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

if (FALSE) cohort2TrajectoryConfiguration(cdm = cdm,
studyName = "TestCohort2Trajectory",
baseUrl = NULL,
pathToStudy = getwd(),
atlasTargetCohort = 0,
atlasStateCohorts = c(1, 2),
stateCohortLabels = c("test_label1", "test_label2"),
) # \dontrun{}