fix documentation

R/aa_helper_functions.R

@@ -670,10 +670,15 @@ create_eucast_ab_documentation <- function() {
   atcs <- ab_atc(ab, only_first = TRUE)
   # only keep ABx with an ATC code:
   ab <- ab[!is.na(atcs)]
+  atcs <- atcs[!is.na(atcs)]
+
+  # sort all vectors on name:
   ab_names <- ab_name(ab, language = NULL, tolower = TRUE)
   ab <- ab[order(ab_names)]
+  atcs <- atcs[order(ab_names)]
   ab_names <- ab_names[order(ab_names)]
-  atc_txt <- paste0("[", atcs[!is.na(atcs)], "](", ab_url(ab), ")")
+  # create the text:
+  atc_txt <- paste0("[", atcs, "](", ab_url(ab), ")")
   out <- paste0(ab_names, " (`", ab, "`, ", atc_txt, ")", collapse = ", ")
   substr(out, 1, 1) <- toupper(substr(out, 1, 1))
   out

R/like.R

@@ -49,8 +49,8 @@
 #' @seealso [grepl()]
 
 #' @examples
-#' # data.table has a more limited version of %like%, so:
-#' detach("package:data.table", unload = TRUE)
+#' # data.table has a more limited version of %like%, so unload it:
+#' try(detach("package:data.table", unload = TRUE), silent = TRUE)
 #' 
 #' a <- "This is a test"
 #' b <- "TEST"

R/zzz.R

@@ -59,16 +59,15 @@ AMR_env$sir_interpretation_history <- data.frame(
   datetime = Sys.time()[0],
   index = integer(0),
   ab_input = character(0),
-  ab_considered = character(0),
+  ab_guideline = set_clean_class(character(0), c("ab", "character")),
   mo_input = character(0),
-  mo_considered = character(0),
+  mo_guideline = set_clean_class(character(0), c("mo", "character")),
   guideline = character(0),
   ref_table = character(0),
   method = character(0),
-  breakpoint_S = double(0),
-  breakpoint_R = double(0),
   input = double(0),
-  interpretation = character(0),
+  outcome = NA_sir_[0],
+  breakpoint_S_R = character(0),
   stringsAsFactors = FALSE
 )
 AMR_env$custom_ab_codes <- character(0)