createCovariateSettings: Create covariate settings
In FeatureExtraction: Generating Features for a Cohort
View source: R/DefaultCovariateSettings.R
createCovariateSettings R Documentation
Create covariate settings
Description
Create covariate settings
Usage
createCovariateSettings(
useDemographicsGender = FALSE,
useDemographicsAge = FALSE,
useDemographicsAgeGroup = FALSE,
useDemographicsRace = FALSE,
useDemographicsEthnicity = FALSE,
useDemographicsIndexYear = FALSE,
useDemographicsIndexMonth = FALSE,
useDemographicsPriorObservationTime = FALSE,
useDemographicsPostObservationTime = FALSE,
useDemographicsTimeInCohort = FALSE,
useDemographicsIndexYearMonth = FALSE,
useCareSiteId = FALSE,
useConditionOccurrenceAnyTimePrior = FALSE,
useConditionOccurrenceLongTerm = FALSE,
useConditionOccurrenceMediumTerm = FALSE,
useConditionOccurrenceShortTerm = FALSE,
useConditionOccurrencePrimaryInpatientAnyTimePrior = FALSE,
useConditionOccurrencePrimaryInpatientLongTerm = FALSE,
useConditionOccurrencePrimaryInpatientMediumTerm = FALSE,
useConditionOccurrencePrimaryInpatientShortTerm = FALSE,
useConditionEraAnyTimePrior = FALSE,
useConditionEraLongTerm = FALSE,
useConditionEraMediumTerm = FALSE,
useConditionEraShortTerm = FALSE,
useConditionEraOverlapping = FALSE,
useConditionEraStartLongTerm = FALSE,
useConditionEraStartMediumTerm = FALSE,
useConditionEraStartShortTerm = FALSE,
useConditionGroupEraAnyTimePrior = FALSE,
useConditionGroupEraLongTerm = FALSE,
useConditionGroupEraMediumTerm = FALSE,
useConditionGroupEraShortTerm = FALSE,
useConditionGroupEraOverlapping = FALSE,
useConditionGroupEraStartLongTerm = FALSE,
useConditionGroupEraStartMediumTerm = FALSE,
useConditionGroupEraStartShortTerm = FALSE,
useDrugExposureAnyTimePrior = FALSE,
useDrugExposureLongTerm = FALSE,
useDrugExposureMediumTerm = FALSE,
useDrugExposureShortTerm = FALSE,
useDrugEraAnyTimePrior = FALSE,
useDrugEraLongTerm = FALSE,
useDrugEraMediumTerm = FALSE,
useDrugEraShortTerm = FALSE,
useDrugEraOverlapping = FALSE,
useDrugEraStartLongTerm = FALSE,
useDrugEraStartMediumTerm = FALSE,
useDrugEraStartShortTerm = FALSE,
useDrugGroupEraAnyTimePrior = FALSE,
useDrugGroupEraLongTerm = FALSE,
useDrugGroupEraMediumTerm = FALSE,
useDrugGroupEraShortTerm = FALSE,
useDrugGroupEraOverlapping = FALSE,
useDrugGroupEraStartLongTerm = FALSE,
useDrugGroupEraStartMediumTerm = FALSE,
useDrugGroupEraStartShortTerm = FALSE,
useProcedureOccurrenceAnyTimePrior = FALSE,
useProcedureOccurrenceLongTerm = FALSE,
useProcedureOccurrenceMediumTerm = FALSE,
useProcedureOccurrenceShortTerm = FALSE,
useDeviceExposureAnyTimePrior = FALSE,
useDeviceExposureLongTerm = FALSE,
useDeviceExposureMediumTerm = FALSE,
useDeviceExposureShortTerm = FALSE,
useMeasurementAnyTimePrior = FALSE,
useMeasurementLongTerm = FALSE,
useMeasurementMediumTerm = FALSE,
useMeasurementShortTerm = FALSE,
useMeasurementValueAnyTimePrior = FALSE,
useMeasurementValueLongTerm = FALSE,
useMeasurementValueMediumTerm = FALSE,
useMeasurementValueShortTerm = FALSE,
useMeasurementRangeGroupAnyTimePrior = FALSE,
useMeasurementRangeGroupLongTerm = FALSE,
useMeasurementRangeGroupMediumTerm = FALSE,
useMeasurementRangeGroupShortTerm = FALSE,
