From d319c8543bf24440d8aa593147095638a7ced783 Mon Sep 17 00:00:00 2001 From: Jennifer Thom Date: Tue, 2 Jul 2024 16:41:52 +0100 Subject: [PATCH] Update running process manually --- .../run_episode_file_1718.R | 71 ++++++++++++++++++- .../run_episode_file_1819.R | 71 ++++++++++++++++++- .../run_episode_file_1920.R | 71 ++++++++++++++++++- .../run_episode_file_2021.R | 71 ++++++++++++++++++- .../run_episode_file_2122.R | 71 ++++++++++++++++++- .../run_episode_file_2223.R | 71 ++++++++++++++++++- .../run_episode_file_2324.R | 71 ++++++++++++++++++- 7 files changed, 483 insertions(+), 14 deletions(-) diff --git a/Run_SLF_Files_manually/run_episode_file_1718.R b/Run_SLF_Files_manually/run_episode_file_1718.R index ab75b94d7..f679ea669 100644 --- a/Run_SLF_Files_manually/run_episode_file_1718.R +++ b/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 ## diff --git a/Run_SLF_Files_manually/run_episode_file_1819.R b/Run_SLF_Files_manually/run_episode_file_1819.R index cd5a7435f..d7a65690e 100644 --- a/Run_SLF_Files_manually/run_episode_file_1819.R +++ b/Run_SLF_Files_manually/run_episode_file_1819.R @@ -3,10 +3,77 @@ library(createslf) year <- "1819" -processed_data_list <- targets::tar_read("processed_data_list_1819", - 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_1819", + store = targets_store + ), + ae = targets::tar_read( + "source_ae_extract_1819", + store = targets_store + ), + cmh = targets::tar_read( + "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 + ), + deaths = targets::tar_read( + "source_nrs_deaths_extract_1819", + store = targets_store + ), + homelessness = targets::tar_read( + "source_homelessness_extract_1819", + store = targets_store + ), + maternity = targets::tar_read( + "source_maternity_extract_1819", + store = targets_store + ), + mental_health = targets::tar_read( + "source_mental_health_extract_1819", + store = targets_store + ), + outpatients = targets::tar_read( + "source_outpatients_extract_1819", + store = targets_store + ), + gp_ooh = targets::tar_read( + "source_ooh_extract_1819", + store = targets_store + ), + prescribing = targets::tar_read( + "source_prescribing_extract_1819", + store = targets_store + ), + care_home = targets::tar_read( + "source_sc_care_home_1819", + store = targets_store + ), + home_care = targets::tar_read( + "source_sc_home_care_1819", + store = targets_store + ), + at = targets::tar_read( + "source_sc_alarms_tele_1819", + store = targets_store + ), + sds = targets::tar_read( + "source_sc_sds_1819", + 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_episode_file_1920.R b/Run_SLF_Files_manually/run_episode_file_1920.R index a9dc591b1..e3c2ebeb0 100644 --- a/Run_SLF_Files_manually/run_episode_file_1920.R +++ b/Run_SLF_Files_manually/run_episode_file_1920.R @@ -3,10 +3,77 @@ library(createslf) year <- "1920" -processed_data_list <- targets::tar_read("processed_data_list_1920", - 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_1920", + store = targets_store + ), + ae = targets::tar_read( + "source_ae_extract_1920", + store = targets_store + ), + cmh = targets::tar_read( + "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 + ), + deaths = targets::tar_read( + "source_nrs_deaths_extract_1920", + store = targets_store + ), + homelessness = targets::tar_read( + "source_homelessness_extract_1920", + store = targets_store + ), + maternity = targets::tar_read( + "source_maternity_extract_1920", + store = targets_store + ), + mental_health = targets::tar_read( + "source_mental_health_extract_1920", + store = targets_store + ), + outpatients = targets::tar_read( + "source_outpatients_extract_1920", + store = targets_store + ), + gp_ooh = targets::tar_read( + "source_ooh_extract_1920", + store = targets_store + ), + prescribing = targets::tar_read( + "source_prescribing_extract_1920", + store = targets_store + ), + care_home = targets::tar_read( + "source_sc_care_home_1920", + store = targets_store + ), + home_care = targets::tar_read( + "source_sc_home_care_1920", + store = targets_store + ), + at = targets::tar_read( + "source_sc_alarms_tele_1920", + store = targets_store + ), + sds = targets::tar_read( + "source_sc_sds_1920", + 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_episode_file_2021.R b/Run_SLF_Files_manually/run_episode_file_2021.R index 37708ee8b..c66f4572d 100644 --- a/Run_SLF_Files_manually/run_episode_file_2021.R +++ b/Run_SLF_Files_manually/run_episode_file_2021.R @@ -3,10 +3,77 @@ library(createslf) year <- "2021" -processed_data_list <- targets::tar_read("processed_data_list_2021", - 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_2021", + store = targets_store + ), + ae = targets::tar_read( + "source_ae_extract_2021", + store = targets_store + ), + cmh = targets::tar_read( + "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 + ), + deaths = targets::tar_read( + "source_nrs_deaths_extract_2021", + store = targets_store + ), + homelessness = targets::tar_read( + "source_homelessness_extract_2021", + store = targets_store + ), + maternity = targets::tar_read( + "source_maternity_extract_2021", + store = targets_store + ), + mental_health = targets::tar_read( + "source_mental_health_extract_2021", + store = targets_store + ), + outpatients = targets::tar_read( + "source_outpatients_extract_2021", + store = targets_store + ), + gp_ooh = targets::tar_read( + "source_ooh_extract_2021", + store = targets_store + ), + prescribing = targets::tar_read( + "source_prescribing_extract_2021", + store = targets_store + ), + care_home = targets::tar_read( + "source_sc_care_home_2021", + store = targets_store + ), + home_care = targets::tar_read( + "source_sc_home_care_2021", + store = targets_store + ), + at = targets::tar_read( + "source_sc_alarms_tele_2021", + store = targets_store + ), + sds = targets::tar_read( + "source_sc_sds_2021", + 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_episode_file_2122.R b/Run_SLF_Files_manually/run_episode_file_2122.R index 47400e2d1..cde974be2 100644 --- a/Run_SLF_Files_manually/run_episode_file_2122.R +++ b/Run_SLF_Files_manually/run_episode_file_2122.R @@ -3,10 +3,77 @@ library(createslf) year <- "2122" -processed_data_list <- targets::tar_read("processed_data_list_2122", - 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_2122", + store = targets_store + ), + ae = targets::tar_read( + "source_ae_extract_2122", + store = targets_store + ), + cmh = targets::tar_read( + "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 + ), + deaths = targets::tar_read( + "source_nrs_deaths_extract_2122", + store = targets_store + ), + homelessness = targets::tar_read( + "source_homelessness_extract_2122", + store = targets_store + ), + maternity = targets::tar_read( + "source_maternity_extract_2122", + store = targets_store + ), + mental_health = targets::tar_read( + "source_mental_health_extract_2122", + store = targets_store + ), + outpatients = targets::tar_read( + "source_outpatients_extract_2122", + store = targets_store + ), + gp_ooh = targets::tar_read( + "source_ooh_extract_2122", + store = targets_store + ), + prescribing = targets::tar_read( + "source_prescribing_extract_2122", + store = targets_store + ), + care_home = targets::tar_read( + "source_sc_care_home_2122", + store = targets_store + ), + home_care = targets::tar_read( + "source_sc_home_care_2122", + store = targets_store + ), + at = targets::tar_read( + "source_sc_alarms_tele_2122", + store = targets_store + ), + sds = targets::tar_read( + "source_sc_sds_2122", + 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_episode_file_2223.R b/Run_SLF_Files_manually/run_episode_file_2223.R index e64a57f32..ee83082f1 100644 --- a/Run_SLF_Files_manually/run_episode_file_2223.R +++ b/Run_SLF_Files_manually/run_episode_file_2223.R @@ -3,10 +3,77 @@ library(createslf) year <- "2223" -processed_data_list <- targets::tar_read("processed_data_list_2223", - 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_2223", + store = targets_store + ), + ae = targets::tar_read( + "source_ae_extract_2223", + store = targets_store + ), + cmh = targets::tar_read( + "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 + ), + deaths = targets::tar_read( + "source_nrs_deaths_extract_2223", + store = targets_store + ), + homelessness = targets::tar_read( + "source_homelessness_extract_2223", + store = targets_store + ), + maternity = targets::tar_read( + "source_maternity_extract_2223", + store = targets_store + ), + mental_health = targets::tar_read( + "source_mental_health_extract_2223", + store = targets_store + ), + outpatients = targets::tar_read( + "source_outpatients_extract_2223", + store = targets_store + ), + gp_ooh = targets::tar_read( + "source_ooh_extract_2223", + store = targets_store + ), + prescribing = targets::tar_read( + "source_prescribing_extract_2223", + store = targets_store + ), + care_home = targets::tar_read( + "source_sc_care_home_2223", + store = targets_store + ), + home_care = targets::tar_read( + "source_sc_home_care_2223", + store = targets_store + ), + at = targets::tar_read( + "source_sc_alarms_tele_2223", + store = targets_store + ), + sds = targets::tar_read( + "source_sc_sds_2223", + 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_episode_file_2324.R b/Run_SLF_Files_manually/run_episode_file_2324.R index 4a7f0ad29..508689f6d 100644 --- a/Run_SLF_Files_manually/run_episode_file_2324.R +++ b/Run_SLF_Files_manually/run_episode_file_2324.R @@ -3,10 +3,77 @@ library(createslf) year <- "2324" -processed_data_list <- targets::tar_read("processed_data_list_2324", - 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_2324", + store = targets_store + ), + ae = targets::tar_read( + "source_ae_extract_2324", + store = targets_store + ), + cmh = targets::tar_read( + "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 + ), + deaths = targets::tar_read( + "source_nrs_deaths_extract_2324", + store = targets_store + ), + homelessness = targets::tar_read( + "source_homelessness_extract_2324", + store = targets_store + ), + maternity = targets::tar_read( + "source_maternity_extract_2324", + store = targets_store + ), + mental_health = targets::tar_read( + "source_mental_health_extract_2324", + store = targets_store + ), + outpatients = targets::tar_read( + "source_outpatients_extract_2324", + store = targets_store + ), + gp_ooh = targets::tar_read( + "source_ooh_extract_2324", + store = targets_store + ), + prescribing = targets::tar_read( + "source_prescribing_extract_2324", + store = targets_store + ), + care_home = targets::tar_read( + "source_sc_care_home_2324", + store = targets_store + ), + home_care = targets::tar_read( + "source_sc_home_care_2324", + store = targets_store + ), + at = targets::tar_read( + "source_sc_alarms_tele_2324", + store = targets_store + ), + sds = targets::tar_read( + "source_sc_sds_2324", + store = targets_store + ) ) # Run episode file create_episode_file(processed_data_list, year = year) %>% process_tests_episode_file(year = year) + +## End of Script ##