Load data for SCCS from the database — getDbSccsData • SelfControlledCaseSeries

Load all data needed to perform an SCCS analysis from the database.

getDbSccsData(
  connectionDetails,
  cdmDatabaseSchema,
  tempEmulationSchema = getOption("sqlRenderTempEmulationSchema"),
  outcomeDatabaseSchema = cdmDatabaseSchema,
  outcomeTable = "condition_era",
  outcomeIds,
  exposureDatabaseSchema = cdmDatabaseSchema,
  exposureTable = "drug_era",
  exposureIds = c(),
  useCustomCovariates = FALSE,
  customCovariateDatabaseSchema = cdmDatabaseSchema,
  customCovariateTable = "cohort",
  customCovariateIds = c(),
  useNestingCohort = FALSE,
  nestingCohortDatabaseSchema = cdmDatabaseSchema,
  nestingCohortTable = "cohort",
  nestingCohortId = NULL,
  deleteCovariatesSmallCount = 0,
  studyStartDate = "",
  studyEndDate = "",
  studyStartDates = c(),
  studyEndDates = c(),
  cdmVersion = "5",
  maxCasesPerOutcome = 0
)

Arguments

connectionDetails: An R object of type ConnectionDetails created using the function 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.
outcomeDatabaseSchema: The name of the database schema that is the location where the data used to define the outcome cohorts is available. If outcomeTable = "condition_era", outcomeDatabaseSchema is not used. Requires read permissions to this database.
outcomeTable: The table name that contains the outcome cohorts. If outcomeTable is not "condition_era", then expectation is outcomeTable has format of cohort table (see details).
outcomeIds: A list of IDs used to define outcomes. If outcomeTable is not "condition_era" the list contains records found in the cohort_definition_id field.
exposureDatabaseSchema: The name of the database schema that is the location where the exposure data used to define the exposure eras is available. If exposureTable = "drug_era", exposureDatabaseSchema is not used but assumed to be equal to cdmDatabaseSchema. Requires read permissions to this database.
exposureTable: The tablename that contains the exposure cohorts. If exposureTable is not "drug_era", then expectation is exposureTable has format of a cohort table (see details).
exposureIds: A list of identifiers to extract from the exposure table. If exposureTable = DRUG_ERA, exposureIds should be CONCEPT_ID. If exposureTable = "drug_era", exposureIds is used to select the drug_concept_id. If no exposure IDs are provided, all drugs or cohorts in the exposureTable are included as exposures.
useCustomCovariates: DEPRECATED. Set customCovariateIds to non-null value to use custom cohorts.
customCovariateDatabaseSchema: The name of the database schema that is the location where the custom covariate data is available.
customCovariateTable: Name of the table holding the custom covariates. This table should have the same structure as the cohort table (see details).
customCovariateIds: A list of cohort definition IDs identifying the records in the customCovariateTable to use for building custom covariates.
useNestingCohort: DEPRECATED. Set nestingCohortId to non-null value to use a nesting cohort.
nestingCohortDatabaseSchema: The name of the database schema that is the location where the nesting cohort is defined.
nestingCohortTable: Name of the table holding the nesting cohort. This table should have the same structure as the cohort table (see details).
nestingCohortId: A cohort definition ID identifying the records in the nestingCohortTable to use as nesting cohort.
deleteCovariatesSmallCount: The minimum count for a covariate to appear in the data to be kept.
studyStartDate: DEPRECATED. Use studyStartDates instead.
studyEndDate: DEPRECATED. Use studyEndDates instead.
studyStartDates: A character object specifying the minimum dates where data is used. Date format is 'yyyymmdd'. Use "" to indicate all time prior. See section for more information.
studyEndDates: A character object specifying the maximum dates where data is used. Date format is 'yyyymmdd'. Use "" to indicate to the end of observation. See section for more information.
cdmVersion: Define the OMOP CDM version used: currently supports "5".
maxCasesPerOutcome: If there are more than this number of cases for a single outcome cases will be sampled to this size. maxCasesPerOutcome = 0 indicates no maximum size.

Value

An SccsData object.

Details

This function downloads several types of information:

Information on the occurrences of the outcome(s) of interest. Note that information for multiple outcomes can be fetched in one go, and later the specific outcome can be specified for which we want to build a model.
Information on the observation time and age for the people with the outcomes.
Information on exposures of interest which we want to include in the model.

Five different database schemas can be specified, for five different types of information: The

cdmDatabaseSchema is used to extract patient age and observation period. The
outcomeDatabaseSchema is used to extract information about the outcomes, the
exposureDatabaseSchema is used to retrieve information on exposures, and the
customCovariateDatabaseSchema is optionally used to find additional, user-defined covariates. All four locations could point to the same database schema.
nestingCohortDatabaseSchema is optionally used to define a cohort in which the analysis is nested, for example a cohort of diabetics patients.

All five locations could point to the same database schema.

Cohort tables are assumed to have the following fields: cohort_definition_id, subject_id, cohort_start_date, and cohort_end_date.

Study period start and end dates

A study start and end date define a period when patient data will be included in the analysis. Multiple non-overlapping periods can be defined, which for example will allow for excluding the time of the COVID pandemic, when most outcome rates were unstable.