new antibiotics

R/count.R

@@ -44,55 +44,55 @@
 #' ?septic_patients
 #'
 #' # Count resistant isolates
-#' count_R(septic_patients$amox)
-#' count_IR(septic_patients$amox)
+#' count_R(septic_patients$AMX)
+#' count_IR(septic_patients$AMX)
 #'
 #' # Or susceptible isolates
-#' count_S(septic_patients$amox)
-#' count_SI(septic_patients$amox)
+#' count_S(septic_patients$AMX)
+#' count_SI(septic_patients$AMX)
 #'
 #' # Count all available isolates
-#' count_all(septic_patients$amox)
-#' n_rsi(septic_patients$amox)
+#' count_all(septic_patients$AMX)
+#' n_rsi(septic_patients$AMX)
 #'
 #' # Since n_rsi counts available isolates, you can
 #' # calculate back to count e.g. non-susceptible isolates.
 #' # This results in the same:
-#' count_IR(septic_patients$amox)
-#' portion_IR(septic_patients$amox) * n_rsi(septic_patients$amox)
+#' count_IR(septic_patients$AMX)
+#' portion_IR(septic_patients$AMX) * n_rsi(septic_patients$AMX)
 #'
 #' library(dplyr)
 #' septic_patients %>%
 #'   group_by(hospital_id) %>%
-#'   summarise(R  = count_R(cipr),
-#'             I  = count_I(cipr),
-#'             S  = count_S(cipr),
-#'             n1 = count_all(cipr), # the actual total; sum of all three
-#'             n2 = n_rsi(cipr),     # same - analogous to n_distinct
+#'   summarise(R  = count_R(CIP),
+#'             I  = count_I(CIP),
+#'             S  = count_S(CIP),
+#'             n1 = count_all(CIP),  # the actual total; sum of all three
+#'             n2 = n_rsi(CIP),      # same - analogous to n_distinct
 #'             total = n())          # NOT the number of tested isolates!
 #'
 #' # Count co-resistance between amoxicillin/clav acid and gentamicin,
 #' # so we can see that combination therapy does a lot more than mono therapy.
 #' # Please mind that `portion_S` calculates percentages right away instead.
-#' count_S(septic_patients$amcl)   # S = 1342 (71.4%)
-#' count_all(septic_patients$amcl) # n = 1879
+#' count_S(septic_patients$AMC)   # S = 1342 (71.4%)
+#' count_all(septic_patients$AMC) # n = 1879
 #'
-#' count_S(septic_patients$gent)   # S = 1372 (74.0%)
-#' count_all(septic_patients$gent) # n = 1855
+#' count_S(septic_patients$GEN)   # S = 1372 (74.0%)
+#' count_all(septic_patients$GEN) # n = 1855
 #'
 #' with(septic_patients,
-#'      count_S(amcl, gent))       # S = 1660 (92.3%)
+#'      count_S(AMC, GEN))         # S = 1660 (92.3%)
 #' with(septic_patients,           # n = 1798
-#'      n_rsi(amcl, gent))
+#'      n_rsi(AMC, GEN))
 #'
 #' # Get portions S/I/R immediately of all rsi columns
 #' septic_patients %>%
-#'   select(amox, cipr) %>%
+#'   select(AMX, CIP) %>%
 #'   count_df(translate = FALSE)
 #'
 #' # It also supports grouping variables
 #' septic_patients %>%
-#'   select(hospital_id, amox, cipr) %>%
+#'   select(hospital_id, AMX, CIP) %>%
 #'   group_by(hospital_id) %>%
 #'   count_df(translate = FALSE)
 #'
@@ -172,7 +172,8 @@ n_rsi <- function(...) {
 #' @importFrom dplyr %>% select_if bind_rows summarise_if mutate group_vars select everything
 #' @export
 count_df <- function(data,
-                     translate_ab = getOption("get_antibiotic_names", "official"),
+                     translate_ab = "name",
+                     language = get_locale(),
                      combine_IR = FALSE) {
 
   if (!"data.frame" %in% class(data)) {
@@ -183,10 +184,9 @@ count_df <- function(data,
     stop("No columns with class 'rsi' found. See ?as.rsi.")
   }
 
-  if (as.character(translate_ab) == "TRUE") {
-    translate_ab <- "official"
+  if (as.character(translate_ab) %in% c("TRUE", "official")) {
+    translate_ab <- "name"
   }
-  options(get_antibiotic_names = translate_ab)
 
   resS <- summarise_if(.tbl = data,
                        .predicate = is.rsi,
@@ -227,10 +227,7 @@ count_df <- function(data,
   }
 
   if (!translate_ab == FALSE) {
-    if (!tolower(translate_ab) %in% tolower(colnames(AMR::antibiotics))) {
-      stop("Parameter `translate_ab` does not occur in the `antibiotics` data set.", call. = FALSE)
-    }
-    res <- res %>% mutate(Antibiotic = abname(Antibiotic, from = "guess", to = translate_ab))
+    res <- res %>% mutate(Antibiotic = ab_property(Antibiotic, property = translate_ab, language = language))
   }
 
   res