# Comparative Cohort Method with Large Scale Propensity and Outcome Models

## Documentation for package ‘CohortMethod’ version 6.0.1

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

adjustedKm | Compute a weight-adjusted Kaplan-Meier curve
checkCmInstallation | Check is CohortMethod and its dependencies are correctly installed
CohortMethodData | Cohort Method Data
CohortMethodData-class | Cohort Method Data
cohortMethodDataSimulationProfile | A simulation profile
computeCovariateBalance | Compute covariate balance before and after PS adjustment
computeEquipoise | Compute fraction in equipoise
computeMdrr | Compute the minimum detectable relative risk
computePsAuc | Compute the area under the ROC curve
convertUntypedListToCmAnalysesSpecifications | Convert untyped list to SccsAnalysesSpecifications
createCmAnalysesSpecifications | Create full CM analysis specifications
createCmAnalysis | Create a CohortMethod analysis specification
createCmDiagnosticThresholds | Create CohortMethod diagnostics thresholds
createCmTable1 | Create a table 1
createCohortMethodDataSimulationProfile | Create simulation profile
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()'
createDefaultMultiThreadingSettings | Create default CohortMethod multi-threading settings
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()'
createMultiThreadingSettings | Create CohortMethod multi-threading settings
createOutcome | Create outcome definition
createPs | Create propensity scores
createResultsDataModel | Create the results data model tables on a database server.
createStratifyByPsArgs | Create a parameter object for the function 'stratifyByPs()'
createStudyPopulation | Create a study population
createTargetComparatorOutcomes | Create target-comparator-outcomes combinations.
createTrimByPsArgs | Create a parameter object for the function 'trimByPs()'
createTruncateIptwArgs | Create a parameter object for the function 'truncateIptw()'
drawAttritionDiagram | Draw the attrition diagram
exportToCsv | Export cohort method results to CSV files
fitOutcomeModel | Create an outcome model, and compute the relative risk
getAttritionTable | Get the attrition table for a population
getDataMigrator | Get database migrations instance
getDbCohortMethodData | Get the cohort data from the server
getDefaultCmTable1Specifications | Get the default table 1 specifications
getDiagnosticsSummary | Get a summary report of the analyses diagnostics
getFileReference | Get file reference
getFollowUpDistribution | Get the distribution of follow-up time
getGeneralizabilityTable | Get information on generalizability
getInteractionResultsSummary | Get a summary report of the analyses results
getOutcomeModel | Get the outcome model
getPsModel | Get the propensity model
getResultsDataModelSpecifications | Get specifications for CohortMethod results data model
getResultsSummary | Get a summary report of the analyses results
isCohortMethodData | Check whether an object is a CohortMethodData object
loadCmAnalysisList | Load a list of CmAnalysis from file
loadCohortMethodData | Load the cohort method data from a file
loadTargetComparatorOutcomesList | Load a list of 'TargetComparatorOutcomes' from file
matchOnPs | Match persons by propensity score
migrateDataModel | Migrate Data model
plotCovariateBalanceOfTopVariables | Plot variables with largest imbalance
plotCovariateBalanceScatterPlot | Create a scatterplot of the covariate balance
plotCovariatePrevalence | Plot covariate prevalence
plotFollowUpDistribution | Plot the distribution of follow-up time
plotKaplanMeier | Plot the Kaplan-Meier curve
plotPs | Plot the propensity score distribution
plotTimeToEvent | Plot time-to-event
runCmAnalyses | Run a list of analyses
saveCmAnalysisList | Save a list of CmAnalysis to file
saveCohortMethodData | Save the cohort method data to file
saveTargetComparatorOutcomesList | Save a list of 'TargetComparatorOutcomes' to file
show-method | Cohort Method Data
simulateCohortMethodData | Generate simulated data
stratifyByPs | Stratify persons by propensity score
summary-method | Cohort Method Data
trimByPs | Trim persons by propensity score
truncateIptw | Truncate IPTW values
uploadResults | Upload results to the database server.