PatientLevelPrediction database details for an omop-duck-db DuckDB file

Wires DuckDB defaults into PatientLevelPrediction::createDatabaseDetails(): DatabaseConnector's native DuckDB connection to db_path, the main schema, and the standard OHDSI cohort table that create_cohort(), build_readmission_cohort() and friends write. The result works with PatientLevelPrediction::getPlpData() and runPlp(), and with DeepPatientLevelPrediction models (including its temporal transformer, whose input is FeatureExtraction::createTemporalSequenceCovariateSettings()).

Usage

plp_database_details(
  db_path,
  target_id,
  outcome_ids,
  cdm_database_schema = "main",
  cohort_database_schema = cdm_database_schema,
  cohort_table = "cohort",
  outcome_database_schema = cohort_database_schema,
  outcome_table = cohort_table,
  cdm_database_id = NULL,
  preflight = TRUE
)

Arguments

db_path

Path to the DuckDB database file. No other process may hold it (see hades_preflight()).

target_id

Target cohort definition id.

outcome_ids

Outcome cohort definition id(s).

cdm_database_schema, cohort_database_schema, outcome_database_schema

Schemas (default "main").

cohort_table, outcome_table

Cohort tables (default "cohort").

cdm_database_id

Identifier recorded with results; default is cdm_source_abbreviation if present, otherwise the file name.

preflight

Run hades_preflight() first and stop on failure (default TRUE).

Value

A databaseDetails object from PatientLevelPrediction.

Details

By default the file is first checked with hades_preflight() and an error is raised if it is not HADES-ready (most importantly: vocabulary tables must be inside the file).