cohort2TrajectoryConfiguration: C2T configuration for initiating the parameter values in the...

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

C2T configuration for initiating the parameter values in the study environment

Description

C2T configuration for initiating the parameter values in the study environment

Usage

cohort2TrajectoryConfiguration(
  cdm = NULL,
  studyName = "Cohort2Trajectory",
  baseUrl = "http://localhost:8080/WebAPI",
  pathToStudy = getwd(),
  atlasTargetCohort = NULL,
  atlasStateCohorts = NULL,
  stateCohortLabels = NULL,
  stateCohortPriorityOrder = NULL,
  stateCohortMandatory = NULL,
  stateCohortAbsorbing = NULL,
  stateSelectionType = NULL,
  oocFix = "None",
  trajectoryType = "Discrete",
  lengthOfStay = NULL,
  outOfCohortAllowed = FALSE,
  runSavedStudy = FALSE,
  useCDM = TRUE,
  trajectoryDataObject = NULL,
  pathToData = "./Cohort2Trajectory/Data/importedData.csv",
  allowedStatesList = createStateList(stateCohortLabels),
  mergeStates = FALSE,
  mergeThreshold = 0.5,
  batchSize = 1000
)

Arguments

cdm	object created with CDMConnector
studyName	name chosen for study, is used as a folder name
baseUrl	the base URL for the WebApi instance
pathToStudy	path to folder which contains folder named after studyName
atlasTargetCohort	the id of the target cohort defined in OHDSI tool ATLAS
atlasStateCohorts	the ids of the state cohorts defined in OHDSI tool ATLAS
stateCohortLabels	vector of the customized labels of the state cohorts
stateCohortPriorityOrder	vector of the customized labels of the state cohorts in priority order
stateCohortMandatory	vector of the customized labels of the state cohorts which are mandatory in trajectory
stateCohortAbsorbing	vector of the customized labels of the state cohorts which are absorbing
stateSelectionType	the type of state selection ("First" - First occurring, "Overlap" - Max overlap, "Priority" - Priority)
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)
trajectoryType	The type of the trajectory ("Discrete" - Discrete time, "Continuous" - Continuous time)
lengthOfStay	The length of stay (days) in one state (Effect only in discrete case)
outOfCohortAllowed	boolean whether the patient trajectory can surpass the target cohort's observation-period
runSavedStudy	running a predefined study from studyName/Settings/trajectorySettings.csv
useCDM	The package can also be run without the OMOP CDM
trajectoryDataObject	When using without OMOP CDM specify the data file (if specified no need for pathToData)
pathToData	When using without OMOP CDM specify the path to data file (if specified no need for trajectoryDataObject)
allowedStatesList	A list object which indicates accessible states from said state
mergeStates	Boolean, if you want to merge states when they overlap
mergeThreshold	Value from 0 to 1. If mergeStates is TRUE the states will be label-merged given they overlap more than the specified threshold. Can be given as vector, then multiple iterations are runned,
batchSize	customizable batch size for cohort generation

Examples

## Not run: cohort2TrajectoryConfiguration(cdm = cdm,
studyName = "TestCohort2Trajectory",
baseUrl = NULL,
pathToStudy = getwd(),
atlasTargetCohort = 0,
atlasStateCohorts = c(1, 2),
stateCohortLabels = c("test_label1", "test_label2"),
)
## End(Not run)

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