Create cohorts used in a reference set.

createReferenceSetCohorts(connectionDetails, oracleTempSchema = NULL,
  cdmDatabaseSchema, outcomeDatabaseSchema = cdmDatabaseSchema,
  outcomeTable = "outcomes", nestingDatabaseSchema = cdmDatabaseSchema,
  nestingTable = "nesting", referenceSet = "ohdsiMethodsBenchmark")

Arguments

connectionDetails

An R object of type ConnectionDetails created using the function createConnectionDetails in the DatabaseConnector package.

oracleTempSchema

Should be used in Oracle to specify a schema where the user has write priviliges for storing temporary tables.

cdmDatabaseSchema

A database schema containing health care data in the OMOP Commond Data Model. Note that for SQL Server, botth the database and schema should be specified, e.g. 'cdm_schema.dbo'

outcomeDatabaseSchema

The database schema where the target outcome table is located. Note that for SQL Server, both the database and schema should be specified, e.g. 'cdm_schema.dbo'

outcomeTable

The name of the table where the outcomes will be stored.

nestingDatabaseSchema

(For the OHDSI Methods Benchmark only) The database schema where the nesting outcome table is located. Note that for SQL Server, both the database and schema should be specified, e.g. 'cdm_schema.dbo'.

nestingTable

(For the OHDSI Methods Benchmark only) The name of the table where the nesting cohorts will be stored.

referenceSet

The name of the reference set for which outcomes need to be created. Currently supported are "omopReferenceSet", "euadrReferenceSet", and "ohdsiMethodsBenchmark".

Details

This function will create the outcomes of interest and nesting cohorts referenced in the various reference sets. The outcomes of interest are derives using information like diagnoses, procedures, and drug prescriptions. The outcomes are stored in a table on the database server.