Proper translations of medical, service sector and provider codes

Utilizing R fuctions from FinnGenUtilsR

Here we provide details on how to translate the medical, service sector and provider codes present in service sector detailed longitudinal BigQuery table. There are three simple R functions in FinnGenUtilsR package within Sandbox that translates the codes using SQL. All these three functions uses a bigquery table called fg_codes_info_v5 which contains code translation information. Please use the latest version of this table as it contains extra codes from different registries.

Users can run these functions on the whole service sector detailed longitudinal BigQuery table but it would take quite a long time to translate all the codes. We recommend to use this after filtering for relevant codes.

Medical codes

Detailed longitudinal data contains medical codes from different finnish health registries representing diagnosis, procedures, measurements and observations. These medical codes comes from international and finnish code sets covering different vocabularies. Users can use the function fg_bq_append_code_info_to_longitudinal_data adds translations to the medical codes present in service sector detailed longitudinal BigQuery table.

fg_bq_append_code_info_to_longitudinal_data(
  bq_project_id, 
  bq_table, 
  fg_codes_info_table
  )  

The function takes into account SOURCE, CODE1, CODE2 and CODE3 columns and translates the code. By default the function takes combination of CODE1 and CODE2 for ICD10 codes present in Hilmo and Avohilmo registries. User can specify to consider only CODE1 column for ICD10 codes.

fg_bq_append_code_info_to_longitudinal_data(
  bq_project_id, 
  bq_table, 
  fg_codes_info_table, 
  ICD10fi_map_to = "CODE1"
  )

Users can also specify the length of the medical code to be translated. By default, ICD10 diagnosis code is of length 5 but user can get parent code translation by specifying the ICD10 diagnosis code length.

fg_bq_append_code_info_to_longitudinal_data(
  bq_project_id, 
  bq_table, 
  fg_codes_info_table, 
  ICD10fi_precision = 4
  )

Default settings and other options the function provides can be viewed using function fg_bq_append_code_info_to_longitudinal_data_sql. Users can checkout tutorials on how to connect to the BigQuery tables and translate the medical codes using FinnGenUtilsR package in the tutorial page.

Service Sector codes

Service sector data contains codes that provide information regarding the type of visit. Users can get proper translation of these service sector codes with help of function fg_bq_append_visit_type_info_to_service_sector_data. Service sector data is only available to two registries HILMO and AVOHILMO and columns CODE5, CODE6, CODE8 and CODE9 contains the service sector codes.

fg_bq_append_visit_type_info_to_service_sector_data(
  bq_project_id, 
  bq_table, 
  fg_codes_info_table
  )  

For HILMO registry, CODE5 is used to translate service sector code but starting from 2019 service sector codes in CODE8 and CODE9 are translated. But there are CODE8 and CODE9 service sector codes available for some medical events before 2019 within HILMO registry. In such scenarios, users can prioritize which service sector codes needs to be translated.

fg_bq_append_visit_type_info_to_service_sector_data(
  bq_project_id, 
  bq_table, 
  fg_codes_info_table,
  prioritise_SRC_Contact_Urgency_over_SRC_Service_Sector # By default TRUE
  )

Default settings and other options the function provides can be viewed using function fg_bq_append_visit_type_info_to_service_sector_data_sql. Users can checkout tutorials on how to connect to the BigQuery tables and translate the service sector codes using FinnGenUtilsR package in the tutorial page.

Provider codes

Service sector data also contains codes for provider specialty and to get proper translation of these codes you can use the function fg_bq_append_provider_info_to_service_sector_data. Only HILMO and AVOHILMO registries gives information on the specialty of the provider. For HILMO registry, the provider specialty code is from column CODE6 and for AVOHILMO registry it is CODE7.

fg_bq_append_provider_info_to_service_sector_data(
  bq_project_id, 
  bq_table, 
  fg_codes_info_table
  ) 

Default settings and other options the function provides can be viewed using function fg_bq_append_provider_info_to_service_sector_data_sql. Users can checkout tutorials on how to connect to the BigQuery tables and translate the provider codes using FinnGenUtilsR package in the tutorial page.