createTrajectories: Generate trajectories using the logic specified in the...

In HealthInformaticsUT/Cohort2Trajectory: Package for creating patient orientated treatment trajectories from cohorts defined in OHDSI ATLAS

Generate trajectories using the logic specified in the configuration

Description

Generate trajectories using the logic specified in the configuration

Usage

createTrajectories(
  cdm = NULL,
  studyEnv = NULL,
  trajectoryType = studyEnv$trajectoryType,
  runSavedStudy = studyEnv$runSavedStudy,
  oocFix = studyEnv$oocFix,
  outOfCohortAllowed = studyEnv$outOfCohortAllowed,
  lengthOfStay = studyEnv$lengthOfStay,
  stateCohortLabels = studyEnv$stateCohortLabels,
  stateCohortPriorityOrder = studyEnv$stateCohortPriorityOrder,
  stateSelectionType = studyEnv$stateSelectionType,
  stateCohortAbsorbing = studyEnv$stateCohortAbsorbing,
  stateCohortMandatory = studyEnv$stateCohortMandatory,
  allowedStatesList = studyEnv$allowedStatesList,
  useCDM = studyEnv$useCDM,
  pathToStudy = studyEnv$pathToStudy,
  batchSize = studyEnv$batchSize,
  updateAutomaticallyForMergedStates = FALSE
)

Arguments

cdm	object created with CDMConnector
studyEnv	environment created with cohort2TrajectoryConfiguration
trajectoryType	The type of the trajectory ("Discrete" - Discrete time, "Continuous" - Continuous time)
runSavedStudy	running a predefined study from studyName/Settings/trajectorySettings.csv
oocFix	the method to use for replacing "OUT OF COHORT" states with more relevant states ("None" -> "OUT OF COHORT"; "Last present state" -> repeat the last one; random str -> used as state)
outOfCohortAllowed	boolean whether the patient trajectory can surpass the target cohort's observation-period
lengthOfStay	The length of stay (days) in one state (Effect only in discrete case)
stateCohortLabels	vector of the customized labels of the state cohorts
stateCohortPriorityOrder	vector of the customized labels of the state cohorts in priority order
stateSelectionType	the type of state selection ("First" - First occurring, "Overlap" - Max overlap, "Priority" - Priority)
stateCohortAbsorbing	vector of the customized labels of the state cohorts which are absorbing
stateCohortMandatory	vector of the customized labels of the state cohorts which are mandatory in trajectory
allowedStatesList	A list object which indicates accessible states from said state
useCDM	The package can also be run without the OMOP CDM
pathToStudy	path to directory that contains study folder
batchSize	customizable batch size for trajectory generation process

Value

dataframe with trajectories

Examples

## Not run: createTrajectories(cdm = cdm, runSavedStudy = F,studyEnv = studyEnv)

HealthInformaticsUT/Cohort2Trajectory documentation built on March 1, 2025, 7:47 p.m.