Runs the main ETL steps for converting AmsterdamUMCdb to the OMOP CDM

This function executes the ETL by creating the CDM and vocabulary tables, loading the vocabulary tables, indexing those tables, loading the source_to_concept_map, loading the data tables, indexing the data tables, creating example cohort tables and running the DataQualityDashboard checks and Achilles aggregation.

Usage

etl(vocabulary = TRUE, mappings = TRUE, achilles = TRUE, dqd = TRUE)

Arguments

vocabulary: Determines whether the vocabulary tables should be processed. Since the vocabularies will not change often, testing run time can be reduced by ignoring these tables. Default: TRUE
mappings: Determines whether the source to concept mappings will be generated using the mappings files created with OHDSI Usagi. Default: TRUE
achilles: Determines whether OHDSI Achilles should be run after loading the data in the CDM to generate table aggregations for use in WebAPI/ATLAS. Setting this to FALSE will significantly reduce testing run time. Default: TRUE
dqd: Determines whether the checks of OHDSI DataQualityDashboard should be run after loading the data in the CDM. Setting this to FALSE will significantly reduce testing run time. Default: TRUE

Details

This function requires a configured config.yaml file created using amstel::create_config().

The ETL for AmsterdamUMCdb is based on the excellent and well-documented ETL of the Sythea project available at: https://github.com/OHDSI/ETL-Synthea.