Generate a set of cohorts

This function generates a set of cohorts in the cohort table.

Usage

generateCohortSet(
  connectionDetails = NULL,
  connection = NULL,
  cdmDatabaseSchema,
  tempEmulationSchema = getOption("sqlRenderTempEmulationSchema"),
  cohortDatabaseSchema = cdmDatabaseSchema,
  cohortTableNames = getCohortTableNames(),
  cohortDefinitionSet = NULL,
  stopOnError = TRUE,
  incremental = FALSE,
  incrementalFolder = NULL
)

Arguments

connectionDetails

An object of type connectionDetails as created using the createConnectionDetails function in the DatabaseConnector package. Can be left NULL if connection is provided.

connection

An object of type connection as created using the connect function in the DatabaseConnector package. Can be left NULL if connectionDetails is provided, in which case a new connection will be opened at the start of the function, and closed when the function finishes.

cdmDatabaseSchema

Schema name where your patient-level data in OMOP CDM format resides. Note that for SQL Server, this should include both the database and schema name, for example 'cdm_data.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.

cohortDatabaseSchema

Schema name where your cohort tables reside. Note that for SQL Server, this should include both the database and schema name, for example 'scratch.dbo'.

cohortTableNames

The names of the cohort tables. See getCohortTableNames for more details.

cohortDefinitionSet

The cohortDefinitionSet argument must be a data frame with the following columns:

cohortId

The unique integer identifier of the cohort

cohortName

The cohort's name

sql

The OHDSI-SQL used to generate the cohort

Optionally, this data frame may contain:

json

The Circe JSON representation of the cohort

stopOnError

If an error happens while generating one of the cohorts in the cohortDefinitionSet, should we stop processing the other cohorts? The default is TRUE; when set to FALSE, failures will be identified in the return value from this function.

incremental

Create only cohorts that haven't been created before?

incrementalFolder

If incremental = TRUE, specify a folder where records are kept of which definition has been executed.

Value

A data.frame consisting of the following columns:

cohortId

The unique integer identifier of the cohort

cohortName

The cohort's name

generationStatus

The status of the generation task which may be one of the following:

COMPLETE

The generation completed successfully

FAILED

The generation failed (see logs for details)

SKIPPED

If using incremental == 'TRUE', this status indicates that the cohort's generation was skipped since it was previously completed.

startTime

The start time of the cohort generation. If the generationStatus == 'SKIPPED', the startTime will be NA.

endTime

The end time of the cohort generation. If the generationStatus == 'FAILED', the endTime will be the time of the failure. If the generationStatus == 'SKIPPED', endTime will be NA.