R/derive_var_afeye.R

In admiralophtha: ADaM in R Asset Library - Ophthalmology

#' Derive Affected Eye
#'
#' Derive Affected Eye (`AFEYE`) in occurrence datasets
#'
#' @param dataset Input dataset
#'
#' `r lifecycle::badge("deprecated")` Please use `dataset` instead.
#'
#' @param loc_var Location variable
#' @param lat_var Laterality variable
#' @param loc_vals `xxLOC` values for which `AFEYE` is derived
#'
#' `r lifecycle::badge("deprecated")` Please simply ensure `xxLAT` values are
#' contained in `c("LEFT", "RIGHT", "BILATERAL")`.
#'
#' @details
#' Affected Eye is derived in the occurrence dataset using laterality and Study
#' Eye. This assumes Study Eye has already been added from ADSL.
#'
#' @author Lucy Palmen
#'
#' @return The input occurrence dataset with Affected Eye (`AFEYE`) added.
#' @keywords der_occds
#' @export
#'
#' @examples
#' library(tibble)
#' library(admiral)
#'
#' adae1 <- tribble(
#'   ~STUDYID, ~USUBJID, ~STUDYEYE, ~AELOC, ~AELAT,
#'   "XXX001", "P01", "RIGHT", "EYE", "RIGHT",
#'   "XXX001", "P01", "RIGHT", "EYE", "LEFT",
#'   "XXX001", "P01", "RIGHT", "EYE", "",
#'   "XXX001", "P01", "RIGHT", "", "RIGHT",
#'   "XXX001", "P02", "LEFT", "", "",
#'   "XXX001", "P02", "LEFT", "EYE", "LEFT",
#'   "XXX001", "P04", "BILATERAL", "EYE", "RIGHT",
#'   "XXX001", "P05", "RIGHT", "EYE", "RIGHT",
#'   "XXX001", "P05", "RIGHT", "EYE", "BILATERAL",
#'   "XXX001", "P06", "BILATERAL", "", "",
#'   "XXX001", "P06", "BILATERAL", "", "RIGHT",
#'   "XXX001", "P07", "BILATERAL", "EYE", "BILATERAL",
#'   "XXX001", "P08", "", "EYE", "BILATERAL",
#'   "XXX001", "P09", "NONSENSE", "EYE", "BILATERAL",
#'   "XXX001", "P09", "BILATERAL", "EYE", "NONSENSE",
#'   "XXX001", "P09", "BILATERAL", "NONSENSE", "BILATERAL",
#'   "XXX001", "P10", "RIGHT", "EYE", "BOTH"
#' )
#'
#' derive_var_afeye(adae1, loc_var = AELOC, lat_var = AELAT)
#'
#' adae2 <- tribble(
#'   ~STUDYID, ~USUBJID, ~STUDYEYE, ~AELOC, ~AELAT,
#'   "XXX001", "P01", "RIGHT", "EYES", "RIGHT",
#'   "XXX001", "P02", "RIGHT", "RETINA", "LEFT",
#'   "XXX001", "P03", "LEFT", "", ""
#' )
#'
#' derive_var_afeye(adae2, loc_var = AELOC, lat_var = AELAT, loc_vals = c("EYES", "RETINA"))
derive_var_afeye <- function(dataset, loc_var, lat_var, loc_vals = "EYE") {
  seye_vals <- c("LEFT", "RIGHT", "BILATERAL")
  lat_vals <- c("LEFT", "RIGHT", "BILATERAL")

  loc_var <- assert_symbol(enexpr(loc_var))
  lat_var <- assert_symbol(enexpr(lat_var))

  assert_data_frame(dataset, required_vars = expr_c(
    loc_var, lat_var,
    exprs(STUDYEYE)
  ))

  dataset %>%
    mutate(AFEYE = case_when(
      toupper(STUDYEYE) %in% seye_vals & !!lat_var == "BILATERAL" &
        !!loc_var %in% loc_vals ~ "Both Eyes",
      toupper(STUDYEYE) == "BILATERAL" & !!lat_var %in% lat_vals &
        !!loc_var %in% loc_vals ~ "Study Eye",
      toupper(!!lat_var) == toupper(STUDYEYE) & toupper(STUDYEYE) %in% seye_vals &
        !!lat_var %in% lat_vals & !!loc_var %in% loc_vals ~ "Study Eye",
      toupper(!!lat_var) != toupper(STUDYEYE) & toupper(STUDYEYE) %in% seye_vals &
        !!lat_var %in% lat_vals & !!loc_var %in% loc_vals ~ "Fellow Eye",
      TRUE ~ NA_character_
    ))
}