createTemporalSequenceCovariateSettings: Create covariate settings

In quinterpriest/FeatureExtraction: Generating Features for a Cohort

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 thetime 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 contructed 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())

quinterpriest/FeatureExtraction documentation built on April 20, 2022, 12:49 a.m.