changes to activity after death flag

R/add_activity_after_death_flag.R

@@ -11,19 +11,22 @@
 add_activity_after_death_flag <- function(
     data,
     year,
-    deaths_data = read_file(all_slf_deaths_lookup_path())) {
-  # Match on BOXI NRS deaths lookup for records without chi
-  data <- data %>%
+    deaths_data = read_file(get_all_slf_deaths_lookup_path())) {
+  death_joined <- data %>%
+    dplyr::select(year, chi, record_keydate1, record_keydate2, death_date, deceased) %>%
     dplyr::filter(!is.na(chi) | chi != "") %>%
     dplyr::left_join(
-      deaths_data,
+      deaths_data %>%
+        slfhelper::get_chi(),
       by = "chi",
       suffix = c("", "_boxi")
-    )
+    ) %>%
+    dplyr::filter(deceased == TRUE | deceased_boxi == TRUE) %>%
+    dplyr::distinct()
 
 
   # Check and print error message for records which already have a death_date in the episode file, but this doesn't match the BOXI death date
-  check_death_date_match <- data %>%
+  check_death_date_match <- death_joined %>%
     dplyr::filter(death_date != death_date_boxi)
 
   if (nrow(check_death_date_match) != 0) {
@@ -32,32 +35,32 @@ add_activity_after_death_flag <- function(
 
 
   # Check and print error message for records which have a record_keydate1 after their BOXI death date
-  check_keydate1_death_date <- data %>%
+  check_keydate1_death_date <- death_joined %>%
     dplyr::filter(record_keydate1 > death_date_boxi)
 
   if (nrow(check_death_date_match) != 0) {
     warning("There were records in the episode file which have a record_keydate1 after the BOXI NRS death date.")
   }
 
 
-  flag_data <- data %>%
+  flag_data <- death_joined %>%
     dplyr::mutate(
-      flag_keydate1 = if_else(record_keydate1 > death_date_boxi, 1, 0),
-      flag_keydate2 = if_else(record_keydate2 > death_date_boxi, 1, 0),
+      flag_keydate1 = dplyr::if_else(record_keydate1 > death_date_boxi, 1, 0),
+      flag_keydate2 = dplyr::if_else(record_keydate2 > death_date_boxi, 1, 0),
 
       # Next flag records with 'ongoing' activity after date of death (available from BOXI) if keydate2 is missing and the death date occurs in
       # in the current or a previous financial year.
-      flag_keydate2_missing = if_else(((is.na(record_keydate2) | record_keydate2 == "") & (death_date_boxi <= paste0("20", substr(year, 3, 4), "-03-31"))), 1, 0),
+      flag_keydate2_missing = dplyr::if_else(((is.na(record_keydate2) | record_keydate2 == "") & (death_date_boxi <= paste0("20", substr(year, 3, 4), "-03-31"))), 1, 0),
 
       # Also flag records without a death_date in the episode file, but the BOXI death date occurs in the current or a previous financial year.
-      flag_deathdate_missing = if_else(((is.na(death_date) | death_date == "") & (death_date_boxi <= paste0("20", substr(year, 3, 4), "-03-31"))), 1, 0)
+      flag_deathdate_missing = dplyr::if_else(((is.na(death_date) | death_date == "") & (death_date_boxi <= paste0("20", substr(year, 3, 4), "-03-31"))), 1, 0)
     ) %>%
     # These should be flagged by one of the two lines of code above, but in these cases, we will also fill in the blank death date if appropriate
 
