Package: SelfControlledCaseSeries 6.1.5

Martijn Schuemie

SelfControlledCaseSeries: Self-Controlled Case Series

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.

Authors:Martijn Schuemie [aut, cre], Patrick Ryan [aut], Trevor Shaddox [aut], Marc Suchard [aut]

SelfControlledCaseSeries_6.1.5.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
SelfControlledCaseSeries/json (API)

# Install 'SelfControlledCaseSeries' in R:
install.packages('SelfControlledCaseSeries', repos = c('https://ohdsi.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ohdsi/selfcontrolledcaseseries/issues

Pkgdown/docs site:https://ohdsi.github.io

Uses libs:
  • c++– GNU Standard C++ Library v3
  • openjdk– OpenJDK Java runtime, using Hotspot JIT

On CRAN:

Conda:

hadescppopenjdk

8.14 score 13 stars 73 scripts 672 downloads 71 exports 73 dependencies

Last updated from:d3c3b489eb. Checks:11 WARNING, 2 OK. Indexed: yes.

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Exports:checkEventExposureIndependenceAssumptioncheckEventObservationIndependenceAssumptioncheckRareOutcomeAssumptioncheckTimeStabilityAssumptioncomputeMdrrcomputePreExposureGainPcomputeTimeStabilityconvertJsonToSccsAnalysesSpecificationsconvertSccsAnalysesSpecificationsToJsonconvertUntypedListToSccsAnalysesSpecificationscreateAgeCovariateSettingscreateCalendarTimeCovariateSettingscreateControlIntervalSettingscreateCreateSccsIntervalDataArgscreateCreateScriIntervalDataArgscreateCreateStudyPopulationArgscreateDefaultSccsMultiThreadingSettingscreateEraCovariateSettingscreateExposurecreateExposuresOutcomecreateFitSccsModelArgscreateGetDbSccsDataArgscreateResultsDataModelcreateSccsAnalysesSpecificationscreateSccsAnalysiscreateSccsDiagnosticThresholdscreateSccsIntervalDatacreateSccsMultiThreadingSettingscreateSccsSimulationSettingscreateScriIntervalDatacreateSeasonalityCovariateSettingscreateSimulationRiskWindowcreateStudyPopulationcyclicSplineDesignexportToCsvfitSccsModelgetAttritionTablegetDataMigratorgetDbSccsDatagetDiagnosticsSummarygetFileReferencegetModelgetResultsDataModelSpecificationsgetResultsSummaryhasAgeEffecthasCalendarTimeEffecthasSeasonalityisSccsDataisSccsIntervalDataloadExposuresOutcomeListloadSccsAnalysisListloadSccsDataloadSccsIntervalDatamigrateDataModelplotAgeEffectplotAgeSpansplotCalendarTimeEffectplotCalendarTimeSpansplotEventObservationDependenceplotEventToCalendarTimeplotExposureCenteredplotSeasonalityrunSccsAnalysessaveExposuresOutcomeListsaveSccsAnalysisListsaveSccsDatasaveSccsIntervalDatashowsimulateSccsDatasummaryuploadResults

Dependencies:Andromedabackportsbitbit64blobcheckmateclicliprcpp11crayonCyclopsDatabaseConnectorDBIdbplyrdigestdplyrduckdbEmpiricalCalibrationfarverfastmapgenericsggplot2gluegridExtragtablehmsisobandjsonlitelabelinglaterlatticelifecyclelubridatemagrittrMatrixmemuseParallelLoggerpillarpkgconfigpoolprettyunitsprogresspurrrR6RColorBrewerRcppRcppEigenreadrResultModelManagerrJavarlangrstudioapiS7scalessnowSqlRenderstringistringrsurvivaltibbletidyrtidyselecttimechangetriebeardtzdburltoolsutf8vctrsviridisLitevroomwithrxml2zip

Results schema of the SelfControlledCaseSeries package
Introduction | Exposures, covariates of interest, and controls | Exposures-outcome-sets, analysis IDs and models | Fields with minimum values | Tables
Rendered fromResultsSchema.Rmdusingknitr::rmarkdown

Last update: 2025-09-03
Started: 2022-12-14

Running multiple analyses at once using the SelfControlledCaseSeries package
Introduction | General approach | Preparation for the example | Specifying exposures-outcome sets | Specifying analyses | Executing multiple analyses | Restarting | Retrieving the results | Diagnostics summary | Negative control distribution | Acknowledgments
Rendered fromMultipleAnalyses.Rmdusingknitr::rmarkdown

Last update: 2025-06-10
Started: 2016-04-25

Single studies using the SelfControlledCaseSeries package
Introduction | Terminology | Installation instructions | Overview | Studies with a single drug | Configuring the connection to the server | Preparing the exposure and outcome of interest | Extracting the data from the server | Saving the data to file | Creating the study population | Defining a simple model | Model fitting | Adding a pre-exposure window | Including seasonality, and calendar time | Removing the COVID blip | Considering event-dependent observation time | Studies with more than one drug | Adding a class of drugs | Adding all drugs | Diagnostics for the main SCCS assumptions | Rare outcome assumption diagnostic | Event-exposure independence assumption diagnostic | Event-observation independence assumption diagnostic | Modeling assumptions diagnostic | Additional diagnostics | Power calculations | Time from exposure start to event | Ages covered per subject | Acknowledgments
Rendered fromSingleStudies.Rmdusingknitr::rmarkdown

