{ "_id": "6a17f02facfb0bcc41da6a5a", "Package": "SelfControlledCaseSeries", "Type": "Package", "Title": "Self-Controlled Case Series", "Version": "6.1.5", "Date": "2026-05-07", "Authors@R": "c(\nperson(\"Martijn\", \"Schuemie\", , \"schuemie@ohdsi.org\", role = c(\"aut\", \"cre\")),\nperson(\"Patrick\", \"Ryan\", role = c(\"aut\")),\nperson(\"Trevor\", \"Shaddox\", role = c(\"aut\")),\nperson(\"Marc\", \"Suchard\", role = c(\"aut\"))\n)", "Maintainer": "Martijn Schuemie ", "Description": "Execute the self-controlled case series (SCCS) design\nusing observational data in the OMOP Common Data Model.\nExtracts all necessary data from the database and transforms it\nto the format required for SCCS. Age and season can be modeled\nusing splines assuming constant hazard within calendar months.\nEvent-dependent censoring of the observation period can be\ncorrected for. Many exposures can be included at once (MSCCS),\nwith regularization on all coefficients except for the exposure\nof interest. Includes diagnostics for all major assumptions of\nthe SCCS.", "VignetteBuilder": "knitr", "URL": "https://ohdsi.github.io/SelfControlledCaseSeries/,\nhttps://github.com/OHDSI/SelfControlledCaseSeries", "BugReports": "https://github.com/OHDSI/SelfControlledCaseSeries/issues", "License": "Apache License 2.0", "NeedsCompilation": "yes", "RoxygenNote": "7.3.3", "Roxygen": "list(markdown = TRUE)", "Encoding": "UTF-8", "Config/pak/sysreqs": "make default-jdk libicu-dev libxml2-dev libx11-dev\nxz-utils", "Repository": "https://ohdsi.r-universe.dev", "Date/Publication": "2026-05-08 11:49:36 UTC", "RemoteUrl": "https://github.com/ohdsi/selfcontrolledcaseseries", "RemoteRef": "HEAD", "RemoteSha": "d3c3b489ebae5dc9f812da10d043822a5c22aef7", "Packaged": { "Date": "2026-05-28 07:21:17 UTC", "User": "root" }, "Author": "Martijn Schuemie [aut, cre],\nPatrick Ryan [aut],\nTrevor Shaddox [aut],\nMarc Suchard [aut]", "MD5sum": "801e6f4bf8122e871ac5c7160340de37", "_user": "ohdsi", "_type": "src", 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a SelfControlledCaseSeries analysis specification", "topics": [ "createSccsAnalysis" ] }, { "page": "createSccsDiagnosticThresholds", "title": "Create SCCS diagnostics thresholds", "topics": [ "createSccsDiagnosticThresholds" ] }, { "page": "createSccsIntervalData", "title": "Create SCCS era data", "topics": [ "createSccsIntervalData" ] }, { "page": "createSccsMultiThreadingSettings", "title": "Create SelfControlledCaseSeries multi-threading settings", "topics": [ "createSccsMultiThreadingSettings" ] }, { "page": "createSccsSimulationSettings", "title": "Create SCCS simulation settings", "topics": [ "createSccsSimulationSettings" ] }, { "page": "createScriIntervalData", "title": "Create Self-Controlled Risk Interval (SCRI) era data", "topics": [ "createScriIntervalData" ] }, { "page": "createSeasonalityCovariateSettings", "title": "Create seasonality settings", "topics": [ "createSeasonalityCovariateSettings" ] }, { "page": "createSimulationRiskWindow", "title": "Create a risk window definition for simulation", "topics": [ "createSimulationRiskWindow" ] }, { "page": "createStudyPopulation", "title": "Create a study population", "topics": [ "createStudyPopulation" ] }, { "page": "cyclicSplineDesign", "title": "Create a design matrix for a cyclic spline", "topics": [ "cyclicSplineDesign" ] }, { "page": "exportToCsv", "title": "Export SCCSresults to CSV files", "topics": [ "exportToCsv" ] }, { "page": "fitSccsModel", "title": "Fit the SCCS model", "topics": [ "fitSccsModel" ] }, { "page": "getAttritionTable", "title": "Get the attrition table for a population", "topics": [ "getAttritionTable" ] }, { "page": "getDataMigrator", "title": "Get database migrations instance", "topics": [ "getDataMigrator" ] }, { "page": "getDbSccsData", "title": "Load data for SCCS from the database", "topics": [ "getDbSccsData" ] }, { "page": "getDiagnosticsSummary", "title": "Get a summary report of the analyses diagnostics", "topics": [ "getDiagnosticsSummary" ] }, { "page": "getFileReference", "title": "Get