Merge branch 'master' into episode/anon_chi

Public-Health-Scotland · Jul 18, 2023 · 9e3505e · 9e3505e
2 parents 2d97da5 + 3b2c54d
commit 9e3505e
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Showing 2 changed files with 28 additions and 19 deletions.
diff --git a/R/fill_geographies.R b/R/fill_geographies.R
@@ -85,7 +85,7 @@ make_gpprac_lookup <- function(data) {
 }
 
 fill_postcode_geogs <- function(data) {
-  spd <- read_file(get_slf_postcode_path())
+  slf_pc_lookup <- read_file(get_slf_postcode_path())
 
   filled_postcodes <- dplyr::left_join(
     data,
@@ -102,7 +102,7 @@ fill_postcode_geogs <- function(data) {
     ) %>%
     # Fill geographies
     dplyr::left_join(
-      spd,
+      slf_pc_lookup,
       by = "postcode",
       suffix = c("_old", "")
     ) %>%
@@ -117,10 +117,11 @@ fill_postcode_geogs <- function(data) {
     cascade_geographies() %>%
     dplyr::mutate(
       hbrescode = dplyr::coalesce(.data$hb2018, .data$hbrescode),
-      hscp = dplyr::coalesce(.data$hscp2018, .data$hscp),
-      lca = dplyr::coalesce(.data$lca, .data$lca_old)
+      hscp2018 = dplyr::coalesce(.data$hscp2018, .data$hscp),
+      lca = dplyr::coalesce(.data$lca, .data$lca_old),
+      datazone2011 = dplyr::coalesce(.data$datazone2011, .data$datazone2011_old)
     ) %>%
-    dplyr::select(!c("hb2018", "hscp2018", "lca_old", "most_recent_postcode"))
+    dplyr::select(!c("hb2018", "hscp", "lca_old", "datazone2011_old", "most_recent_postcode"))
 
   return(filled_postcodes)
 }

diff --git a/_targets.R b/_targets.R
@@ -59,7 +59,8 @@ list(
     process_lookup_sc_demographics(
       sc_demog_data,
       write_to_disk = write_to_disk
-    )
+    ),
+    priority = 0.9
   ),
   tar_target(
     tests_sc_demog_lookup,
@@ -70,7 +71,8 @@ list(
     process_it_chi_deaths(
       data = it_chi_deaths_extract,
       write_to_disk = write_to_disk
-    )
+    ),
+    priority = 0.9
   ),
   tar_target(
     tests_it_chi_deaths,
@@ -83,7 +85,8 @@ list(
       gpprac_ref_path = gpprac_ref_path,
       spd_path = spd_path,
       write_to_disk = write_to_disk
-    )
+    ),
+    priority = 0.9
   ),
   tar_target(
     tests_source_gp_lookup,
@@ -96,16 +99,17 @@ list(
       simd_path = simd_path,
       locality_path = locality_path,
       write_to_disk = write_to_disk
-    )
+    ),
+    priority = 0.9
   ),
   tar_target(
     tests_source_pc_lookup,
     process_tests_lookup_pc(source_pc_lookup)
   ),
   ## Cost Lookups ##
-  tar_target(ch_cost_lookup, process_costs_ch_rmd()),
-  tar_target(dn_cost_lookup, process_costs_dn_rmd()),
-  tar_target(hc_cost_lookup, process_costs_hc_rmd()),
+  tar_target(ch_cost_lookup, process_costs_ch_rmd(), priority = 0.8),
+  tar_target(dn_cost_lookup, process_costs_dn_rmd(), priority = 0.8),
+  tar_target(hc_cost_lookup, process_costs_hc_rmd(), priority = 0.8),
   tar_target(gp_ooh_cost_lookup, process_costs_gp_ooh_rmd()),
   ## Social Care - 'All' data ##
   tar_target(
@@ -122,7 +126,8 @@ list(
       all_at_extract,
       sc_demog_lookup = sc_demog_lookup,
       write_to_disk = write_to_disk
-    )
+    ),
+    priority = 0.5
   ),
   tar_target(
     all_home_care_extract,
@@ -138,7 +143,8 @@ list(
       all_home_care_extract,
       sc_demog_lookup = sc_demog_lookup,
       write_to_disk = write_to_disk
-    )
+    ),
+    priority = 0.5
   ),
   tar_target(
     all_care_home_extract,
@@ -157,7 +163,8 @@ list(
       ch_name_lookup_path = slf_ch_name_lookup_path,
       spd_path = spd_path,
       write_to_disk = write_to_disk
-    )
+    ),
+    priority = 0.5
   ),
   tar_target(
     tests_all_care_home,
@@ -177,7 +184,8 @@ list(
       all_sds_extract,
       sc_demog_lookup = sc_demog_lookup,
       write_to_disk = write_to_disk
-    )
+    ),
+    priority = 0.5
   ),
   tar_map(
     list(year = years_to_run),
@@ -256,14 +264,14 @@ list(
       get_boxi_extract_path(year = year, type = "GP_OoH-c"),
       format = "file"
     ),
-    tar_target(ooh_data,
+    tar_qs(
+      ooh_data,
       read_extract_gp_ooh(
         year,
         diagnosis_data_path,
         outcomes_data_path,
         consultations_data_path
-      ),
-      format = "rds"
+      )
     ),
     ### Target source processed extracts ###
     tar_target(source_acute_extract, process_extract_acute(