View source: R/DefaultTemporalCovariateSettings.R
createTemporalCovariateSettings | R Documentation |
Create covariate settings
createTemporalCovariateSettings(
useDemographicsGender = FALSE,
useDemographicsAge = FALSE,
useDemographicsAgeGroup = FALSE,
useDemographicsRace = FALSE,
useDemographicsEthnicity = FALSE,
useDemographicsIndexYear = FALSE,
useDemographicsIndexMonth = FALSE,
useDemographicsPriorObservationTime = FALSE,
useDemographicsPostObservationTime = FALSE,
useDemographicsTimeInCohort = FALSE,
useDemographicsIndexYearMonth = FALSE,
useCareSiteId = FALSE,
useConditionOccurrence = FALSE,
useConditionOccurrencePrimaryInpatient = FALSE,
useConditionEraStart = FALSE,
useConditionEraOverlap = FALSE,
useConditionEraGroupStart = FALSE,
useConditionEraGroupOverlap = FALSE,
useDrugExposure = FALSE,
useDrugEraStart = FALSE,
useDrugEraOverlap = FALSE,
useDrugEraGroupStart = FALSE,
useDrugEraGroupOverlap = FALSE,
useProcedureOccurrence = FALSE,
useDeviceExposure = FALSE,
useMeasurement = FALSE,
useMeasurementValue = FALSE,
useMeasurementRangeGroup = FALSE,
useMeasurementValueAsConcept = FALSE,
useObservation = FALSE,
useObservationValueAsConcept = FALSE,
useCharlsonIndex = FALSE,
useDcsi = FALSE,
useChads2 = FALSE,
useChads2Vasc = FALSE,
useHfrs = FALSE,
useDistinctConditionCount = FALSE,
useDistinctIngredientCount = FALSE,
useDistinctProcedureCount = FALSE,
useDistinctMeasurementCount = FALSE,
useDistinctObservationCount = FALSE,
useVisitCount = FALSE,
useVisitConceptCount = FALSE,
temporalStartDays = -365:-1,
temporalEndDays = -365:-1,
includedCovariateConceptIds = c(),
addDescendantsToInclude = FALSE,
excludedCovariateConceptIds = c(),
addDescendantsToExclude = FALSE,
includedCovariateIds = c()
)
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) |
useDemographicsPriorObservationTime |
Number of days of observation time preceding the index date. (analysis ID 8) |
useDemographicsPostObservationTime |
Number of days of observation time preceding the index date. (analysis ID 9) |
useDemographicsTimeInCohort |
Number of days of observation time preceding the index date. (analysis ID 10) |
useDemographicsIndexYearMonth |
Calendar month of the index date. (analysis ID 11) |
useCareSiteId |
Care site associated with the cohort start, pulled from the visit_detail, visit_occurrence, or person table, in that order. (analysis ID 12) |
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) |
useConditionEraOverlap |
One covariate per condition in the condition_era table overlapping with any part of the time window. (analysis ID 202) |
useConditionEraGroupStart |
One covariate per condition era rolled up to SNOMED groups in the condition_era table starting in the time window. (analysis ID 203) |
useConditionEraGroupOverlap |
One covariate per condition era rolled up to SNOMED groups in the condition_era table overlapping with any part of the time window. (analysis ID 204) |
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) |
useDrugEraOverlap |
One covariate per drug in the drug_era table overlapping with any part of the time window. (analysis ID 402) |
useDrugEraGroupStart |
One covariate per drug rolled up to ATC groups in the drug_era table starting in the time window. (analysis ID 403) |
useDrugEraGroupOverlap |
One covariate per drug rolled up to ATC groups in the drug_era table overlapping with any part of the time window. (analysis ID 404) |
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) |
useMeasurementRangeGroup |
Covariates indicating whether measurements are below, within, or above normal range within the time period. (analysis ID 703) |
useMeasurementValueAsConcept |
One covariate per measurement-value concept combination within the time period. (analysis ID 704) |
useObservation |
One covariate per observation in the observation table in the time window. (analysis ID 801) |
