A sample version of an OMOP compliant input file for the Valueset Conformance 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
vs_input_omop
A dataframe or CSV file with 6 columns
- check_id
A short string "code" used to identify the specific check (ex: de, de_rx)
- 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
- valueset_name
The name of the CSV file (stored in the pre-defined file subdirectory) defining the acceptable values for the valueset
- concept_field
The *_concept_id field with the concepts that make up the valueset (ex: race_concept_id, ethnicity_concept_id)
- 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 evaluate the valueset for prescription drugs)