useMeasurementValueAsConceptAnyTimePrior = FALSE,
useMeasurementValueAsConceptLongTerm = FALSE,
useMeasurementValueAsConceptMediumTerm = FALSE,
useMeasurementValueAsConceptShortTerm = FALSE,
useObservationAnyTimePrior = FALSE,
useObservationLongTerm = FALSE,
useObservationMediumTerm = FALSE,
useObservationShortTerm = FALSE,
useObservationValueAsConceptAnyTimePrior = FALSE,
useObservationValueAsConceptLongTerm = FALSE,
useObservationValueAsConceptMediumTerm = FALSE,
useObservationValueAsConceptShortTerm = FALSE,
useCharlsonIndex = FALSE,
useDcsi = FALSE,
useChads2 = FALSE,
useChads2Vasc = FALSE,
useHfrs = FALSE,
useDistinctConditionCountLongTerm = FALSE,
useDistinctConditionCountMediumTerm = FALSE,
useDistinctConditionCountShortTerm = FALSE,
useDistinctIngredientCountLongTerm = FALSE,
useDistinctIngredientCountMediumTerm = FALSE,
useDistinctIngredientCountShortTerm = FALSE,
useDistinctProcedureCountLongTerm = FALSE,
useDistinctProcedureCountMediumTerm = FALSE,
useDistinctProcedureCountShortTerm = FALSE,
useDistinctMeasurementCountLongTerm = FALSE,
useDistinctMeasurementCountMediumTerm = FALSE,
useDistinctMeasurementCountShortTerm = FALSE,
useDistinctObservationCountLongTerm = FALSE,
useDistinctObservationCountMediumTerm = FALSE,
useDistinctObservationCountShortTerm = FALSE,
useVisitCountLongTerm = FALSE,
useVisitCountMediumTerm = FALSE,
useVisitCountShortTerm = FALSE,
useVisitConceptCountLongTerm = FALSE,
useVisitConceptCountMediumTerm = FALSE,
useVisitConceptCountShortTerm = FALSE,
longTermStartDays = -365,
mediumTermStartDays = -180,
shortTermStartDays = -30,
endDays = 0,
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)
useDemographicsPriorObservationTime
Number of continuous days of observation
time preceding the index date. (analysis
ID 8)
useDemographicsPostObservationTime
Number of continuous days of observation
time following the index date. (analysis
ID 9)
useDemographicsTimeInCohort
Number of days of observation time
during cohort period. (analysis ID 10)
useDemographicsIndexYearMonth
Both calendar year and month of the
index date in a single variable.
(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)
useConditionOccurrenceAnyTimePrior
One covariate per condition in the
condition_occurrence table starting any
time prior to index. (analysis ID 101)
useConditionOccurrenceLongTerm
One covariate per condition in the
condition_occurrence table starting in
the long term window. (analysis ID 102)
useConditionOccurrenceMediumTerm
One covariate per condition in the
condition_occurrence table starting in
the medium term window. (analysis ID
103)
useConditionOccurrenceShortTerm
One covariate per condition in the
condition_occurrence table starting in
the short term window. (analysis ID 104)
useConditionOccurrencePrimaryInpatientAnyTimePrior
One covariate per condition observed as
a primary diagnosis in an inpatient
setting in the condition_occurrence
table starting any time prior to index.
(analysis ID 105)
useConditionOccurrencePrimaryInpatientLongTerm
One covariate per condition observed as
a primary diagnosis in an inpatient
setting in the condition_occurrence
table starting in the long term window.
