))`, see [microorganisms].
@@ -163,7 +163,7 @@ interpretive_rules <- function(x,
                                rules = getOption("AMR_interpretive_rules", default = c("breakpoints", "expected_phenotypes")),
                                guideline = getOption("AMR_guideline", "EUCAST"),
                                verbose = FALSE,
-                               version_breakpoints = 15.0,
+                               version_breakpoints = 16.0,
                                version_expected_phenotypes = 1.2,
                                version_expertrules = 3.3,
                                ampc_cephalosporin_resistance = NA,

R/mo.R

@@ -249,7 +249,7 @@ as.mo <- function(x,
   if (length(which(ind)) > 0 && isTRUE(info) && message_not_thrown_before("as.mo_microorganisms.codes", is.na(out), toupper(x))) {
     message_(
       "Retrieved value", ifelse(sum(ind) > 1, "s", ""),
-      " from the {.help [microorganisms.codes](AMR::microorganisms.codes)} data set for ", vector_and(paste0("{.val ", toupper(x)[ind], "}"), quotes = FALSE), "."
+      " from the {.help [microorganisms.codes](AMR::microorganisms.codes)} data set for ", vector_and(toupper(x)[ind]), "."
     )
   }
   # From SNOMED ----

R/sir.R

@@ -1079,8 +1079,8 @@ get_guideline <- function(guideline, reference_data) {
   guideline_param[guideline_param %unlike% " "] <- gsub("([a-z]+)([0-9]+)", "\\1 \\2", guideline_param[guideline_param %unlike% " "], ignore.case = TRUE)
 
   stop_ifnot(guideline_param %in% reference_data$guideline,
-    "invalid guideline: '", guideline,
-    "'.\nValid guidelines are: ", vector_and(reference_data$guideline, quotes = TRUE, reverse = TRUE),
+    "invalid guideline: {.val ", guideline,
+    "}.\nValid guidelines are: ", vector_and(reference_data$guideline, reverse = TRUE),
     call = FALSE
   )