Tidy the NRS deaths functions (#699)

* Rename the IT CHI deaths file functions

* Clean up the NRS processing functions

* Update documentation

* [check-spelling] Update metadata

Update for https://github.com/Public-Health-Scotland/source-linkage-files/actions/runs/5331571060/attempts/1
Accepted in #699 (comment)

Signed-off-by: check-spelling-bot <[email protected]>

---------

Signed-off-by: check-spelling-bot <[email protected]>
Co-authored-by: Moohan <[email protected]>
Co-authored-by: Jennit07 <[email protected]>

R/process_extract_nrs_deaths.R

@@ -1,8 +1,7 @@
 #' Process the Nation Records of Scotland (NRS) Deaths extract
 #'
-#' @description This will read and process the
-#' NRS deaths extract, it will return the final data
-#' but also write this out an rds.
+#' @description This will process the NRS deaths extract, it will return the
+#' final data and write this out.
 #'
 #' @param data The extract to process
 #' @param year The year to process, in FY format.
@@ -13,27 +12,20 @@
 #' @export
 #' @family process extracts
 process_extract_nrs_deaths <- function(data, year, write_to_disk = TRUE) {
-  # Only run for a single year
   stopifnot(length(year) == 1L)
 
-  # Check that the supplied year is in the correct format
   year <- check_year_format(year)
 
-  # Data Cleaning  ---------------------------------------
-
   deaths_clean <- data %>%
-    dplyr::mutate(record_keydate2 = .data$record_keydate1) %>%
-    # create recid and year variables
     dplyr::mutate(
+      record_keydate2 = .data$record_keydate1,
       recid = "NRS",
-      year = year
-    ) %>%
-    # fix dummy gpprac codes
-    dplyr::mutate(gpprac = convert_eng_gpprac_to_dummy(.data$gpprac)) %>%
-    dplyr::mutate(smrtype = add_smr_type(.data$recid))
+      year = year,
+      gpprac = convert_eng_gpprac_to_dummy(.data$gpprac),
+      smrtype = add_smr_type(.data$recid)
+    )
 
   if (write_to_disk) {
-    # Save as rds file
     deaths_clean %>%
       write_file(get_source_extract_path(year, "Deaths", check_mode = "write"))
   }

R/read_extract_nrs_deaths.R

@@ -3,9 +3,9 @@
 #' @inherit read_extract_acute
 #'
 #' @export
-#'
-read_extract_nrs_deaths <- function(year, file_path = get_boxi_extract_path(year = year, type = "Deaths")) {
-  # Read BOXI extract
+read_extract_nrs_deaths <- function(
+    year,
+    file_path = get_boxi_extract_path(year = year, type = "Deaths")) {
   extract_nrs_deaths <- read_file(file_path,
     col_types = cols_only(
       "Death Location Code" = col_character(),
@@ -36,7 +36,6 @@ read_extract_nrs_deaths <- function(year, file_path = get_boxi_extract_path(year
       "GP practice code(99)" = col_character()
     )
   ) %>%
-    # rename variables
     dplyr::rename(
       death_location_code = "Death Location Code",
       lca = "Geo Council Area Code",