Synthea to OMOP ETL

Source: R/etl_to_omop.R

Synthea to OMOP ETL

etl_to_omop(
  user = NULL,
  password = NULL,
  server = NULL,
  port = NULL,
  omop_cdm_schema = "omop_cdm",
  synthea_schema = "native_synthea",
  path_to_synthea_csvs = "synthea_output/2020-12-20 20:12:56/csv/",
  path_to_omop_vocab_csvs = ""
)

Arguments

omop_cdm_schema

Destination schema for the OMOP Vocabulary Tables and ETL'd Synthea data
synthea_schema

Schema where the native synthea csvs will be loaded for the ETL.
path_to_synthea_csvs

Path to the csvs produced by run_synthea.
path_to_omop_vocab_csvs

Path to csvs downloaded the reconstituted (if CPT4 is desired) from athena.ohdsi.org.
connDetails

Connection Details object, Default: cd

See also

typewrite DropVocabTables,DropEventTables,DropSyntheaTables,DropMapAndRollupTables,CreateVocabTables,CreateEventTables,CreateSyntheaTables,LoadSyntheaTables,LoadVocabFromCsv,CreateVocabMapTables,CreateVisitRollupTables,LoadEventTables