Reference

Aggregate Covariate Analysis This analysis calculates the aggregate characteristics for a Target cohort (T), an Outcome cohort (O) and combiations of T with O during time at risk and T without O during time at risk.
createAggregateCovariateSettings()	Create aggregate covariate study settings
Dechallenge Rechallenge Analysis For a given Target cohort (T) and Outcome cohort (O) find any occurrances of a dechallenge (when the T cohort stops close to when O started) and a rechallenge (when T restarts and O starts again) This is useful for investigating causality between drugs and events.
computeDechallengeRechallengeAnalyses()	Compute dechallenge rechallenge study
computeRechallengeFailCaseSeriesAnalyses()	Compute fine the subjects that fail the dechallenge rechallenge study
createDechallengeRechallengeSettings()	Create dechallenge rechallenge study settings
Time to Event Analysis This analysis calculates the timing between the Target cohort (T) and an Outcome cohort (O).
computeTimeToEventAnalyses()	Compute time to event study
createTimeToEventSettings()	Create time to event study settings
Run Large Scale Characterization Study Run multipe aggregate covariate analysis, time to event and dechallenge/rechallenge studies.
createCharacterizationSettings()	Create the settings for a large scale characterization study
loadCharacterizationSettings()	Load the characterization settings previously saved as a json file
runCharacterizationAnalyses()	execute a large-scale characterization study
saveCharacterizationSettings()	Save the characterization settings as a json
Save Load Functions to save the analysis settings and the results (as sqlite or csv files).
exportDechallengeRechallengeToCsv()	export the DechallengeRechallenge results as csv
exportRechallengeFailCaseSeriesToCsv()	export the RechallengeFailCaseSeries results as csv
exportTimeToEventToCsv()	export the TimeToEvent results as csv
Insert into Database Functions to insert the results into a database.
createCharacterizationTables()	Create the results tables to store characterization results into a database
createSqliteDatabase()	Create an sqlite database connection
insertResultsToDatabase()	Upload the results into a result database
Shiny App Functions to interactively exlore the results from runCharacterizationAnalyses().
viewCharacterization()	viewCharacterization - Interactively view the characterization results
Custom covariates Code to create covariates during cohort start and end
createDuringCovariateSettings()	Create during covariate settings
getDbDuringCovariateData()	Extracts covariates that occur during a cohort
Incremental Code to run incremetal model
cleanIncremental()	Removes csv files from folders that have not been marked as completed and removes the record of the execution file
cleanNonIncremental()	Removes csv files from the execution folder as there should be no csv files when running in non-incremental model