Last update: 2025-06-10
Started: 2015-11-18

Readme and manuals

Help Manual

Help pageTopics
Check diagnostic for event-dependent exposurecheckEventExposureIndependenceAssumption
Check diagnostic for event-dependent observation endcheckEventObservationIndependenceAssumption
Check if rare outcome assumption is violatedcheckRareOutcomeAssumption
Check stability of outcome rate over timecheckTimeStabilityAssumption
Compute the minimum detectable relative riskcomputeMdrr
Compute P for pre-exposure risk gaincomputePreExposureGainP
Check stability of outcome rate over timecomputeTimeStability
Convert JSON to SccsAnalysesSpecificationsconvertJsonToSccsAnalysesSpecifications
Convert SccsAnalysesSpecifications to JSONconvertSccsAnalysesSpecificationsToJson
Convert untyped list to SccsAnalysesSpecificationsconvertUntypedListToSccsAnalysesSpecifications
Create age covariate settingscreateAgeCovariateSettings
Create calendar time settingscreateCalendarTimeCovariateSettings
Create control interval settingscreateControlIntervalSettings
Create a parameter object for the 'createSccsIntervalData()' functioncreateCreateSccsIntervalDataArgs
Create a parameter object for the 'createScriIntervalData()' functioncreateCreateScriIntervalDataArgs
Create a parameter object for the 'createStudyPopulation()' functioncreateCreateStudyPopulationArgs
Create default SelfControlledCaseSeries multi-threading settingscreateDefaultSccsMultiThreadingSettings
Create era covariate settingscreateEraCovariateSettings
Create exposure definitioncreateExposure
Create a exposures-outcome combination.createExposuresOutcome
Create a parameter object for the function fitSccsModelcreateFitSccsModelArgs
Create a parameter object for the function getDbSccsDatacreateGetDbSccsDataArgs
Create the results data model tables on a database server.createResultsDataModel
Create full SCCS analysis specificationscreateSccsAnalysesSpecifications
Create a SelfControlledCaseSeries analysis specificationcreateSccsAnalysis
Create SCCS diagnostics thresholdscreateSccsDiagnosticThresholds
Create SCCS era datacreateSccsIntervalData
Create SelfControlledCaseSeries multi-threading settingscreateSccsMultiThreadingSettings
Create SCCS simulation settingscreateSccsSimulationSettings
Create Self-Controlled Risk Interval (SCRI) era datacreateScriIntervalData
Create seasonality settingscreateSeasonalityCovariateSettings
Create a risk window definition for simulationcreateSimulationRiskWindow
Create a study populationcreateStudyPopulation
Create a design matrix for a cyclic splinecyclicSplineDesign
Export SCCSresults to CSV filesexportToCsv
Fit the SCCS modelfitSccsModel
Get the attrition table for a populationgetAttritionTable
Get database migrations instancegetDataMigrator
Load data for SCCS from the databasegetDbSccsData
Get a summary report of the analyses diagnosticsgetDiagnosticsSummary
Get file referencegetFileReference
Output the full modelgetModel
Get specifications for SelfControlledCaseSeries results data modelgetResultsDataModelSpecifications
Get a summary report of the analyses resultsgetResultsSummary
Does the model contain an age effect?hasAgeEffect
Does the model contain a calendar time effect?hasCalendarTimeEffect
Does the model contain a seasonality effect?hasSeasonality
Check whether an object is a SccsData objectisSccsData
Check whether an object is a SccsIntervalData objectisSccsIntervalData
Load a list of 'ExposuresOutcome' from fileloadExposuresOutcomeList
Load a list of sccsAnalysis from fileloadSccsAnalysisList
Load the cohort method data from a fileloadSccsData
Load the cohort method data from a fileloadSccsIntervalData
Migrate Data modelmigrateDataModel
Plot the age effectplotAgeEffect
Plot the age ranges spanned by each observation period.plotAgeSpans
Plot the calendar time effectplotCalendarTimeEffect
Plot the calendar time ranges spanned by each observation period.plotCalendarTimeSpans
Plot time from event to observation end for censored and uncensored time.plotEventObservationDependence
Plot the ratio of observed to expected events over calendar time.plotEventToCalendarTime
Plot information centered around the start of exposureplotExposureCentered
Plot the seasonality effectplotSeasonality
Run a list of analysesrunSccsAnalyses
Save a list of 'ExposuresOutcome' to filesaveExposuresOutcomeList
Save a list of SccsAnalysis to filesaveSccsAnalysisList
Save the cohort method data to filesaveSccsData
Save the cohort method data to filesaveSccsIntervalData
SCCS DataSccsData SccsData-class show,SccsData-method summary,SccsData-method
SCCS Interval DataSccsIntervalData SccsIntervalData-class show,SccsIntervalData-method summary,SccsIntervalData-method
Simulate SCCS datasimulateSccsData
Upload results to the database server.uploadResults