(analysis ID 106)
useConditionOccurrencePrimaryInpatientMediumTerm
One covariate per condition observed as
a primary diagnosis in an inpatient
setting in the condition_occurrence
table starting in the medium term
window. (analysis ID 107)
useConditionOccurrencePrimaryInpatientShortTerm
One covariate per condition observed as
a primary diagnosis in an inpatient
setting in the condition_occurrence
table starting in the short term window.
(analysis ID 108)
useConditionEraAnyTimePrior
One covariate per condition in the
condition_era table overlapping with any
time prior to index. (analysis ID 201)
useConditionEraLongTerm
One covariate per condition in the
condition_era table overlapping with any
part of the long term window. (analysis
ID 202)
useConditionEraMediumTerm
One covariate per condition in the
condition_era table overlapping with any
part of the medium term window.
(analysis ID 203)
useConditionEraShortTerm
One covariate per condition in the
condition_era table overlapping with any
part of the short term window. (analysis
ID 204)
useConditionEraOverlapping
One covariate per condition in the
condition_era table overlapping with the
end of the risk window. (analysis ID
205)
useConditionEraStartLongTerm
One covariate per condition in the
condition_era table starting in the long
term window. (analysis ID 206)
useConditionEraStartMediumTerm
One covariate per condition in the
condition_era table starting in the
medium term window. (analysis ID 207)
useConditionEraStartShortTerm
One covariate per condition in the
condition_era table starting in the
short term window. (analysis ID 208)
useConditionGroupEraAnyTimePrior
One covariate per condition era rolled
up to groups in the condition_era table
overlapping with any time prior to
index. (analysis ID 209)
useConditionGroupEraLongTerm
One covariate per condition era rolled
up to groups in the condition_era table
overlapping with any part of the long
term window. (analysis ID 210)
useConditionGroupEraMediumTerm
One covariate per condition era rolled
up to groups in the condition_era table
overlapping with any part of the medium
term window. (analysis ID 211)
useConditionGroupEraShortTerm
One covariate per condition era rolled
up to groups in the condition_era table
overlapping with any part of the short
term window. (analysis ID 212)
useConditionGroupEraOverlapping
One covariate per condition era rolled
up to groups in the condition_era table
overlapping with the end of the risk
window. (analysis ID 213)
useConditionGroupEraStartLongTerm
One covariate per condition era rolled
up to groups in the condition_era table
starting in the long term window.
(analysis ID 214)
useConditionGroupEraStartMediumTerm
One covariate per condition era rolled
up to groups in the condition_era table
starting in the medium term window.
(analysis ID 215)
useConditionGroupEraStartShortTerm
One covariate per condition era rolled
up to groups in the condition_era table
starting in the short term window.
(analysis ID 216)
useDrugExposureAnyTimePrior
One covariate per drug in the
drug_exposure table starting any time
prior to index. (analysis ID 301)
useDrugExposureLongTerm
One covariate per drug in the
drug_exposure table starting in the long
term window. (analysis ID 302)
useDrugExposureMediumTerm
One covariate per drug in the
drug_exposure table starting in the
medium term window. (analysis ID 303)
useDrugExposureShortTerm
One covariate per drug in the
drug_exposure table starting in the
short term window. (analysis ID 304)
useDrugEraAnyTimePrior
One covariate per drug in the drug_era
table overlapping with any time prior to
index. (analysis ID 401)
useDrugEraLongTerm
One covariate per drug in the drug_era
table overlapping with any part of the
long term window. (analysis ID 402)
useDrugEraMediumTerm
One covariate per drug in the drug_era
table overlapping with any part of the
medium term window. (analysis ID 403)
useDrugEraShortTerm
One covariate per drug in the drug_era
table overlapping with any part of the
short term window. (analysis ID 404)
useDrugEraOverlapping
One covariate per drug in the drug_era
table overlapping with the end of the
risk window. (analysis ID 405)
useDrugEraStartLongTerm
One covariate per drug in the drug_era
table starting in the long term window.
