Runs a comprehensive preflight verification of OMOP CDM vocabulary coverage, ATC hierarchies, unmapped concept 0 rates across clinical tables, and drug exposure types.
Source:R/integrity.R
vocabulary_preflight.RdRuns a comprehensive preflight verification of OMOP CDM vocabulary coverage, ATC hierarchies, unmapped concept 0 rates across clinical tables, and drug exposure types.
Usage
vocabulary_preflight(
con,
required = c("RxNorm", "ATC", "LOINC", "SNOMED"),
max_unmapped_rate = 0.5,
fail_fast = TRUE,
vocab_schema = NULL,
vocab_db = NULL,
prescribed_type_concept_ids = NULL,
administered_type_concept_ids = NULL,
dispensed_type_concept_ids = NULL
)Arguments
- con
DuckDB OMOP database connection.
- required
Required vocabulary IDs (default: RxNorm, ATC, LOINC, SNOMED).
- max_unmapped_rate
Maximum allowable share of concept 0 unmapped rows before flagging (default 0.50 = 50%).
- fail_fast
If TRUE, raises an error if any required vocabulary is missing.
- vocab_schema
Optional schema or attached database name for vocabulary tables.
- vocab_db
Alias for vocab_schema.
- prescribed_type_concept_ids
Optional integer vector of prescribed concept IDs (default: 32838, 38000177, 32817).
- administered_type_concept_ids
Optional integer vector of administered concept IDs (default: 38000180, 32828).
- dispensed_type_concept_ids
Optional integer vector of dispensed concept IDs (default: 38000175, 32823).