Update run_slf_manually scripts

Public-Health-Scotland · Aug 28, 2024 · 0e19c5f · 0e19c5f
1 parent bfed637
commit 0e19c5f
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Showing 9 changed files with 84 additions and 28 deletions.
diff --git a/Run_SLF_Files_manually/run_episode_file_1718.R b/Run_SLF_Files_manually/run_episode_file_1718.R
@@ -18,10 +18,6 @@ processed_data_list <- list(
     "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

diff --git a/Run_SLF_Files_manually/run_episode_file_1819.R b/Run_SLF_Files_manually/run_episode_file_1819.R
@@ -18,10 +18,6 @@ processed_data_list <- list(
     "source_cmh_extract_1819",
     store = targets_store
   ),
-  cmh = targets::tar_read(
-    "source_cmh_extract_1819",
-    store = targets_store
-  ),
   dn = targets::tar_read(
     "source_dn_extract_1819",
     store = targets_store

diff --git a/Run_SLF_Files_manually/run_episode_file_1920.R b/Run_SLF_Files_manually/run_episode_file_1920.R
@@ -18,10 +18,6 @@ processed_data_list <- list(
     "source_cmh_extract_1920",
     store = targets_store
   ),
-  cmh = targets::tar_read(
-    "source_cmh_extract_1920",
-    store = targets_store
-  ),
   dn = targets::tar_read(
     "source_dn_extract_1920",
     store = targets_store

diff --git a/Run_SLF_Files_manually/run_episode_file_2021.R b/Run_SLF_Files_manually/run_episode_file_2021.R
@@ -18,10 +18,6 @@ processed_data_list <- list(
     "source_cmh_extract_2021",
     store = targets_store
   ),
-  cmh = targets::tar_read(
-    "source_cmh_extract_2021",
-    store = targets_store
-  ),
   dn = targets::tar_read(
     "source_dn_extract_2021",
     store = targets_store

diff --git a/Run_SLF_Files_manually/run_episode_file_2122.R b/Run_SLF_Files_manually/run_episode_file_2122.R
@@ -18,10 +18,6 @@ processed_data_list <- list(
     "source_cmh_extract_2122",
     store = targets_store
   ),
-  cmh = targets::tar_read(
-    "source_cmh_extract_2122",
-    store = targets_store
-  ),
   dn = targets::tar_read(
     "source_dn_extract_2122",
     store = targets_store

diff --git a/Run_SLF_Files_manually/run_episode_file_2223.R b/Run_SLF_Files_manually/run_episode_file_2223.R
@@ -18,10 +18,6 @@ processed_data_list <- list(
     "source_cmh_extract_2223",
     store = targets_store
   ),
-  cmh = targets::tar_read(
-    "source_cmh_extract_2223",
-    store = targets_store
-  ),
   dn = targets::tar_read(
     "source_dn_extract_2223",
     store = targets_store

diff --git a/Run_SLF_Files_manually/run_episode_file_2324.R b/Run_SLF_Files_manually/run_episode_file_2324.R
@@ -18,10 +18,6 @@ processed_data_list <- list(
     "source_cmh_extract_2324",
     store = targets_store
   ),
-  cmh = targets::tar_read(
-    "source_cmh_extract_2324",
-    store = targets_store
-  ),
   dn = targets::tar_read(
     "source_dn_extract_2324",
     store = targets_store

diff --git a/Run_SLF_Files_manually/run_episode_file_2425.R b/Run_SLF_Files_manually/run_episode_file_2425.R
@@ -0,0 +1,75 @@
+library(targets)
+library(createslf)
+
+year <- "2425"
+
+targets_store <- fs::path("/conf/sourcedev/Source_Linkage_File_Updates/", "_targets")
+
+processed_data_list <- list(
+  acute = targets::tar_read(
+    "source_acute_extract_2425",
+    store = targets_store
+  ),
+  ae = targets::tar_read(
+    "source_ae_extract_2425",
+    store = targets_store
+  ),
+  cmh = targets::tar_read(
+    "source_cmh_extract_2425",
+    store = targets_store
+  ),
+  dn = targets::tar_read(
+    "source_dn_extract_2425",
+    store = targets_store
+  ),
+  deaths = targets::tar_read(
+    "source_nrs_deaths_extract_2425",
+    store = targets_store
+  ),
+  homelessness = targets::tar_read(
+    "source_homelessness_extract_2425",
+    store = targets_store
+  ),
+  maternity = targets::tar_read(
+    "source_maternity_extract_2425",
+    store = targets_store
+  ),
+  mental_health = targets::tar_read(
+    "source_mental_health_extract_2425",
+    store = targets_store
+  ),
+  outpatients = targets::tar_read(
+    "source_outpatients_extract_2425",
+    store = targets_store
+  ),
+  gp_ooh = targets::tar_read(
+    "source_ooh_extract_2425",
+    store = targets_store
+  ),
+  prescribing = targets::tar_read(
+    "source_prescribing_extract_2425",
+    store = targets_store
+  ),
+  care_home = targets::tar_read(
+    "source_sc_care_home_2425",
+    store = targets_store
+  ),
+  home_care = targets::tar_read(
+    "source_sc_home_care_2425",
+    store = targets_store
+  ),
+  at = targets::tar_read(
+    "source_sc_alarms_tele_2425",
+    store = targets_store
+  ),
+  sds = targets::tar_read(
+    "source_sc_sds_2425",
+    store = targets_store
+  )
+)
+
+# Run episode file
+create_episode_file(processed_data_list, year = year) %>%
+  process_tests_episode_file(year = year)
+
+## End of Script ##
diff --git a/Run_SLF_Files_manually/run_individual_file_2425.R b/Run_SLF_Files_manually/run_individual_file_2425.R
@@ -0,0 +1,9 @@
+library(createslf)
+
+year <- "2425"
+
+episode_file <- arrow::read_parquet(get_slf_episode_path(year))
+
+# Run individual file
+create_individual_file(episode_file, year = year) %>%
+  process_tests_individual_file(year = year)