Import the data from CDM for the study
getDataForStudy.RdImport the data from CDM for the study
Usage
getDataForStudy(
runSavedStudy = studyEnv$runSavedStudy,
useCDM = studyEnv$useCDM,
trajectoryDataObject = NULL,
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,
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)