(analysis ID 406)
useDrugEraStartMediumTerm
One covariate per drug in the drug_era
table starting in the medium term
window. (analysis ID 407)
useDrugEraStartShortTerm
One covariate per drug in the drug_era
table starting in the short term window.
(analysis ID 408)
useDrugGroupEraAnyTimePrior
One covariate per drug rolled up to ATC
groups in the drug_era table overlapping
with any time prior to index. (analysis
ID 409)
useDrugGroupEraLongTerm
One covariate per drug rolled up to ATC
groups in the drug_era table overlapping
with any part of the long term window.
(analysis ID 410)
useDrugGroupEraMediumTerm
One covariate per drug rolled up to ATC
groups in the drug_era table overlapping
with any part of the medium term window.
(analysis ID 411)
useDrugGroupEraShortTerm
One covariate per drug rolled up to ATC
groups in the drug_era table overlapping
with any part of the short term window.
(analysis ID 412)
useDrugGroupEraOverlapping
One covariate per drug rolled up to ATC
groups in the drug_era table overlapping
with the end of the risk window.
(analysis ID 413)
useDrugGroupEraStartLongTerm
One covariate per drug rolled up to ATC
groups in the drug_era table starting in
the long term window. (analysis ID 414)
useDrugGroupEraStartMediumTerm
One covariate per drug rolled up to ATC
groups in the drug_era table starting in
the medium term window. (analysis ID
415)
useDrugGroupEraStartShortTerm
One covariate per drug rolled up to ATC
groups in the drug_era table starting in
the short term window. (analysis ID 416)
useProcedureOccurrenceAnyTimePrior
One covariate per procedure in the
procedure_occurrence table any time
prior to index. (analysis ID 501)
useProcedureOccurrenceLongTerm
One covariate per procedure in the
procedure_occurrence table in the long
term window. (analysis ID 502)
useProcedureOccurrenceMediumTerm
One covariate per procedure in the
procedure_occurrence table in the medium
term window. (analysis ID 503)
useProcedureOccurrenceShortTerm
One covariate per procedure in the
procedure_occurrence table in the short
term window. (analysis ID 504)
useDeviceExposureAnyTimePrior
One covariate per device in the device
exposure table starting any time prior
to index. (analysis ID 601)
useDeviceExposureLongTerm
One covariate per device in the device
exposure table starting in the long term
window. (analysis ID 602)
useDeviceExposureMediumTerm
One covariate per device in the device
exposure table starting in the medium
term window. (analysis ID 603)
useDeviceExposureShortTerm
One covariate per device in the device
exposure table starting in the short
term window. (analysis ID 604)
useMeasurementAnyTimePrior
One covariate per measurement in the
measurement table any time prior to
index. (analysis ID 701)
useMeasurementLongTerm
One covariate per measurement in the
measurement table in the long term
window. (analysis ID 702)
useMeasurementMediumTerm
One covariate per measurement in the
measurement table in the medium term
window. (analysis ID 703)
useMeasurementShortTerm
One covariate per measurement in the
measurement table in the short term
window. (analysis ID 704)
useMeasurementValueAnyTimePrior
One covariate containing the value per
measurement-unit combination any time
prior to index. (analysis ID 705)
useMeasurementValueLongTerm
One covariate containing the value per
measurement-unit combination in the long
term window. (analysis ID 706)
useMeasurementValueMediumTerm
One covariate containing the value per
measurement-unit combination in the
medium term window. (analysis ID 707)
useMeasurementValueShortTerm
One covariate containing the value per
measurement-unit combination in the
short term window. (analysis ID 708)
useMeasurementRangeGroupAnyTimePrior
Covariates indicating whether
measurements are below, within, or above
normal range any time prior to index.
(analysis ID 709)
useMeasurementRangeGroupLongTerm
Covariates indicating whether
measurements are below, within, or above
normal range in the long term window.
