createSccsAnalysesSpecifications: Create full SCCS analysis specifications

Description

Create full SCCS analysis specifications

Usage

createSccsAnalysesSpecifications(
  sccsAnalysisList,
  exposuresOutcomeList,
  analysesToExclude = NULL,
  combineDataFetchAcrossOutcomes = FALSE,
  sccsDiagnosticThresholds = SelfControlledCaseSeries::createSccsDiagnosticThresholds(),
  controlType = "outcome"
)

Value

An object of type SccsAnalysesSpecifications.

Arguments

sccsAnalysisList: A list of objects of type SccsAnalysis as created using the createSccsAnalysis() function.
exposuresOutcomeList: A list of objects of type ExposuresOutcome as created using the createExposuresOutcome() function.
analysesToExclude: Analyses to exclude. See the Analyses to Exclude section for details.
combineDataFetchAcrossOutcomes: Should fetching data from the database be done one outcome at a time, or for all outcomes in one fetch? Combining fetches will be more efficient if there is large overlap in the subjects that have the different outcomes.
sccsDiagnosticThresholds: An object of type SccsDiagnosticThresholds as created using createSccsDiagnosticThresholds().
controlType: Type of negative (and positive) controls. Can be "outcome" or "exposure". When set to "outcome", controls with the same exposure (and nesting cohort) are grouped together for calibration. When set to "exposure", controls with the same outcome are grouped together.

Details

Analyses to Exclude

Normally, runSccsAnalyses will run all combinations of exposures-outcome-analyses settings. However, sometimes we may not need all those combinations. Using the analysesToExclude argument, we can remove certain items from the full matrix. This argument should be a data frame with at least one of the following columns:

exposureId
outcomeId
nestingCohortId
analysisId

This data frame will be joined to the outcome model reference table before executing, and matching rows will be removed. For example, if one specifies only one exposure ID and analysis ID, then any analyses with that exposure and that analysis ID will be skipped.