createAggregateCovariateSettings: Create aggregate covariate study settings

In Characterization: Implement Descriptive Studies Using the Common Data Model

Create aggregate covariate study settings

Description

Create aggregate covariate study settings

Usage

createAggregateCovariateSettings(
  targetIds,
  outcomeIds,
  minPriorObservation = 0,
  outcomeWashoutDays = 0,
  riskWindowStart = 1,
  startAnchor = "cohort start",
  riskWindowEnd = 365,
  endAnchor = "cohort start",
  covariateSettings = FeatureExtraction::createCovariateSettings(useDemographicsGender =
    TRUE, useDemographicsAge = TRUE, useDemographicsAgeGroup = TRUE, useDemographicsRace
    = TRUE, useDemographicsEthnicity = TRUE, useDemographicsIndexYear = TRUE,
    useDemographicsIndexMonth = TRUE, useDemographicsTimeInCohort = TRUE,
    useDemographicsPriorObservationTime = TRUE, useDemographicsPostObservationTime =
    TRUE, useConditionGroupEraLongTerm = TRUE, useDrugGroupEraOverlapping = TRUE,
    useDrugGroupEraLongTerm = TRUE, useProcedureOccurrenceLongTerm = TRUE, 
    
    useMeasurementLongTerm = TRUE, useObservationLongTerm = TRUE,
    useDeviceExposureLongTerm = TRUE, useVisitConceptCountLongTerm = TRUE,
    useConditionGroupEraShortTerm = TRUE, useDrugGroupEraShortTerm = TRUE,
    useProcedureOccurrenceShortTerm = TRUE, useMeasurementShortTerm = TRUE,
    useObservationShortTerm = TRUE, useDeviceExposureShortTerm = TRUE,
    useVisitConceptCountShortTerm = TRUE, endDays = 0, longTermStartDays = -365,
    shortTermStartDays = -30),
  caseCovariateSettings = createDuringCovariateSettings(useConditionGroupEraDuring =
    TRUE, useDrugGroupEraDuring = TRUE, useProcedureOccurrenceDuring = TRUE,
    useDeviceExposureDuring = TRUE, useMeasurementDuring = TRUE, useObservationDuring =
    TRUE, useVisitConceptCountDuring = TRUE),
  casePreTargetDuration = 365,
  casePostOutcomeDuration = 365,
  extractNonCaseCovariates = TRUE
)

Arguments

targetIds	A list of cohortIds for the target cohorts
outcomeIds	A list of cohortIds for the outcome cohorts
minPriorObservation	The minimum time (in days) in the database a patient in the target cohorts must be observed prior to index
outcomeWashoutDays	Patients with the outcome within outcomeWashout days prior to index are excluded from the risk factor analysis
riskWindowStart	The start of the risk window (in days) relative to the 'startAnchor'.
startAnchor	The anchor point for the start of the risk window. Can be '"cohort start"' or '"cohort end"'.
riskWindowEnd	The end of the risk window (in days) relative to the 'endAnchor'.
endAnchor	The anchor point for the end of the risk window. Can be '"cohort start"' or '"cohort end"'.
covariateSettings	An object created using FeatureExtraction::createCovariateSettings
caseCovariateSettings	An object created using createDuringCovariateSettings
casePreTargetDuration	The number of days prior to case index we use for FeatureExtraction
casePostOutcomeDuration	The number of days prior to case index we use for FeatureExtraction
extractNonCaseCovariates	Whether to extract aggregate covariates and counts for patients in the targets and outcomes in addition to the cases

Value

A list with the settings

Examples

aggregateSetting <- createAggregateCovariateSettings(
  targetIds = c(1,2),
  outcomeIds = c(3),
  minPriorObservation = 365,
  outcomeWashoutDays = 90,
  riskWindowStart = 1,
  startAnchor = "cohort start",
  riskWindowEnd = 365,
  endAnchor = "cohort start",
  casePreTargetDuration = 365,
  casePostOutcomeDuration = 365
)

Characterization documentation built on April 4, 2025, 2:02 a.m.