file reference", "topics": [ "getFileReference" ] }, { "page": "getModel", "title": "Output the full model", "topics": [ "getModel" ] }, { "page": "getResultsDataModelSpecifications", "title": "Get specifications for SelfControlledCaseSeries results data model", "topics": [ "getResultsDataModelSpecifications" ] }, { "page": "getResultsSummary", "title": "Get a summary report of the analyses results", "topics": [ "getResultsSummary" ] }, { "page": "hasAgeEffect", "title": "Does the model contain an age effect?", "topics": [ "hasAgeEffect" ] }, { "page": "hasCalendarTimeEffect", "title": "Does the model contain a calendar time effect?", "topics": [ "hasCalendarTimeEffect" ] }, { "page": "hasSeasonality", "title": "Does the model contain a seasonality effect?", "topics": [ "hasSeasonality" ] }, { "page": "isSccsData", "title": "Check whether an object is a SccsData object", "topics": [ "isSccsData" ] }, { "page": "isSccsIntervalData", "title": "Check whether an object is a SccsIntervalData object", "topics": [ "isSccsIntervalData" ] }, { "page": "loadExposuresOutcomeList", "title": "Load a list of 'ExposuresOutcome' from file", "topics": [ "loadExposuresOutcomeList" ] }, { "page": "loadSccsAnalysisList", "title": "Load a list of sccsAnalysis from file", "topics": [ "loadSccsAnalysisList" ] }, { "page": "loadSccsData", "title": "Load the cohort method data from a file", "topics": [ "loadSccsData" ] }, { "page": "loadSccsIntervalData", "title": "Load the cohort method data from a file", "topics": [ "loadSccsIntervalData" ] }, { "page": "migrateDataModel", "title": "Migrate Data model", "topics": [ "migrateDataModel" ] }, { "page": "plotAgeEffect", "title": "Plot the age effect", "topics": [ "plotAgeEffect" ] }, { "page": "plotAgeSpans", "title": "Plot the age ranges spanned by each observation period.", "topics": [ "plotAgeSpans" ] }, { "page": "plotCalendarTimeEffect", "title": "Plot the calendar time effect", "topics": [ "plotCalendarTimeEffect" ] }, { "page": "plotCalendarTimeSpans", "title": "Plot the calendar time ranges spanned by each observation period.", "topics": [ "plotCalendarTimeSpans" ] }, { "page": "plotEventObservationDependence", "title": "Plot time from event to observation end for censored and uncensored time.", "topics": [ "plotEventObservationDependence" ] }, { "page": "plotEventToCalendarTime", "title": "Plot the ratio of observed to expected events over calendar time.", "topics": [ "plotEventToCalendarTime" ] }, { "page": "plotExposureCentered", "title": "Plot information centered around the start of exposure", "topics": [ "plotExposureCentered" ] }, { "page": "plotSeasonality", "title": "Plot the seasonality effect", "topics": [ "plotSeasonality" ] }, { "page": "runSccsAnalyses", "title": "Run a list of analyses", "topics": [ "runSccsAnalyses" ] }, { "page": "saveExposuresOutcomeList", "title": "Save a list of 'ExposuresOutcome' to file", "topics": [ "saveExposuresOutcomeList" ] 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Schuemie", "engine": "knitr::rmarkdown", "headings": [ "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" ], "created": "2016-04-25 13:31:56", "modified": "2025-06-10 03:50:18", "commits": 27 }, { "source": "ResultsSchema.Rmd", "filename": "ResultsSchema.html", "title": "Results schema of the SelfControlledCaseSeries package", "author": "Martijn J. Schuemie", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Exposures, covariates of interest, and controls", "Exposures-outcome-sets, analysis IDs and models", "Fields with minimum values", "Tables" ], "created": "2022-12-14 14:10:52", "modified": "2025-09-03 04:06:34", "commits": 8 }, { "source": "SingleStudies.Rmd", "filename": "SingleStudies.html", "title": "Single studies using the SelfControlledCaseSeries package", "author": "Martijn J. Schuemie, Marc A. Suchard and Patrick Ryan", "engine": "knitr::rmarkdown", "headings": [ "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" 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