(v2.1.1.9123) add EFF code to antibiotics data set

R/ab.R

@@ -687,3 +687,30 @@ get_translate_ab <- function(translate_ab) {
     translate_ab
   }
 }
+
+create_AB_AV_lookup <- function(df) {
+  new_df <- df
+  new_df$generalised_name <- generalise_antibiotic_name(new_df$name)
+  new_df$generalised_synonyms <- lapply(new_df$synonyms, generalise_antibiotic_name)
+  if ("abbreviations" %in% colnames(df)) {
+    new_df$generalised_abbreviations <- lapply(new_df$abbreviations, generalise_antibiotic_name)
+  }
+  new_df$generalised_loinc <- lapply(new_df$loinc, generalise_antibiotic_name)
+  new_df$generalised_all <- unname(lapply(
+    as.list(as.data.frame(
+      t(new_df[,
+               c(
+                 colnames(new_df)[colnames(new_df) %in% c("ab", "av", "atc", "cid", "name")],
+                 colnames(new_df)[colnames(new_df) %like% "generalised"]
+               ),
+               drop = FALSE
+      ]),
+      stringsAsFactors = FALSE
+    )),
+    function(x) {
+      x <- generalise_antibiotic_name(unname(unlist(x)))
+      x[x != ""]
+    }
+  ))
+  new_df[, colnames(new_df)[colnames(new_df) %like% "^generalised"]]
+}

R/ab_selectors.R

@@ -48,7 +48,7 @@
 #' `r paste0(" * ", na.omit(sapply(DEFINED_AB_GROUPS, function(ab) ifelse(tolower(gsub("^AB_", "", ab)) %in% ls(envir = asNamespace("AMR")), paste0("[", tolower(gsub("^AB_", "", ab)), "()] can select: \\cr ", vector_and(paste0(ab_name(eval(parse(text = ab), envir = asNamespace("AMR")), language = NULL, tolower = TRUE), " (", eval(parse(text = ab), envir = asNamespace("AMR")), ")"), quotes = FALSE, sort = TRUE)), character(0)), USE.NAMES = FALSE)), "\n", collapse = "")`
 #' @rdname antibiotic_class_selectors
 #' @name antibiotic_class_selectors
-#' @return When used inside selecting or filtering, this returns a [character] vector of column names, with additional class `"ab_selector"`. When used individually, this returns an ['ab' vector][as.ab()] with all possible antimicrobial that the function would be able to select or filter.
+#' @return When used inside selecting or filtering, this returns a [character] vector of column names, with additional class `"ab_selector"`. When used individually, this returns an ['ab' vector][as.ab()] with all possible antimicrobials that the function would be able to select or filter.
 #' @export
 #' @inheritSection AMR Reference Data Publicly Available
 #' @examples
@@ -418,6 +418,13 @@ penicillins <- function(only_sir_columns = FALSE, ...) {
   ab_select_exec("penicillins", only_sir_columns = only_sir_columns)
 }
 
+#' @rdname antibiotic_class_selectors
+#' @export
+phenicols <- function(only_sir_columns = FALSE, ...) {
+  meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
+  ab_select_exec("phenicols", only_sir_columns = only_sir_columns)
+}
+
 #' @rdname antibiotic_class_selectors
 #' @export
 polymyxins <- function(only_sir_columns = FALSE, only_treatable = TRUE, ...) {
@@ -675,17 +682,16 @@ ab_select_exec <- function(function_name,
   }
   
   if (is.null(vars_df)) {
-    # no data found, no antimicrobials, so no input. Can happen if users run e.g. `aminoglycosides()` as a separate command.
+    # no data found, no antimicrobials, so no input. Happens if users run e.g. `aminoglycosides()` as a separate command.
     examples <- paste0(
-      ", e.g.:\n",
       "  ", AMR_env$bullet_icon, " your_data %>% select(", function_name, "())\n",
       "  ", AMR_env$bullet_icon, " your_data %>% select(column_a, column_b, ", function_name, "())\n",
       "  ", AMR_env$bullet_icon, " your_data %>% filter(any(", function_name, "() == \"R\"))\n",
       "  ", AMR_env$bullet_icon, " your_data[, ", function_name, "()]\n",
-      "  ", AMR_env$bullet_icon, " your_data[, c(\"column_a\", \"column_b\", ", function_name, "())]"
-    )
-    message_("The function `" , function_name, "()` should be used inside a `dplyr` verb or `data.frame` call",
-             examples, "\n\nNow returning a vector of all possible antimicrobials that `" , function_name, "()` can select.")
+      "  ", AMR_env$bullet_icon, " your_data[, c(\"column_a\", \"column_b\", ", function_name, "())]")
+    message_("The function `" , function_name, "()` should be used inside a `dplyr` verb or `data.frame` call, e.g.:\n",
+             examples,
+             "\n\nNow returning a vector of all possible antimicrobials that `" , function_name, "()` can select.")
     return(sort(abx))
   }
 

R/zzz.R

@@ -200,10 +200,14 @@ AMR_env$cli_abort <- import_fn("cli_abort", "cli", error_on_fail = FALSE)
   if (pkg_is_available("tibble")) {
     try(loadNamespace("tibble"), silent = TRUE)
   }
-
+  
   # reference data - they have additional data to improve algorithm speed
   # they cannot be part of R/sysdata.rda since CRAN thinks it would make the package too large (+3 MB)
-  AMR_env$AB_lookup <- cbind(AMR::antibiotics, AB_LOOKUP)
+  if (NROW(AB_LOOKUP) != NROW(AMR::antibiotics)) {
+    # antibiotics data set was updated - run create_AB_AV_lookup() again
+    AB_LOOKUP <- create_AB_AV_lookup(AMR::antibiotics)
+  }
+  AMR_env$AB_lookup <- cbind(AMR::antibiotics, AB_LOOKUP)  
   AMR_env$AV_lookup <- cbind(AMR::antivirals, AV_LOOKUP)
 }