Merge branch 'september-2024' into add_client_flags

.github/actions/spelling/expect.txt

@@ -3,7 +3,7 @@ Accom
 Admissio
 admloc
 admtype
-ADPE
+adpe
 adtf
 alstr
 arrivalmode
@@ -20,12 +20,12 @@ bodyloc
 boxi
 CAK
 callr
-Canx
+canx
 carehome
 careinspectorate
 categorises
 cattend
-CCYY
+ccyy
 cdn
 cennum
 CEREBROVASC
@@ -36,9 +36,9 @@ chpstart
 cij
 Classificat
 cmh
-CNWs
+cnws
 codecov
-Comhairle
+comhairle
 commhosp
 congen
 copd
@@ -158,7 +158,7 @@ keytime
 kis
 knitr
 lcap
-LCHO
+lcho
 lgl
 linetype
 lintr
@@ -168,8 +168,8 @@ ltd
 lubridate
 magrittr
 markdownguide
-Matern
-Mcbride
+matern
+mcbride
 mcmahon
 microsoft
 MIU
@@ -215,7 +215,7 @@ PLICS
 popluation
 Posix
 postcodes
-PPAs
+ppas
 prac
 praccode
 ptypes
@@ -268,7 +268,7 @@ simd
 slf
 slfhelper
 smr
-SMRA
+smra
 smrtype
 sourcedev
 sparra

NAMESPACE

@@ -88,11 +88,11 @@ export(midpoint_fy)
 export(next_fy)
 export(phs_db_connection)
 export(previous_update)
+export(process_combined_deaths_lookup)
 export(process_costs_ch_rmd)
 export(process_costs_dn_rmd)
 export(process_costs_gp_ooh_rmd)
 export(process_costs_hc_rmd)
-export(process_deaths_lookup)
 export(process_extract_acute)
 export(process_extract_ae)
 export(process_extract_alarms_telecare)

R/add_activity_after_death_flag.R

@@ -125,8 +125,8 @@ add_activity_after_death_flag <- function(
 #'
 #'
 # Read data------------------------------------------------
-process_deaths_lookup <- function(update = latest_update(),
-                                  write_to_disk = TRUE, ...) {
+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",

R/get_boxi_extract_path.R

@@ -16,12 +16,14 @@ get_boxi_extract_path <- function(
       "ae",
       "ae_cup",
       "acute",
+      "acute_cup",
       "cmh",
       "deaths",
       "dn",
       "gp_ooh-c",
       "gp_ooh-d",
       "gp_ooh-o",
+      "gp_ooh_cup",
       "homelessness",
       "maternity",
       "mh",
@@ -44,11 +46,13 @@ get_boxi_extract_path <- function(
     "ae" ~ "anon-A&E-episode-level-extract",
     "ae_cup" ~ "anon-A&E-UCD-CUP-extract",
     "acute" ~ "anon-Acute-episode-level-extract",
+    "acute_cup" ~ "anon-Acute-cup-extract",
     "cmh" ~ "anon-Community-MH-contact-level-extract",
     "dn" ~ "anon-District-Nursing-contact-level-extract",
     "gp_ooh-c" ~ "anon-GP-OoH-consultations-extract",
     "gp_ooh-d" ~ "anon-GP-OoH-diagnosis-extract",
     "gp_ooh-o" ~ "anon-GP-OoH-outcomes-extract",
+    "gp_ooh_cup" ~ "anon-GP-OoH-cup-extract",
     "homelessness" ~ "anon-Homelessness-extract",
     "maternity" ~ "anon-Maternity-episode-level-extract",
     "mh" ~ "anon-Mental-Health-episode-level-extract",

R/process_extract_acute.R

@@ -12,7 +12,10 @@
 #' @return the final data as a [tibble][tibble::tibble-package].
 #' @export
 #' @family process extracts
-process_extract_acute <- function(data, year, write_to_disk = TRUE) {
+process_extract_acute <- function(data,
+                                  year,
+                                  acute_cup_path = get_boxi_extract_path(year, "acute_cup"),
+                                  write_to_disk = TRUE) {
   # Only run for a single year
   stopifnot(length(year) == 1L)
 
