Get the cohort data from the server — getDbCohortMethodData • CohortMethod

This function executes a large set of SQL statements against the database in OMOP CDM format to extract the data needed to perform the analysis.

Usage

getDbCohortMethodData(
  connectionDetails,
  cdmDatabaseSchema,
  tempEmulationSchema = getOption("sqlRenderTempEmulationSchema"),
  targetId,
  comparatorId,
  outcomeIds,
  exposureDatabaseSchema = cdmDatabaseSchema,
  exposureTable = "drug_era",
  outcomeDatabaseSchema = cdmDatabaseSchema,
  outcomeTable = "condition_occurrence",
  nestingCohortDatabaseSchema = cdmDatabaseSchema,
  nestingCohortTable = "cohort",
  getDbCohortMethodDataArgs = createGetDbCohortMethodDataArgs()
)

Arguments

connectionDetails: An R object of type connectionDetails created using the DatabaseConnector::createConnectionDetails() function.
cdmDatabaseSchema: The name of the database schema that contains the OMOP CDM instance. Requires read permissions to this database. On SQL Server, this should specify both the database and the schema, so for example 'cdm_instance.dbo'.
tempEmulationSchema: Some database platforms like Oracle and Impala do not truly support temp tables. To emulate temp tables, provide a schema with write privileges where temp tables can be created.
targetId: A unique identifier to define the target cohort. If exposureTable = DRUG_ERA, targetId is a concept ID and all descendant concepts within that concept ID will be used to define the cohort. If exposureTable <> DRUG_ERA, targetId is used to select the COHORT_DEFINITION_ID in the cohort-like table.
comparatorId: A unique identifier to define the comparator cohort. If exposureTable = DRUG_ERA, comparatorId is a concept ID and all descendant concepts within that concept ID will be used to define the cohort. If exposureTable <> DRUG_ERA, comparatorId is used to select the COHORT_DEFINITION_ID in the cohort-like table.
outcomeIds: A list of cohort IDs used to define outcomes.
exposureDatabaseSchema: The name of the database schema that is the location where the exposure data used to define the exposure cohorts is available.
exposureTable: The tablename that contains the exposure cohorts. If exposureTable <> DRUG_ERA, then expectation is exposureTable has format of COHORT table: COHORT_DEFINITION_ID, SUBJECT_ID, COHORT_START_DATE, COHORT_END_DATE.
outcomeDatabaseSchema: The name of the database schema that is the location where the data used to define the outcome cohorts is available.
outcomeTable: The tablename that contains the outcome cohorts. If outcomeTable <> CONDITION_OCCURRENCE, then expectation is outcomeTable has format of COHORT table: COHORT_DEFINITION_ID, SUBJECT_ID, COHORT_START_DATE, COHORT_END_DATE.
nestingCohortDatabaseSchema: The name of the database schema that is the location where the data used to define the nesting cohorts is available.
nestingCohortTable: The tablename that contains the nesting cohorts. Must have the format of COHORT table: COHORT_DEFINITION_ID, SUBJECT_ID, COHORT_START_DATE, COHORT_END_DATE.
getDbCohortMethodDataArgs: An object of type GetDbCohortMethodDataArgs as created by the createGetDbCohortMethodDataArgs() function.

Value

A CohortMethodData object.

Details

Based on the arguments, the treatment and comparator cohorts are retrieved, as well as outcomes occurring in exposed subjects. The treatment and comparator cohorts can be identified using the DRUG_ERA table, or through user-defined cohorts in a cohort table either inside the CDM schema or in a separate schema. Similarly, outcomes are identified using the CONDITION_ERA table or through user-defined cohorts in a cohort table either inside the CDM schema or in a separate schema. Optionally, the target and comparator cohorts can be restricted to be within a nesting cohort, which can reside in a different database schema and table.