(v2.1.1.9247) CLSI/EUCAST 2025!

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(
+  "15.0" = list(
+    version_txt = "v15.0",
+    year = 2025,
+    title = "'EUCAST Clinical Breakpoint Tables'",
+    url = "https://www.eucast.org/clinical_breakpoints/"
+  ),
   "14.0" = list(
     version_txt = "v14.0",
     year = 2024,

R/eucast_rules.R

@@ -167,7 +167,7 @@ eucast_rules <- function(x,
                          info = interactive(),
                          rules = getOption("AMR_eucastrules", default = c("breakpoints", "expected_phenotypes")),
                          verbose = FALSE,
-                         version_breakpoints = 14.0,
+                         version_breakpoints = 15.0,
                          version_expected_phenotypes = 1.2,
                          version_expertrules = 3.3,
                          ampc_cephalosporin_resistance = NA,
@@ -1242,7 +1242,7 @@ edit_sir <- function(x,
 
 #' @rdname eucast_rules
 #' @export
-eucast_dosage <- function(ab, administration = "iv", version_breakpoints = 12.0) {
+eucast_dosage <- function(ab, administration = "iv", version_breakpoints = 15) {
   meet_criteria(ab, allow_class = c("character", "numeric", "integer", "factor"))
   meet_criteria(administration, allow_class = "character", is_in = dosage$administration[!is.na(dosage$administration)], has_length = 1)
   meet_criteria(version_breakpoints, allow_class = c("numeric", "integer"), has_length = 1, is_in = as.double(names(EUCAST_VERSION_BREAKPOINTS)))

R/mic.R

@@ -214,8 +214,8 @@ as.mic <- function(x, na.rm = FALSE, keep_operators = "all") {
   x <- gsub("=>", ">=", x, fixed = TRUE)
   # Remove leading == and =
   x <- gsub("^=+", "", x)
-  # retrieve signs and remove them from input
-  x_signs <- trimws(gsub("[^>=<]", "", x))
+  # retrieve operators and remove them from input
+  x_operators <- trimws(gsub("[^>=<]", "", x))
   x <- trimws(gsub("[>=<]", "", x))
   # dots without a leading zero must start with 0
   x <- gsub("([^0-9]|^)[.]", "\\10.", x, perl = TRUE)
@@ -238,8 +238,8 @@ as.mic <- function(x, na.rm = FALSE, keep_operators = "all") {
   x <- gsub("[.]$", "", x, perl = TRUE)
   # remove scientific notation
   x[x %like% "[0-9]e[-]?[0-9]"] <- trimws(format(suppressWarnings(as.double(x[x %like% "[0-9]e[-]?[0-9]"])), scientific = FALSE))
-  # add signs again
-  x <- paste0(x_signs, x)
+  # add operators again
+  x <- paste0(x_operators, x)
   # remove NAs introduced by format()
   x <- gsub("(NA)+", "", x)
   # trim it

R/plotting.R

@@ -52,7 +52,7 @@
 #' @details
 #' ### The `scale_*_mic()` Functions
 #'
-#' The functions [scale_x_mic()], [scale_y_mic()], [scale_colour_mic()], and [scale_fill_mic()] functions allow to plot the [mic][as.mic()] class (MIC values) on a continuous, logarithmic scale. They also allow to rescale the MIC range with an 'inside' or 'outside' range if required, and retain the signs in MIC values if desired. Missing intermediate log2 levels will be plotted too.
+#' The functions [scale_x_mic()], [scale_y_mic()], [scale_colour_mic()], and [scale_fill_mic()] functions allow to plot the [mic][as.mic()] class (MIC values) on a continuous, logarithmic scale. They also allow to rescale the MIC range with an 'inside' or 'outside' range if required, and retain the operators in MIC values (such as `>=`) if desired. Missing intermediate log2 levels will be plotted too.
 #'
 #' ### The `scale_*_sir()` Functions
 #'