@@ -59,7 +62,48 @@ process_extract_acute <- function(data, year, write_to_disk = TRUE) {
     # Add oldtadm as a factor with labels
     dplyr::mutate(oldtadm = factor(.data$oldtadm,
       levels = 0L:8L
-    ))
+    )) %>%
+    dplyr::mutate(
+      unique_row_num = dplyr::row_number()
+    )
+
+  acute_cup <- read_file(
+    path = acute_cup_path,
+    col_type = readr::cols(
+      "anon_chi" = readr::col_character(),
+      "Acute Admission Date" = readr::col_date(format = "%Y/%m/%d %T"),
+      "Acute Discharge Date" = readr::col_date(format = "%Y/%m/%d %T"),
+      "Acute Admission Type Code" = readr::col_character(),
+      "Acute Discharge Type Code" = readr::col_character(),
+      "Case Reference Number [C]" = readr::col_character(),
+      "CUP Marker" = readr::col_integer(),
+      "CUP Pathway Name" = readr::col_character()
+    )
+  ) %>%
+    dplyr::select(
+      anon_chi = "anon_chi",
+      case_reference_number = "Case Reference Number [C]",
+      record_keydate1 = "Acute Admission Date",
+      record_keydate2 = "Acute Discharge Date",
+      tadm = "Acute Admission Type Code",
+      disch = "Acute Discharge Type Code",
+      cup_marker = "CUP Marker",
+      cup_pathway = "CUP Pathway Name"
+    ) %>%
+    dplyr::distinct() %>%
+    slfhelper::get_chi()
+
+  acute_clean <- acute_clean %>%
+    dplyr::left_join(acute_cup,
+      by = c(
+        "record_keydate1",
+        "record_keydate2",
+        "case_reference_number",
+        "chi",
+        "tadm",
+        "disch"
+      )
+    )
 
   acute_processed <- acute_clean %>%
     dplyr::select(
@@ -106,7 +150,9 @@ process_extract_acute <- function(data, year, write_to_disk = TRUE) {
       "cost_total_net",
       tidyselect::ends_with("_beddays"),
       tidyselect::ends_with("_cost"),
-      "uri"
+      "uri",
+      "cup_marker",
+      "cup_pathway"
     ) %>%
     dplyr::arrange(.data$chi, .data$record_keydate1) %>%
     slfhelper::get_anon_chi()

R/process_extract_alarms_telecare.R

@@ -41,12 +41,12 @@ process_extract_alarms_telecare <- function(
       "smrtype",
       "chi",
       "dob",
+      "person_id",
       "gender",
       "postcode",
       "sc_send_lca",
       "record_keydate1",
       "record_keydate2",
-      "person_id",
       "sc_latest_submission"
     ) %>%
     slfhelper::get_anon_chi()

R/process_extract_gp_ooh.R

@@ -12,7 +12,10 @@
 #' @return the final data as a [tibble][tibble::tibble-package].
 #' @export
 #' @family process extracts
-process_extract_gp_ooh <- function(year, data_list, write_to_disk = TRUE) {
+process_extract_gp_ooh <- function(year,
+                                   data_list,
+                                   gp_ooh_cup_path = get_boxi_extract_path(year, "gp_ooh_cup"),
+                                   write_to_disk = TRUE) {
   diagnosis_extract <- process_extract_ooh_diagnosis(data_list[["diagnosis"]], year)
   outcomes_extract <- process_extract_ooh_outcomes(data_list[["outcomes"]], year)
   consultations_extract <- process_extract_ooh_consultations(data_list[["consultations"]], year)
@@ -93,6 +96,39 @@ process_extract_gp_ooh <- function(year, data_list, write_to_disk = TRUE) {
     ) %>%
     dplyr::ungroup()
 
+  ## Link CUP Marker -----
+  gp_ooh_cup_file <- read_file(
+    path = gp_ooh_cup_path,
+    col_type = readr::cols(
+      "GP OOH Consultation Start Date" = readr::col_date(format = "%Y/%m/%d %T"),
+      "GP OOH Consultation Start Time" = readr::col_time(""),
+      "GUID" = readr::col_character(),
+      "CUP Marker" = readr::col_integer(),
+      "CUP Pathway Name" = readr::col_character()
+    )
+  ) %>%
+    dplyr::select(
+      record_keydate1 = "GP OOH Consultation Start Date",
+      keytime1 = "GP OOH Consultation Start Time",
+      ooh_case_id = "GUID",
+      cup_marker = "CUP Marker",
+      cup_pathway = "CUP Pathway Name"
+    ) %>%
+    dplyr::distinct(
+      .data$record_keydate1,
+      .data$keytime1,
+      .data$ooh_case_id,
+      .keep_all = TRUE
+    )
+
+  ooh_clean <- ooh_clean %>%
+    dplyr::left_join(gp_ooh_cup_file,
+      by = dplyr::join_by(
+        "ooh_case_id",
+        "record_keydate1",
+        "keytime1"
+      )
+    )
 
