Package index • SelfControlledCaseSeries

Getting data and creating a study population

Functions for getting the necessary data from the database in Common Data Model, and creating a study population.

show(<SccsData>) summary(<SccsData>): SCCS Data

getDbSccsData(): Load data for SCCS from the database

saveSccsData(): Save the cohort method data to file

loadSccsData(): Load the cohort method data from a file

isSccsData(): Check whether an object is a SccsData object

createStudyPopulation(): Create a study population

Interval data

Functions for creating interval data.

show(<SccsIntervalData>) summary(<SccsIntervalData>): SCCS Interval Data

createEraCovariateSettings(): Create era covariate settings

createAgeCovariateSettings(): Create age covariate settings

createSeasonalityCovariateSettings(): Create seasonality settings

createCalendarTimeCovariateSettings(): Create calendar time settings

createControlIntervalSettings(): Create control interval settings

createSccsIntervalData(): Create SCCS era data

createScriIntervalData(): Create Self-Controlled Risk Interval (SCRI) era data

saveSccsIntervalData(): Save the cohort method data to file

loadSccsIntervalData(): Load the cohort method data from a file

isSccsIntervalData(): Check whether an object is a SccsIntervalData object

Model fitting

Functions for creating and viewing models.

fitSccsModel(): Fit the SCCS model

getModel(): Output the full model

plotAgeEffect(): Plot the age effect

plotSeasonality(): Plot the seasonality effect

plotCalendarTimeEffect(): Plot the calendar time effect

hasAgeEffect(): Does the model contain an age effect?

hasSeasonality(): Does the model contain a seasonality effect?

hasCalendarTimeEffect(): Does the model contain a calendar time effect?

Diagnostics

Functions for producing various study diagnostics.

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

getAttritionTable(): Get the attrition table for a population

plotAgeSpans(): Plot the age ranges spanned by each observation period.

plotCalendarTimeSpans(): Plot the calendar time ranges spanned by each observation period.

plotEventObservationDependence(): Plot time from event to observation end for censored and uncensored time.

plotEventToCalendarTime(): Plot the ratio of observed to expected events over calendar time.

plotExposureCentered(): Plot information centered around the start of exposure

Running multiple analyses

Functions for running multiple analyses in an efficient way.

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

createFitSccsModelArgs(): Create a parameter object for the function fitSccsModel

createGetDbSccsDataArgs(): Create a parameter object for the function getDbSccsData

createExposure(): Create exposure definition

createExposuresOutcome(): Create a exposures-outcome combination.

createSccsAnalysesSpecifications(): Create full SCCS analysis specifications

saveExposuresOutcomeList(): Save a list of ExposuresOutcome to file

loadExposuresOutcomeList(): Load a list of ExposuresOutcome from file

createSccsAnalysis(): Create a SelfControlledCaseSeries analysis specification

saveSccsAnalysisList(): Save a list of SccsAnalysis to file

loadSccsAnalysisList(): Load a list of sccsAnalysis from file

convertJsonToSccsAnalysesSpecifications(): Convert JSON to SccsAnalysesSpecifications

convertSccsAnalysesSpecificationsToJson(): Convert SccsAnalysesSpecifications to JSON

convertUntypedListToSccsAnalysesSpecifications(): Convert untyped list to SccsAnalysesSpecifications

createSccsMultiThreadingSettings(): Create SelfControlledCaseSeries multi-threading settings

createDefaultSccsMultiThreadingSettings(): Create default SelfControlledCaseSeries multi-threading settings

runSccsAnalyses(): Run a list of analyses

getFileReference(): Get file reference

getResultsSummary(): Get a summary report of the analyses results

getDiagnosticsSummary(): Get a summary report of the analyses diagnostics

createSccsDiagnosticThresholds(): Create SCCS diagnostics thresholds

exportToCsv(): Export SCCSresults to CSV files

Result upload

Uploading results to a database.

createResultsDataModel(): Create the results data model tables on a database server.

getDataMigrator(): Get database migrations instance

getResultsDataModelSpecifications(): Get specifications for SelfControlledCaseSeries results data model

migrateDataModel(): Migrate Data model

uploadResults(): Upload results to the database server.

Simulation

Functions for simulating cohort method data objects.

createSimulationRiskWindow(): Create a risk window definition for simulation

createSccsSimulationSettings(): Create SCCS simulation settings

simulateSccsData(): Simulate SCCS data

Helper functions

Various helper functions

cyclicSplineDesign(): Create a design matrix for a cyclic spline