eraFyCohorts: Era-fy cohort(s)

Description

Given a table with cohort_definition_id, subject_id, cohort_start_date, cohort_end_date execute era logic. This will delete and replace the original rows with the cohort_definition_id(s). edit privileges to the cohort table is required.

Usage

eraFyCohorts(
  connectionDetails = NULL,
  connection = NULL,
  sourceCohortDatabaseSchema = NULL,
  sourceCohortTable = "cohort",
  targetCohortDatabaseSchema = NULL,
  targetCohortTable,
  oldCohortIds,
  newCohortId,
  eraconstructorpad = 0,
  cdmDatabaseSchema = NULL,
  purgeConflicts = FALSE,
  isTempTable = FALSE,
  tempEmulationSchema = getOption("sqlRenderTempEmulationSchema")
)

Value

Nothing is returned

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.
sourceCohortDatabaseSchema: Schema name where your source cohort tables reside. Note that for SQL Server, this should include both the database and schema name, for example 'scratch.dbo'.
sourceCohortTable: The name of the source cohort table.
targetCohortDatabaseSchema: Schema name where your target cohort tables reside. Note that for SQL Server, this should include both the database and schema name, for example 'scratch.dbo'.
targetCohortTable: The name of the target cohort table.
oldCohortIds: An array of 1 or more integer id representing the cohort id of the cohort on which the function will be applied.
newCohortId: The cohort id of the output cohort.
eraconstructorpad: Optional value to pad cohort era construction logic. Default = 0. i.e. no padding.
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'.
purgeConflicts: If there are conflicts in the target cohort table i.e. the target cohort table already has records with newCohortId, do you want to purge and replace them with transformed. By default - it will not be replaced, and an error message is thrown.
isTempTable: Is the output a temp table. If yes, a new temp table is created. This will required an active connection. Any old temp table is dropped and replaced.
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.