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Load data for SCCS from the database

Source: R/DataLoadingSaving.R
getDbSccsData.Rd

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

Usage

getDbSccsData(
  connectionDetails,
  cdmDatabaseSchema,
  tempEmulationSchema = getOption("sqlRenderTempEmulationSchema"),
  outcomeDatabaseSchema = cdmDatabaseSchema,
  outcomeTable = "condition_era",
  outcomeIds,
  exposureDatabaseSchema = cdmDatabaseSchema,
  exposureTable = "drug_era",
  customCovariateDatabaseSchema = cdmDatabaseSchema,
  customCovariateTable = "cohort",
  nestingCohortDatabaseSchema = cdmDatabaseSchema,
  nestingCohortTable = "cohort",
  getDbSccsDataArgs
)

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).

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).

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).

getDbSccsDataArgs

An object of type GetDbSccsDataArgs as created by the createGetDbSccsDataArgs() function.

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.