Merge branch 'development' into 00_Sort_BI_Extracts

Public-Health-Scotland · Oct 3, 2023 · 17f0d00 · 17f0d00
2 parents 196340a + e5335c4
commit 17f0d00
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Showing 48 changed files with 13 additions and 302 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -67,7 +67,9 @@ export(get_slf_ch_name_lookup_path)
 export(get_slf_chi_deaths_path)
 export(get_slf_deaths_lookup_path)
 export(get_slf_dir)
+export(get_slf_episode_path)
 export(get_slf_gpprac_path)
+export(get_slf_individual_path)
 export(get_slf_postcode_path)
 export(get_source_extract_path)
 export(get_sparra_path)

diff --git a/R/create_episode_file.R b/R/create_episode_file.R
@@ -171,7 +171,7 @@ create_episode_file <- function(
   }
 
   if (write_to_disk) {
-    write_file(episode_file, slf_episode_path)
+    write_file(episode_file, get_slf_episode_path(year, check_mode = "write"))
   }
 
   return(episode_file)
@@ -428,5 +428,3 @@ join_cohort_lookups <- function(
 
   return(join_cohort_lookups)
 }
-
-slf_episode_path <- get_slf_episode_path(year, check_mode = "write")
diff --git a/R/get_source_extract_path.R b/R/get_source_extract_path.R
@@ -31,7 +31,6 @@ get_source_extract_path <- function(year,
                                       "sds"
                                     ),
                                     ...) {
-
   if (year %in% type) {
     cli::cli_abort("{.val {year}} was supplied to the {.arg year} argument.")
   }
@@ -64,8 +63,7 @@ get_source_extract_path <- function(year,
     "outpatients" ~ "outpatients_for_source",
     "pis" ~ "prescribing_file_for_source",
     "sds" ~ "sds-for-source"
-  )
- %>%
+  ) %>%
     stringr::str_glue("-{year}.parquet")
 
   source_extract_path <- get_file_path(

diff --git a/R/process_extract_ae.R b/R/process_extract_ae.R
@@ -192,7 +192,7 @@ process_extract_ae <- function(data, year, write_to_disk = TRUE) {
   # Read in data---------------------------------------
 
   ae_cup_file <- read_file(
-    path = get_boxi_extract_path(year, "ae_cup),
+    path = get_boxi_extract_path(year, "ae_cup"),
     col_type = readr::cols(
       "ED Arrival Date" = readr::col_date(format = "%Y/%m/%d %T"),
       "ED Arrival Time" = readr::col_time(""),
@@ -292,12 +292,11 @@ process_extract_ae <- function(data, year, write_to_disk = TRUE) {
     )
 
   if (write_to_disk) {
-
     write_file(
       ae_processed,
       get_source_extract_path(year, "ae", check_mode = "write")
     )
- }
+  }
 
   return(ae_processed)
 }
diff --git a/R/process_tests_sc_demographics.R b/R/process_tests_sc_demographics.R
@@ -41,6 +41,7 @@ produce_sc_demog_lookup_tests <- function(data) {
       n_missing_sending_loc = is.na(.data$sending_location),
       n_missing_sc_id = is.na(.data$social_care_id)
     ) %>%
+    create_sending_location_test_flags(.data$sending_location) %>%
     # remove variables that won't be summed
     dplyr::select(
       -c(

diff --git a/_SPSS_archived/All_years/04-Social_Care/03-Alarms_Telecare_data.R b/_SPSS_archived/All_years/04-Social_Care/03-Alarms_Telecare_data.R
@@ -46,8 +46,6 @@ at_full_data <- tbl(
     service_end_date
   ) %>%
   # fix bad period (2017, 2020 & 2021)
-  # TODO - ask SC team as last meeting they said to look at extract date - these dont relate.
-  # e.g. extract date later than period
   mutate(
     period = if_else(period == "2017", "2017Q4", period),
     period = if_else(period == "2020", "2020Q4", period),

diff --git a/man/add_acute_columns.Rd b/man/add_acute_columns.Rd
diff --git a/man/add_ae_columns.Rd b/man/add_ae_columns.Rd
diff --git a/man/add_all_columns.Rd b/man/add_all_columns.Rd
diff --git a/man/add_at_columns.Rd b/man/add_at_columns.Rd
diff --git a/man/add_ch_columns.Rd b/man/add_ch_columns.Rd
diff --git a/man/add_cij_columns.Rd b/man/add_cij_columns.Rd
diff --git a/man/add_cmh_columns.Rd b/man/add_cmh_columns.Rd
diff --git a/man/add_dd_columns.Rd b/man/add_dd_columns.Rd
diff --git a/man/add_dn_columns.Rd b/man/add_dn_columns.Rd
diff --git a/man/add_gls_columns.Rd b/man/add_gls_columns.Rd
diff --git a/man/add_hc_columns.Rd b/man/add_hc_columns.Rd
diff --git a/man/add_hl1_columns.Rd b/man/add_hl1_columns.Rd
diff --git a/man/add_ipdc_cols.Rd b/man/add_ipdc_cols.Rd
diff --git a/man/add_mat_columns.Rd b/man/add_mat_columns.Rd
diff --git a/man/add_mh_columns.Rd b/man/add_mh_columns.Rd
diff --git a/man/add_nrs_columns.Rd b/man/add_nrs_columns.Rd
diff --git a/man/add_nsu_cohort.Rd b/man/add_nsu_cohort.Rd
diff --git a/man/add_nsu_columns.Rd b/man/add_nsu_columns.Rd
diff --git a/man/add_ooh_columns.Rd b/man/add_ooh_columns.Rd
diff --git a/man/add_op_columns.Rd b/man/add_op_columns.Rd
diff --git a/man/add_pis_columns.Rd b/man/add_pis_columns.Rd
diff --git a/man/add_ppa_flag.Rd b/man/add_ppa_flag.Rd
diff --git a/man/add_sds_columns.Rd b/man/add_sds_columns.Rd
diff --git a/man/add_standard_cols.Rd b/man/add_standard_cols.Rd
diff --git a/man/aggregate_by_chi.Rd b/man/aggregate_by_chi.Rd
diff --git a/man/aggregate_ch_episodes.Rd b/man/aggregate_ch_episodes.Rd