A sample version of an OMOP compliant input file for the Best Mapped Concepts data quality module. This exact file is also included as a CSV in the package if the user wishes to use it, or the structure can be copied to produce a custom list of checks.
Format
bmc_input_omop
A dataframe or CSV file with 7 columns
- check_id
A short string "code" used to identify the specific check (ex: de, de_rx)
- check_description
A longer description of the check (ex: full drug_exposure table, prescribed drugs based on drug_type_concept_id)
- schema
The schema where the data is kept. Use
cdmto use the pre-configuredcdm_schema,resultto use the preconfiguredresults_schema, or input the exact name of the schema.- table
The name of the CDM or pre-computed results table where the relevant data is kept
- concept_field
The *_concept_id field with the concepts that make up the valueset (ex: drug_concept_id, drug_source_concept_id)
- concept_table_field
OPTIONAL The field in OMOP's vocabulary concept table that should be used to identify the concept_ids in the concept_field (i.e. concept_name, concept_class_id); only needed if concept_tbl is not NULL
- filter_logic
OPTIONAL The logic that should be applied to the provided table in order to tailor the tables to the desired check assessment (ex: if you only want to assess prescription drugs)