SelfControlledCaseSeries6.1.0 package

Self-Controlled Case Series

checkEventExposureIndependenceAssumption

Check diagnostic for event-dependent exposure

checkEventObservationIndependenceAssumption

Check diagnostic for event-dependent observation end

checkRareOutcomeAssumption

Check if rare outcome assumption is violated

checkTimeStabilityAssumption

Check stability of outcome rate over time

computeMdrr

Compute the minimum detectable relative risk

computePreExposureGainP

Compute P for pre-exposure risk gain

computeTimeStability

Check stability of outcome rate over time

convertJsonToSccsAnalysesSpecifications

Convert JSON to SccsAnalysesSpecifications

convertSccsAnalysesSpecificationsToJson

Convert SccsAnalysesSpecifications to JSON

convertUntypedListToSccsAnalysesSpecifications

Convert untyped list to SccsAnalysesSpecifications

createAgeCovariateSettings

Create age covariate settings

createCalendarTimeCovariateSettings

Create calendar time settings

createControlIntervalSettings

Create control interval settings

createCreateSccsIntervalDataArgs

Create a parameter object for the createSccsIntervalData() function

createCreateScriIntervalDataArgs

Create a parameter object for the createScriIntervalData() function

createCreateStudyPopulationArgs

Create a parameter object for the createStudyPopulation() function

createDefaultSccsMultiThreadingSettings

Create default SelfControlledCaseSeries multi-threading settings

createEraCovariateSettings

Create era covariate settings

createExposure

Create exposure definition

createExposuresOutcome

Create a exposures-outcome combination.

createFitSccsModelArgs

Create a parameter object for the function fitSccsModel

createGetDbSccsDataArgs

Create a parameter object for the function getDbSccsData

createResultsDataModel

Create the results data model tables on a database server.

createSccsAnalysesSpecifications

Create full SCCS analysis specifications

createSccsAnalysis

Create a SelfControlledCaseSeries analysis specification

createSccsDiagnosticThresholds

Create SCCS diagnostics thresholds

createSccsIntervalData

Create SCCS era data

createSccsMultiThreadingSettings

Create SelfControlledCaseSeries multi-threading settings

createSccsSimulationSettings

Create SCCS simulation settings

createScriIntervalData

Create Self-Controlled Risk Interval (SCRI) era data

createSeasonalityCovariateSettings

Create seasonality settings

createSimulationRiskWindow

Create a risk window definition for simulation

createStudyPopulation

Create a study population

cyclicSplineDesign

Create a design matrix for a cyclic spline

exportToCsv

Export SCCSresults to CSV files

fitSccsModel

Fit the SCCS model

getAttritionTable

Get the attrition table for a population

getDataMigrator

Get database migrations instance

getDbSccsData

Load data for SCCS from the database

getDiagnosticsSummary

Get a summary report of the analyses diagnostics

getFileReference

Get file reference

getModel

Output the full model

getResultsDataModelSpecifications

Get specifications for SelfControlledCaseSeries results data model

getResultsSummary

Get a summary report of the analyses results

hasAgeEffect

Does the model contain an age effect?

hasCalendarTimeEffect

Does the model contain a calendar time effect?

hasSeasonality

Does the model contain a seasonality effect?

isSccsData

Check whether an object is a SccsData object

isSccsIntervalData

Check whether an object is a SccsIntervalData object

loadExposuresOutcomeList

Load a list of ExposuresOutcome from file

loadSccsAnalysisList

Load a list of sccsAnalysis from file

loadSccsData

Load the cohort method data from a file

loadSccsIntervalData

Load the cohort method data from a file

migrateDataModel

Migrate Data model

plotAgeEffect

Plot the age effect

plotAgeSpans

Plot the age ranges spanned by each observation period.

plotCalendarTimeEffect

Plot the calendar time effect

plotCalendarTimeSpans

Plot the calendar time ranges spanned by each observation period.

plotEventObservationDependence

Plot time from event to observation end for censored and uncensored ti...

plotEventToCalendarTime

Plot the ratio of observed to expected events over calendar time.

plotExposureCentered

Plot information centered around the start of exposure

plotSeasonality

Plot the seasonality effect

runSccsAnalyses

Run a list of analyses

saveExposuresOutcomeList

Save a list of ExposuresOutcome to file

saveSccsAnalysisList

Save a list of SccsAnalysis to file

saveSccsData

Save the cohort method data to file

saveSccsIntervalData

Save the cohort method data to file

SccsData-class

SCCS Data

SccsIntervalData-class

SCCS Interval Data

SelfControlledCaseSeries-package

SelfControlledCaseSeries: Self-Controlled Case Series

simulateSccsData

Simulate SCCS data

uploadResults

Upload results to the database server.

Execute the self-controlled case series (SCCS) design using observational data in the OMOP Common Data Model. Extracts all necessary data from the database and transforms it to the format required for SCCS. Age and season can be modeled using splines assuming constant hazard within calendar months. Event-dependent censoring of the observation period can be corrected for. Many exposures can be included at once (MSCCS), with regularization on all coefficients except for the exposure of interest. Includes diagnostics for all major assumptions of the SCCS.

  • Maintainer: Martijn Schuemie
  • License: Apache License 2.0
  • Last published: 2025-09-03