useObservationValueAsConcept |
One covariate per observation-value concept combination within the time period. (analysis ID 802) |
useCharlsonIndex |
The Charlson comorbidity index (Romano adaptation) using all conditions prior to the window end. (analysis ID 901) |
useDcsi |
The Diabetes Comorbidity Severity Index (DCSI) using all conditions prior to the window end. (analysis ID 902) |
useChads2 |
The CHADS2 score using all conditions prior to the window end. (analysis ID 903) |
useChads2Vasc |
The CHADS2VASc score using all conditions prior to the window end. (analysis ID 904) |
useHfrs |
The Hospital Frailty Risk Score score using all conditions prior to the window end. (analysis ID 926) |
useDistinctConditionCount |
The number of distinct condition concepts observed in the time window. (analysis ID 905) |
useDistinctIngredientCount |
The number of distinct ingredients observed in the time window. (analysis ID 906) |
useDistinctProcedureCount |
The number of distinct procedures observed in the time window. (analysis ID 907) |
useDistinctMeasurementCount |
The number of distinct measurements observed in the time window. (analysis ID 908) |
useDistinctObservationCount |
The number of distinct observations in the time window. (analysis ID 909) |
useVisitCount |
The number of visits observed in the time window. (analysis ID 910) |
useVisitConceptCount |
The number of visits observed in the time window, stratified by visit concept ID. (analysis ID 911) |
temporalStartDays |
A list of integers representing the start of a time period, relative to the index date. 0 indicates the index date, -1 indicates the day before the index date, etc. The start day is included in the time period. |
temporalEndDays |
A list of integers representing the end of a time period, relative to the index date. 0 indicates the index date, -1 indicates the day before the index date, etc. The end day is included in the time period. |
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. |
creates an object specifying how covariates should be constructed from data in the CDM model.
An object of type covariateSettings
, to be used in other functions.
settings <- createTemporalCovariateSettings(
useDemographicsGender = TRUE,
useDemographicsAge = FALSE,
useDemographicsAgeGroup = TRUE,
useDemographicsRace = TRUE,
useDemographicsEthnicity = TRUE,
useDemographicsIndexYear = TRUE,
useDemographicsIndexMonth = TRUE,
useDemographicsPriorObservationTime = FALSE,
useDemographicsPostObservationTime = FALSE,
useDemographicsTimeInCohort = FALSE,
useDemographicsIndexYearMonth = FALSE,
useCareSiteId = FALSE,
useConditionOccurrence = FALSE,
useConditionOccurrencePrimaryInpatient = FALSE,
useConditionEraStart = FALSE,
useConditionEraOverlap = FALSE,
useConditionEraGroupStart = FALSE,
useConditionEraGroupOverlap = TRUE,
useDrugExposure = FALSE,
useDrugEraStart = FALSE,
useDrugEraOverlap = FALSE,
useDrugEraGroupStart = FALSE,
useDrugEraGroupOverlap = TRUE,
useProcedureOccurrence = TRUE,
useDeviceExposure = TRUE,
useMeasurement = TRUE,
useMeasurementValue = FALSE,
useMeasurementRangeGroup = TRUE,
useMeasurementValueAsConcept = TRUE,
useObservation = TRUE,
useObservationValueAsConcept = TRUE,
useCharlsonIndex = TRUE,
useDcsi = TRUE,
useChads2 = TRUE,
useChads2Vasc = TRUE,
useHfrs = FALSE,
useDistinctConditionCount = FALSE,
useDistinctIngredientCount = FALSE,
useDistinctProcedureCount = FALSE,
useDistinctMeasurementCount = FALSE,
useDistinctObservationCount = FALSE,
useVisitCount = FALSE,
useVisitConceptCount = FALSE,
temporalStartDays = -365:-1,
temporalEndDays = -365:-1,
includedCovariateConceptIds = c(),
addDescendantsToInclude = FALSE,
excludedCovariateConceptIds = c(),
addDescendantsToExclude = FALSE,
includedCovariateIds = c()
)
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