getDataForStudy: Import the data from CDM for the study

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

Import the data from CDM for the study

Description

Import the data from CDM for the study

Usage

getDataForStudy(
  runSavedStudy = studyEnv$runSavedStudy,
  useCDM = studyEnv$useCDM,
  trajectoryDataObject = studyEnv$trajectoryDataObject,
  cdm = NULL,
  studyEnv = NULL,
  atlasStateCohorts = studyEnv$atlasStateCohorts,
  atlasTargetCohort = studyEnv$atlasTargetCohort,
  stateCohortLabels = studyEnv$stateCohortLabels,
  baseUrl = studyEnv$baseUrl,
  outOfCohortAllowed = studyEnv$outOfCohortAllowed,
  stateCohortMandatory = studyEnv$stateCohortMandatory,
  stateCohortPriorityOrder = studyEnv$stateCohortPriorityOrder,
  mergeStates = studyEnv$mergeStates,
  mergeThreshold = studyEnv$mergeThreshold,
  allowedStatesList = studyEnv$allowedStatesList,
  stateCohortAbsorbing = studyEnv$stateCohortAbsorbing,
  pathToData = NULL
)

Arguments

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)
cdm	object created with CDMConnector
studyEnv	environment created with cohort2TrajectoryConfiguration
atlasStateCohorts	the ids of the state cohorts defined in OHDSI tool ATLAS
atlasTargetCohort	the id of the target cohort defined in OHDSI tool ATLAS
stateCohortLabels	vector of the customized labels of the state cohorts
baseUrl	the base URL for the WebApi instance
outOfCohortAllowed	boolean whether the patient trajectory can surpass the target cohort's observation-period
stateCohortMandatory	vector of the customized labels of the state cohorts which are mandatory in trajectory
stateCohortPriorityOrder	vector of the customized labels of the state cohorts in priority order
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,
pathToData	When using without OMOP CDM specify the path to data file (if specified no need for trajectoryDataObject)

Value

log info

Examples

## Not run: getDataForStudy(cdm = cdm,studyEnv = studyEnv)

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