createTemporalSequenceCovariateSettings: Create covariate settings
In FeatureExtraction: Generating Features for a Cohort

View source: R/DefaultTemporalSequenceCovariateSettings.R

createTemporalSequenceCovariateSettings

R Documentation

Create covariate settings

Description

Create covariate settings

Usage

createTemporalSequenceCovariateSettings(
  useDemographicsGender = FALSE,
  useDemographicsAge = FALSE,
  useDemographicsAgeGroup = FALSE,
  useDemographicsRace = FALSE,
  useDemographicsEthnicity = FALSE,
  useDemographicsIndexYear = FALSE,
  useDemographicsIndexMonth = FALSE,
  useConditionOccurrence = FALSE,
  useConditionOccurrencePrimaryInpatient = FALSE,
  useConditionEraStart = FALSE,
  useConditionEraGroupStart = FALSE,
  useDrugExposure = FALSE,
  useDrugEraStart = FALSE,
  useDrugEraGroupStart = FALSE,
  useProcedureOccurrence = FALSE,
  useDeviceExposure = FALSE,
  useMeasurement = FALSE,
  useMeasurementValue = FALSE,
  useObservation = FALSE,
  timePart = "month",
  timeInterval = 1,
  sequenceEndDay = -1,
  sequenceStartDay = -730,
  includedCovariateConceptIds = c(),
  addDescendantsToInclude = FALSE,
  excludedCovariateConceptIds = c(),
  addDescendantsToExclude = FALSE,
  includedCovariateIds = c()
)

Arguments

`useDemographicsGender`	Gender of the subject. (analysis ID 1)
`useDemographicsAge`	Age of the subject on the index date (in years). (analysis ID 2)
`useDemographicsAgeGroup`	Age of the subject on the index date (in 5 year age groups) (analysis ID 3)
`useDemographicsRace`	Race of the subject. (analysis ID 4)
`useDemographicsEthnicity`	Ethnicity of the subject. (analysis ID 5)
`useDemographicsIndexYear`	Year of the index date. (analysis ID 6)
`useDemographicsIndexMonth`	Month of the index date. (analysis ID 7)
`useConditionOccurrence`	One covariate per condition in the condition_occurrence table starting in the time window. (analysis ID 101)
`useConditionOccurrencePrimaryInpatient`	One covariate per condition observed as a primary diagnosis in an inpatient setting in the condition_occurrence table starting in the time window. (analysis ID 102)
`useConditionEraStart`	One covariate per condition in the condition_era table starting in the time window. (analysis ID 201)
`useConditionEraGroupStart`	One covariate per condition era rolled up to SNOMED groups in the condition_era table starting in the time window. (analysis ID 203)
`useDrugExposure`	One covariate per drug in the drug_exposure table starting in the time window. (analysis ID 301)
`useDrugEraStart`	One covariate per drug in the drug_era table starting in the time window. (analysis ID 401)
`useDrugEraGroupStart`	One covariate per drug rolled up to ATC groups in the drug_era table starting in the time window. (analysis ID 403)
`useProcedureOccurrence`	One covariate per procedure in the procedure_occurrence table in the time window. (analysis ID 501)
`useDeviceExposure`	One covariate per device in the device exposure table starting in the timewindow. (analysis ID 601)
`useMeasurement`	One covariate per measurement in the measurement table in the time window. (analysis ID 701)
`useMeasurementValue`	One covariate containing the value per measurement-unit combination in the time window. If multiple values are found, the last is taken. (analysis ID 702)
`useObservation`	One covariate per observation in the observation table in the time window. (analysis ID 801)
`timePart`	The interval scale ('DAY', 'MONTH', 'YEAR')
`timeInterval`	Fixed interval length for timeId using the 'timePart' scale. For example, a 'timePart' of DAY with 'timeInterval' 30 has timeIds where timeId 1 is day 0 to day 29, timeId 2 is day 30 to day 59, etc.
`sequenceEndDay`	What is the end day (relative to the index date) of the data extraction?
`sequenceStartDay`	What is the start day (relative to the index date) of the data extraction?
`includedCovariateConceptIds`	A list of concept IDs that should be used to construct covariates.
`addDescendantsToInclude`	Should descendant concept IDs be added to the list of concepts to include?
`excludedCovariateConceptIds`	A list of concept IDs that should NOT be used to construct covariates.
`addDescendantsToExclude`	Should descendant concept IDs be added to the list of concepts to exclude?
`includedCovariateIds`	A list of covariate IDs that should be restricted to.

Details

creates an object specifying how covariates should be constructed from data in the CDM model.

Value

An object of type covariateSettings, to be used in other functions.

Examples

settings <- createTemporalSequenceCovariateSettings(
  useDemographicsGender = TRUE,
  useDemographicsAge = FALSE,
  useDemographicsAgeGroup = TRUE,
  useDemographicsRace = TRUE,
  useDemographicsEthnicity = TRUE,
  useDemographicsIndexYear = TRUE,
  useDemographicsIndexMonth = TRUE,
  useConditionOccurrence = FALSE,
  useConditionOccurrencePrimaryInpatient = FALSE,
  useConditionEraStart = FALSE,
  useConditionEraGroupStart = FALSE,
  useDrugExposure = FALSE,
  useDrugEraStart = FALSE,
  useDrugEraGroupStart = FALSE,
  useProcedureOccurrence = TRUE,
  useDeviceExposure = TRUE,
  useMeasurement = TRUE,
  useMeasurementValue = FALSE,
  useObservation = TRUE,
  timePart = "DAY",
  timeInterval = 1,
  sequenceEndDay = -1,
  sequenceStartDay = -730,
  includedCovariateConceptIds = c(),
  addDescendantsToInclude = FALSE,
  excludedCovariateConceptIds = c(),
  addDescendantsToExclude = FALSE,
  includedCovariateIds = c()
)

FeatureExtraction documentation built on Oct. 18, 2024, 9:06 a.m.