R/sir.R

@@ -115,9 +115,12 @@
 #'
 #' ### Supported Guidelines
 #'
-#' For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are for **clinical microbiology**: EUCAST `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST" & type == "human")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST" & type == "human")$guideline)))` and CLSI `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "human")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "human")$guideline)))`, and for **veterinary microbiology**: EUCAST `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST" & type == "animal")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST" & type == "animal")$guideline)))` and CLSI `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "animal")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "animal")$guideline)))`.
+#' For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are:
+#' - For **clinical microbiology**: EUCAST `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST" & type == "human")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST" & type == "human")$guideline)))` and CLSI `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "human")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "human")$guideline)))`;
+#' - For **veterinary microbiology**: EUCAST `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST" & type == "animal")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST" & type == "animal")$guideline)))` and CLSI `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "animal")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "animal")$guideline)))`;
+#' - For **ECOFFs** (Epidemiological Cut-off Values): EUCAST `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST" & type == "ECOFF")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST" & type == "ECOFF")$guideline)))` and CLSI `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "ECOFF")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "ECOFF")$guideline)))`.
 #'
-#' Thus, the `guideline` argument must be set to e.g., ``r paste0('"', subset(AMR::clinical_breakpoints, guideline %like% "EUCAST")$guideline[1], '"')`` or ``r paste0('"', subset(AMR::clinical_breakpoints, guideline %like% "CLSI")$guideline[1], '"')``. By simply using `"EUCAST"` (the default) or `"CLSI"` as input, the latest included version of that guideline will automatically be selected. Importantly, using a column name of your data instead, allows for straightforward interpretation of historical data, which must be analysed in the context of, for example, different years.
+#' The `guideline` argument must be set to e.g., ``r paste0('"', subset(AMR::clinical_breakpoints, guideline %like% "EUCAST")$guideline[1], '"')`` or ``r paste0('"', subset(AMR::clinical_breakpoints, guideline %like% "CLSI")$guideline[1], '"')``. By simply using `"EUCAST"` (the default) or `"CLSI"` as input, the latest included version of that guideline will automatically be selected. Importantly, using a column name of your data instead, allows for straightforward interpretation of historical data that must be analysed in the context of, for example, different years.
 #'
 #' You can set your own data set using the `reference_data` argument. The `guideline` argument will then be ignored.
 #'
@@ -1611,17 +1614,17 @@ as_sir_method <- function(method_short,
         ),
         "\n",
         ifelse(method == "mic" & capped_mic_handling %in% c("conservative", "inverse") & as.character(values_bak) %like% "^[<][0-9]",
-          paste0("MIC values with the sign '<' are all considered 'S' since capped_mic_handling = \"", capped_mic_handling, "\""),
+          paste0("MIC values with the operator '<' are all considered 'S' since capped_mic_handling = \"", capped_mic_handling, "\""),
           ""
         ),
         "\n",
         ifelse(method == "mic" & capped_mic_handling %in% c("conservative", "inverse") & as.character(values_bak) %like% "^[>][0-9]",
-          paste0("MIC values with the sign '>' are all considered 'R' since capped_mic_handling = \"", capped_mic_handling, "\""),
+          paste0("MIC values with the operator '>' are all considered 'R' since capped_mic_handling = \"", capped_mic_handling, "\""),
           ""
         ),
         "\n",
         ifelse(method == "mic" & capped_mic_handling %in% c("conservative", "standard") & as.character(values_bak) %like% "^[><]=[0-9]" & as.double(values) > breakpoints_current$breakpoint_S & as.double(values) < breakpoints_current$breakpoint_R,
-          paste0("MIC values within the breakpoint guideline range with the sign '<=' or '>=' are considered 'NI' since capped_mic_handling = \"", capped_mic_handling, "\""),
+          paste0("MIC values within the breakpoint guideline range with the operator '<=' or '>=' are considered 'NI' since capped_mic_handling = \"", capped_mic_handling, "\""),
           ""
         )
       )