   ## Save Outfile -------------------------------------
 
@@ -122,7 +158,9 @@ process_extract_gp_ooh <- function(year, data_list, write_to_disk = TRUE) {
       tidyselect::starts_with("ooh_outcome"),
       "cost_total_net",
       tidyselect::ends_with("_cost"),
-      "ooh_case_id"
+      "ooh_case_id",
+      cup_marker,
+      cup_pathway
     ) %>%
     slfhelper::get_anon_chi()
 

R/process_extract_sds.R

@@ -41,11 +41,13 @@ process_extract_sds <- function(
       "smrtype",
       "chi",
       "dob",
+      "person_id",
       "gender",
       "postcode",
+      "sc_send_lca",
       "record_keydate1",
       "record_keydate2",
-      "sc_send_lca"
+      "sc_latest_submission"
     ) %>%
     slfhelper::get_anon_chi()
 

R/read_extract_acute.R

@@ -149,6 +149,7 @@ read_extract_acute <- function(year, file_path = get_boxi_extract_path(year = ye
       ipdc = "Inpatient Day Case Identifier Code",
       cij_ipdc = "CIJ Inpatient Day Case Identifier Code (01)",
       lineno = "Line Number (01)",
+      case_reference_number = "Case Reference Number [C]",
       GLS_record = "GLS Record"
     ) %>%
     # replace NA in cost_total_net by 0

R/read_lookup_sc_client.R

@@ -44,6 +44,7 @@ read_lookup_sc_client <- function(fyyear,
       "day_care"
     ) %>%
     dplyr::filter(.data$financial_year == year) %>%
+    dplyr::collect() %>%
     dplyr::mutate(
       dplyr::across(
         c(

Run_SLF_Files_manually/run_episode_file_1718.R

@@ -3,10 +3,77 @@ library(createslf)
 
 year <- "1718"
 
-processed_data_list <- targets::tar_read("processed_data_list_1718",
-  store = fs::path("/conf/sourcedev/Source_Linkage_File_Updates/", "_targets")
+targets_store <- fs::path("/conf/sourcedev/Source_Linkage_File_Updates/", "_targets")
+
+processed_data_list <- list(
+  acute = targets::tar_read(
+    "source_acute_extract_1718",
+    store = targets_store
+  ),
+  ae = targets::tar_read(
+    "source_ae_extract_1718",
+    store = targets_store
+  ),
+  cmh = targets::tar_read(
+    "source_cmh_extract_1718",
+    store = targets_store
+  ),
+  cmh = targets::tar_read(
+    "source_cmh_extract_1718",
+    store = targets_store
+  ),
+  dn = targets::tar_read(
+    "source_dn_extract_1718",
+    store = targets_store
+  ),
+  deaths = targets::tar_read(
+    "source_nrs_deaths_extract_1718",
+    store = targets_store
+  ),
+  homelessness = targets::tar_read(
+    "source_homelessness_extract_1718",
+    store = targets_store
+  ),
+  maternity = targets::tar_read(
+    "source_maternity_extract_1718",
+    store = targets_store
+  ),
+  mental_health = targets::tar_read(
+    "source_mental_health_extract_1718",
+    store = targets_store
+  ),
+  outpatients = targets::tar_read(
+    "source_outpatients_extract_1718",
+    store = targets_store
+  ),
+  gp_ooh = targets::tar_read(
+    "source_ooh_extract_1718",
+    store = targets_store
+  ),
+  prescribing = targets::tar_read(
+    "source_prescribing_extract_1718",
+    store = targets_store
+  ),
+  care_home = targets::tar_read(
+    "source_sc_care_home_1718",
+    store = targets_store
+  ),
+  home_care = targets::tar_read(
+    "source_sc_home_care_1718",
+    store = targets_store
+  ),
+  at = targets::tar_read(
+    "source_sc_alarms_tele_1718",
+    store = targets_store
+  ),
+  sds = targets::tar_read(
+    "source_sc_sds_1718",
+    store = targets_store
+  )
 )
 
 # Run episode file
 create_episode_file(processed_data_list, year = year) %>%
   process_tests_episode_file(year = year)
+
+## End of Script ##