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 an age effect?

hasCalendarTimeEffect()

Does the model contain an age effect?

Diagnostics

Functions for producing various study diagnostics.

computeMdrr()

Compute the minimum detectable relative risk

computePreExposureGainP()

Compute P for pre-exposure risk gain

computeTimeStability()

Compute 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 function createSccsIntervalData

createCreateScriIntervalDataArgs()

Create a parameter object for the function createScriIntervalData

createCreateStudyPopulationArgs()

Create a parameter object for the function createStudyPopulation

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.

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

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

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