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",
customCovariateDatabaseSchema = cdmDatabaseSchema,
customCovariateTable = "cohort",
nestingCohortDatabaseSchema = cdmDatabaseSchema,
nestingCohortTable = "cohort",
getDbSccsDataArgs
)An SccsData object.
An R object of type ConnectionDetails created using
the function DatabaseConnector::createConnectionDetails() function.
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'.
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.
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.
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).
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.
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.
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).
The name of the database schema that is the location where the custom covariate data is available.
Name of the table holding the custom covariates. This table should have the same structure as the cohort table (see details).
The name of the database schema that is the location where the nesting cohort is defined.
Name of the table holding the nesting cohort. This table should have the same structure as the cohort table (see details).
An object of type GetDbSccsDataArgs as created by the createGetDbSccsDataArgs()
function.
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.
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.