Package index • CohortMethod

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.
`getDbCohortMethodData()`	Get the cohort data from the server
`show(<CohortMethodData>)` `summary(<CohortMethodData>)`	Cohort Method Data
`isCohortMethodData()`	Check whether an object is a CohortMethodData object
`saveCohortMethodData()`	Save the cohort method data to file
`loadCohortMethodData()`	Load the cohort method data from a file
`createStudyPopulation()`	Create a study population
Propensity scores Functions for creating and using propensity scores.
`createPs()`	Create propensity scores
`getPsModel()`	Get the propensity model
`matchOnPs()`	Match persons by propensity score
`matchOnPsAndCovariates()`	Match by propensity score as well as other covariates
`trimByPs()`	Trim persons by propensity score
`trimByPsToEquipoise()`	Keep only persons in clinical equipoise
`trimByIptw()`	Remove subjects with a high IPTW
`stratifyByPs()`	Stratify persons by propensity score
`stratifyByPsAndCovariates()`	Stratify persons by propensity score and other covariates
`truncateIptw()`	Truncate IPTW values
Outcome models Functions for creating and viewing outcome models.
`fitOutcomeModel()`	Create an outcome model, and compute the relative risk
`getOutcomeModel()`	Get the outcome model
`adjustedKm()`	Compute a weight-adjusted Kaplan-Meier curve
`plotKaplanMeier()`	Plot the Kaplan-Meier curve
Diagnostics Functions for producing various study diagnostics.
`computeMdrr()`	Compute the minimum detectable relative risk
`getAttritionTable()`	Get the attrition table for a population
`drawAttritionDiagram()`	Draw the attrition diagram
`plotFollowUpDistribution()`	Plot the distribution of follow-up time
`createCmTable1()`	Create a table 1
`getDefaultCmTable1Specifications()`	Get the default table 1 specifications
`getFollowUpDistribution()`	Get the distribution of follow-up time
`plotPs()`	Plot the propensity score distribution
`computeEquipoise()`	Compute fraction in equipoise
`computePsAuc()`	Compute the area under the ROC curve
`computeCovariateBalance()`	Compute covariate balance before and after PS adjustment
`plotCovariateBalanceOfTopVariables()`	Plot variables with largest imbalance
`plotCovariateBalanceScatterPlot()`	Create a scatterplot of the covariate balance
`plotCovariatePrevalence()`	Plot covariate prevalence
`plotTimeToEvent()`	Plot time-to-event
`getGeneralizabilityTable()`	Get information on generalizability
Running multiple analyses Functions for running multiple analyses in an efficient way.
`createComputeCovariateBalanceArgs()`	Create a parameter object for the function computeCovariateBalance
`createCreatePsArgs()`	Create a parameter object for the function createPs
`createCreateStudyPopulationArgs()`	Create a parameter object for the function createStudyPopulation
`createFitOutcomeModelArgs()`	Create a parameter object for the function fitOutcomeModel
`createGetDbCohortMethodDataArgs()`	Create a parameter object for the function getDbCohortMethodData
`createMatchOnPsAndCovariatesArgs()`	Create a parameter object for the function matchOnPsAndCovariates
`createMatchOnPsArgs()`	Create a parameter object for the function matchOnPs
`createStratifyByPsAndCovariatesArgs()`	Create a parameter object for the function stratifyByPsAndCovariates
`createStratifyByPsArgs()`	Create a parameter object for the function stratifyByPs
`createTrimByIptwArgs()`	Create a parameter object for the function trimByIptw
`createTrimByPsArgs()`	Create a parameter object for the function trimByPs
`createTrimByPsToEquipoiseArgs()`	Create a parameter object for the function trimByPsToEquipoise
`createTruncateIptwArgs()`	Create a parameter object for the function truncateIptw
`createCmAnalysis()`	Create a CohortMethod analysis specification
`saveCmAnalysisList()`	Save a list of cmAnalysis to file
`loadCmAnalysisList()`	Load a list of cmAnalysis from file
`createOutcome()`	Create outcome definition
`createTargetComparatorOutcomes()`	Create target-comparator-outcomes combinations.
`saveTargetComparatorOutcomesList()`	Save a list of targetComparatorOutcomes to file
`loadTargetComparatorOutcomesList()`	Load a list of targetComparatorOutcomes from file
`createMultiThreadingSettings()`	Create CohortMethod multi-threading settings
`createDefaultMultiThreadingSettings()`	Create default CohortMethod multi-threading settings
`runCmAnalyses()`	Run a list of analyses
Results of multiple analyses Functions for viewing results of multiple analyses.
`getFileReference()`	Get file reference
`getResultsSummary()`	Get a summary report of the analyses results
`getInteractionResultsSummary()`	Get a summary report of the analyses results
`createCmDiagnosticThresholds()`	Create CohortMethod diagnostics thresholds
`exportToCsv()`	Export cohort method results to CSV files
`getResultsDataModelSpecifications()`	Get specifications for CohortMethod results data model
`insertExportedResultsInSqlite()`	Insert exported results into a SQLite database
`launchResultsViewerUsingSqlite()`	Launch Shiny app using a SQLite database
`createResultsDataModel()`	Create the results data model tables on a database server.
`migrateDataModel()`	Migrate Data model
`getDataMigrator()`	Get database migrations instance
`uploadResults()`	Upload results to the database server.
`launchResultsViewer()`	Launch Shiny app using
Simulation Functions for simulating cohort method data objects.
`createCohortMethodDataSimulationProfile()`	Create simulation profile
`simulateCohortMethodData()`	Generate simulated data
`cohortMethodDataSimulationProfile`	A simulation profile
Helper functions Various helper functions
`checkCmInstallation()`	Check is CohortMethod and its dependencies are correctly installed

Reference

Getting data and creating a study population

Propensity scores

Outcome models

Diagnostics

Running multiple analyses

Results of multiple analyses

Simulation

Helper functions