A sample version of an PCORnet compliant input file for the Unmapped 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
uc_input_pcornet
A dataframe or CSV file with 8 columns
- check_id
A short string "code" used to identify the specific check (ex: dr_admin, dr_rx)
- check_description
A longer description of the check (ex: full med_admin table, full prescribing table)
- 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: rxnorm_cui, raw_rxnorm_cui)
- source_value_field
For analyses where
produce_mapped_list == TRUE, the *_source_value field linked to the concept_field of interest to be used to produce a list of source values associated with unmapped concepts- date_field
For analyses where
by_year == TRUE, the date field to be used to retrieve the year associted with the unmapped concepts- 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 identify billed procedures that are unmapped)