(analysis ID 710)
useMeasurementRangeGroupMediumTerm
Covariates indicating whether
measurements are below, within, or above
normal range in the medium term window.
(analysis ID 711)
useMeasurementRangeGroupShortTerm
Covariates indicating whether
measurements are below, within, or above
normal range in the short term window.
(analysis ID 712)
useMeasurementValueAsConceptAnyTimePrior
One covariate per measurement-value
concept combination any time prior to
index. (analysis ID 713)
useMeasurementValueAsConceptLongTerm
One covariate per measurement-value
concept combination in the long term
window. (analysis ID 714)
useMeasurementValueAsConceptMediumTerm
One covariate per measurement-value
concept combination in the medium term
window. (analysis ID 715)
useMeasurementValueAsConceptShortTerm
One covariate per measurement-value
concept combination in the short term
window. (analysis ID 716)
useObservationAnyTimePrior
One covariate per observation in the
observation table any time prior to
index. (analysis ID 801)
useObservationLongTerm
One covariate per observation in the
observation table in the long term
window. (analysis ID 802)
useObservationMediumTerm
One covariate per observation in the
observation table in the medium term
window. (analysis ID 803)
useObservationShortTerm
One covariate per observation in the
observation table in the short term
window. (analysis ID 804)
useObservationValueAsConceptAnyTimePrior
One covariate per observation-value
concept combination any time prior to
index. (analysis ID 805)
useObservationValueAsConceptLongTerm
One covariate per observation-value
concept combination in the long term
window. (analysis ID 806)
useObservationValueAsConceptMediumTerm
One covariate per observation-value
concept combination in the medium term
window. (analysis ID 807)
useObservationValueAsConceptShortTerm
One covariate per observation-value
concept combination in the short term
window. (analysis ID 808)
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)
useDistinctConditionCountLongTerm
The number of distinct condition
concepts observed in the long term
window. (analysis ID 905)
useDistinctConditionCountMediumTerm
The number of distinct condition
concepts observed in the medium term
window. (analysis ID 906)
useDistinctConditionCountShortTerm
The number of distinct condition
concepts observed in the short term
window. (analysis ID 907)
useDistinctIngredientCountLongTerm
The number of distinct ingredients
observed in the long term window.
(analysis ID 908)
useDistinctIngredientCountMediumTerm
The number of distinct ingredients
observed in the medium term window.
(analysis ID 909)
useDistinctIngredientCountShortTerm
The number of distinct ingredients
observed in the short term window.
(analysis ID 910)
useDistinctProcedureCountLongTerm
The number of distinct procedures
observed in the long term window.
(analysis ID 911)
useDistinctProcedureCountMediumTerm
The number of distinct procedures
observed in the medium term window.
(analysis ID 912)
useDistinctProcedureCountShortTerm
The number of distinct procedures
observed in the short term window.
(analysis ID 913)
useDistinctMeasurementCountLongTerm
The number of distinct measurements
observed in the long term window.
(analysis ID 914)
useDistinctMeasurementCountMediumTerm
The number of distinct measurements
observed in the medium term window.
(analysis ID 915)
useDistinctMeasurementCountShortTerm
The number of distinct measurements
observed in the short term window.
(analysis ID 916)
useDistinctObservationCountLongTerm
The number of distinct observations
observed in the long term window.
(analysis ID 917)
useDistinctObservationCountMediumTerm
The number of distinct observations
observed in the medium term window.
(analysis ID 918)
useDistinctObservationCountShortTerm
The number of distinct observations
observed in the short term window.
