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
trimByPs(): Trim persons by propensity score
stratifyByPs(): Stratify persons by propensity score
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()
createMatchOnPsArgs(): Create a parameter object for the function matchOnPs()
createStratifyByPsArgs(): Create a parameter object for the function stratifyByPs()
createTrimByPsArgs(): Create a parameter object for the function trimByPs()
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
createCmDiagnosticThresholds(): Create CohortMethod diagnostics thresholds
createCmAnalysesSpecifications(): Create full CM analysis specifications
convertUntypedListToCmAnalysesSpecifications(): Convert untyped list to SccsAnalysesSpecifications
createMultiThreadingSettings(): Create CohortMethod multi-threading settings
createDefaultMultiThreadingSettings(): Create default CohortMethod multi-threading settings
runCmAnalyses(): Run a list of analyses
getFileReference(): Get file reference
getResultsSummary(): Get a summary report of the analyses results
getInteractionResultsSummary(): Get a summary report of the analyses results
getDiagnosticsSummary(): Get a summary report of the analyses diagnostics
exportToCsv(): Export cohort method results to CSV files

Results upload

Uploading results to a database.

getResultsDataModelSpecifications(): Get specifications for CohortMethod results data model
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.

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