remove redundant combine death function

R/add_activity_after_death_flag.R

@@ -108,87 +108,3 @@ add_activity_after_death_flag <- function(
 
   return(final_data)
 }
-
-
-#' Create and read SLF Deaths lookup from processed BOXI NRS deaths extracts
-#'
-#' @description The BOXI NRS deaths extract lookup should be created after the extract files for all years have been processed,
-# but before an episode file has been produced. Therefore, all BOXI NRS years should be run before running episode files.
-#'
-#' @param ... additional arguments passed to [get_slf_deaths_lookup_path()]
-#' @param update the update month (defaults to use [latest_update()])
-#'
-#' @param write_to_disk (optional) Should the data be written to disk default is
-#' `TRUE` i.e. write the data to disk.
-#'
-#' @return the final data as a [tibble][tibble::tibble-package].
-#' @export
-#'
-#'
-#'
-# Read data------------------------------------------------
-
-process_combined_deaths_lookup <- function(update = latest_update(),
-                                           write_to_disk = TRUE, ...) {
-  dir_folder <- "/conf/hscdiip/SLF_Extracts/Deaths"
-  file_names <- list.files(dir_folder,
-    pattern = "^anon-slf_deaths_lookup_.*parquet",
-    full.names = TRUE
-  )
-
-  # read all year specific deaths lookups and bind them together
-  all_boxi_deaths <- lapply(file_names, arrow::read_parquet) %>%
-    data.table::rbindlist() %>%
-    # convert to chi for processing
-    slfhelper::get_chi() %>%
-    # Remove rows with missing or blank CHI number - could also use na.omit?
-    # na.omit(all_boxi_deaths)
-    dplyr::filter(!is.na(.data$chi) | .data$chi != "")
-
-  # Check all CHI numbers are valid
-  chi_check <- all_boxi_deaths %>%
-    dplyr::pull(.data$chi) %>%
-    phsmethods::chi_check()
-
-  if (!all(chi_check %in% c("Valid CHI", "Missing (Blank)", "Missing (NA)"))) {
-    # There are some Missing (NA) values in the extracts, but I have excluded them above as they cannot be matched to episode file
-    stop("There were bad CHI numbers in the BOXI NRS file")
-  }
-
-  # Check and print error message for chi numbers with more than one death date
-  duplicates <- all_boxi_deaths %>%
-    janitor::get_dupes(.data$chi)
-
-  if (nrow(duplicates) != 0) {
-    # There are some Missing (NA) values in the extracts, but I have excluded them above as they cannot be matched to episode file
-    warning("There were duplicate death dates in the BOXI NRS file.")
-  }
-
-
-  # We decided to include duplicates as unable to determine which is correct date (unless IT can tell us, however, they don't seem to know
-  # the process well enough), and overall impact will be negligible
-  # Get anon_chi and use this to match onto episode file later
-  all_boxi_deaths <- all_boxi_deaths %>%
-    slfhelper::get_anon_chi()
-
-  # Save out duplicates for further investigation if needed (as anon_chi)
-  if (!missing(duplicates)) {
-    write_file(
-      duplicates,
-      fs::path(get_slf_dir(), "Deaths",
-        file_name = stringr::str_glue("slf_deaths_duplicates_{update}.parquet")
-      )
-    )
-  }
-
-  # Maybe save as its own function
-  # Write the all BOXI NRS deaths lookup file to disk, so this can be used to populate activity after death flag in each episode file
-  if (write_to_disk) {
-    write_file(
-      all_boxi_deaths,
-      get_combined_slf_deaths_lookup_path()
-    )
-  }
-
-  return(all_boxi_deaths)
-}