This function generates a set of cohorts in the cohort table.
generateCohortSet(
connectionDetails = NULL,
connection = NULL,
cdmDatabaseSchema,
tempEmulationSchema = getOption("sqlRenderTempEmulationSchema"),
cohortDatabaseSchema = cdmDatabaseSchema,
cohortTableNames = getCohortTableNames(),
cohortDefinitionSet = NULL,
stopOnError = TRUE,
incremental = FALSE,
incrementalFolder = NULL
)
An object of type connectionDetails
as created using the
createConnectionDetails
function in the
DatabaseConnector package. Can be left NULL if connection
is
provided.
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.
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'.
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.
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'.
The names of the cohort tables. See getCohortTableNames
for more details.
The cohortDefinitionSet
argument must be a data frame with
the following columns:
The unique integer identifier of the cohort
The cohort's name
The OHDSI-SQL used to generate the cohort
Optionally, this data frame may contain:
The Circe JSON representation of the cohort
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.
Create only cohorts that haven't been created before?
If incremental = TRUE
, specify a folder where records are
kept of which definition has been executed.
A data.frame consisting of the following columns:
The unique integer identifier of the cohort
The cohort's name
The status of the generation task which may be one of the following:
The generation completed successfully
The generation failed (see logs for details)
If using incremental == 'TRUE', this status indicates that the cohort's generation was skipped since it was previously completed.
The start time of the cohort generation. If the generationStatus == 'SKIPPED', the startTime will be NA.
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.