     # Search all variables beginning with "flag_" for value "1" and create new variable to flag cases where 1 is present
     # Multiplying by 1 changes flag from true/false to 1/0
     dplyr::mutate(activity_after_death = purrr::pmap_dbl(
-      select(., contains("flag_")),
+      dplyr::select(., contains("flag_")),
       ~ any(grepl("^1$", c(...)),
         na.rm = TRUE
       ) * 1
@@ -77,18 +80,17 @@ add_activity_after_death_flag <- function(
   # Fill in date of death if missing in the episode file but available in BOXI lookup, due to historic dates of death not being carried
   # over from previous financial years
   flag_data <- flag_data %>%
-    dplyr::mutate(death_date = if_else(((is.na(death_date) | death_date == "") & (death_date_boxi <= paste0("20", substr(year, 1, 2), "-03-31"))), death_date_boxi, death_date)) %>%
-    dplyr::mutate(deceased = if_else(((is.na(deceased) | deceased == "") & (deceased_boxi == TRUE)), deceased_boxi, deceased)) %>%
+    dplyr::filter(activity_after_death == 1) %>%
     # Remove temporary flag variables used to create activity after death flag and fill in missing death_date
-    dplyr::select(-c(death_date_boxi, deceased_boxi, flag_keydate1, flag_keydate2, flag_keydate2_missing, flag_deathdate_missing))
+    dplyr::select(year, chi, record_keydate1, record_keydate2, activity_after_death) %>%
+    dplyr::distinct()
 
   # Match activity after death flag back to episode file
   final_data <- data %>%
     dplyr::left_join(
       flag_data,
-      by = "chi",
-      na_matches = "never",
-      relationship = "many-to-one"
+      by = c("year", "chi", "record_keydate1", "record_keydate2"),
+      na_matches = "never"
     )
 
 
@@ -113,7 +115,8 @@ add_activity_after_death_flag <- function(
 #'
 #'
 # Read data------------------------------------------------
-process_deaths_lookup <- function(update = latest_update(), ...) {
+process_deaths_lookup <- function(update = latest_update(),
+                                  write_to_disk = TRUE, ...) {
   all_boxi_deaths <- read_file(get_slf_deaths_lookup_path("1415")) %>%
     rbind(read_file(get_slf_deaths_lookup_path("1516"))) %>%
     rbind(read_file(get_slf_deaths_lookup_path("1617"))) %>%
@@ -125,7 +128,7 @@ process_deaths_lookup <- function(update = latest_update(), ...) {
     rbind(read_file(get_slf_deaths_lookup_path("2223"))) %>%
     rbind(read_file(get_slf_deaths_lookup_path("2324"))) %>%
     # Can this be automated to pick up files starting with name "get_slf_deaths_lookup_path"?
-
+    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(chi) | chi != "")
@@ -169,8 +172,12 @@ process_deaths_lookup <- function(update = latest_update(), ...) {
   # 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) {
-    all_boxi_deaths %>%
-      write_file(get_all_slf_deaths_lookup_path())
+    write_file(
+      all_boxi_deaths,
+      fs::path(get_slf_dir(), "Deaths",
+        file_name = stringr::str_glue("anon-all_slf_deaths_lookup_{update}.parquet")
+      )
+    )
   }
 
   return(all_boxi_deaths)

R/get_slf_lookup_paths.R

@@ -63,7 +63,7 @@ get_slf_deaths_lookup_path <- function(year, ...) {
   # Review the naming convention of this path and file
   slf_deaths_lookup_path <- get_file_path(
     directory = fs::path(get_slf_dir(), "Deaths"),
-    file_name = stringr::str_glue("slf_deaths_lookup_{year}.parquet"),
+    file_name = stringr::str_glue("anon-slf_deaths_lookup_{year}.parquet"),
     ...
   )
 
@@ -82,19 +82,20 @@ get_slf_deaths_lookup_path <- function(year, ...) {
 #' @family slf lookup file path
 #' @seealso [get_file_path()] for the generic function.
 
-get_all_slf_deaths_lookup_path <- function(update = latest_update()) {
+get_all_slf_deaths_lookup_path <- function(update = latest_update(), ...) {
   # Note this name is very similar to the existing slf_deaths_lookup_path which returnsthe path for
   # the processed BOXI extract for each financial year. This function will return the combined financial
   # years lookup i.e. all years put together.
   all_slf_deaths_lookup_path <- get_file_path(
-    directory = fs::path(get_slf_dir(), "Deaths",
-      file_name = stringr::str_glue("all_slf_deaths_lookup_{update}.parquet")
-    )
+    directory = fs::path(get_slf_dir(), "Deaths"),
+    file_name = stringr::str_glue("anon-all_slf_deaths_lookup_{update}.parquet"),
+    ...
   )
-
   return(all_slf_deaths_lookup_path)
 }
 
+
+
 #' SLF CHI Deaths File Path
 #'
 #' @description Get the full path to the CHI deaths file