(analysis ID 919)
useVisitCountLongTerm
The number of visits observed in the
long term window. (analysis ID 920)
useVisitCountMediumTerm
The number of visits observed in the
medium term window. (analysis ID 921)
useVisitCountShortTerm
The number of visits observed in the
short term window. (analysis ID 922)
useVisitConceptCountLongTerm
The number of visits observed in the
long term window, stratified by visit
concept ID. (analysis ID 923)
useVisitConceptCountMediumTerm
The number of visits observed in the
medium term window, stratified by visit
concept ID. (analysis ID 924)
useVisitConceptCountShortTerm
The number of visits observed in the
short term window, stratified by visit
concept ID. (analysis ID 925)
longTermStartDays
What is the start day (relative to the
index date) of the long-term window?
mediumTermStartDays
What is the start day (relative to the
index date) of the medium-term window?
shortTermStartDays
What is the start day (relative to the
index date) of the short-term window?
endDays
What is the end day (relative to the
index date) of the window?
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 <- createCovariateSettings(
useDemographicsGender = TRUE,
useDemographicsAge = FALSE,
useDemographicsAgeGroup = TRUE,
useDemographicsRace = TRUE,
useDemographicsEthnicity = TRUE,
useDemographicsIndexYear = TRUE,
useDemographicsIndexMonth = TRUE,
useDemographicsPriorObservationTime = FALSE,
useDemographicsPostObservationTime = FALSE,
useDemographicsTimeInCohort = FALSE,
useDemographicsIndexYearMonth = FALSE,
useCareSiteId = FALSE,
useConditionOccurrenceAnyTimePrior = FALSE,
useConditionOccurrenceLongTerm = FALSE,
useConditionOccurrenceMediumTerm = FALSE,
useConditionOccurrenceShortTerm = FALSE,
useConditionOccurrencePrimaryInpatientAnyTimePrior = FALSE,
useConditionOccurrencePrimaryInpatientLongTerm = FALSE,
useConditionOccurrencePrimaryInpatientMediumTerm = FALSE,
useConditionOccurrencePrimaryInpatientShortTerm = FALSE,
useConditionEraAnyTimePrior = FALSE,
useConditionEraLongTerm = FALSE,
useConditionEraMediumTerm = FALSE,
useConditionEraShortTerm = FALSE,
useConditionEraOverlapping = FALSE,
useConditionEraStartLongTerm = FALSE,
useConditionEraStartMediumTerm = FALSE,
useConditionEraStartShortTerm = FALSE,
useConditionGroupEraAnyTimePrior = FALSE,
useConditionGroupEraLongTerm = TRUE,
useConditionGroupEraMediumTerm = FALSE,
useConditionGroupEraShortTerm = TRUE,
useConditionGroupEraOverlapping = FALSE,
useConditionGroupEraStartLongTerm = FALSE,
useConditionGroupEraStartMediumTerm = FALSE,
useConditionGroupEraStartShortTerm = FALSE,
useDrugExposureAnyTimePrior = FALSE,
useDrugExposureLongTerm = FALSE,
useDrugExposureMediumTerm = FALSE,
useDrugExposureShortTerm = FALSE,
useDrugEraAnyTimePrior = FALSE,
useDrugEraLongTerm = FALSE,
useDrugEraMediumTerm = FALSE,
useDrugEraShortTerm = FALSE,
useDrugEraOverlapping = FALSE,
useDrugEraStartLongTerm = FALSE,
useDrugEraStartMediumTerm = FALSE,
useDrugEraStartShortTerm = FALSE,
useDrugGroupEraAnyTimePrior = FALSE,
useDrugGroupEraLongTerm = TRUE,
useDrugGroupEraMediumTerm = FALSE,
useDrugGroupEraShortTerm = TRUE,
useDrugGroupEraOverlapping = TRUE,
useDrugGroupEraStartLongTerm = FALSE,
useDrugGroupEraStartMediumTerm = FALSE,
useDrugGroupEraStartShortTerm = FALSE,
useProcedureOccurrenceAnyTimePrior = FALSE,
useProcedureOccurrenceLongTerm = TRUE,
useProcedureOccurrenceMediumTerm = FALSE,
useProcedureOccurrenceShortTerm = TRUE,
useDeviceExposureAnyTimePrior = FALSE,
useDeviceExposureLongTerm = TRUE,
useDeviceExposureMediumTerm = FALSE,
useDeviceExposureShortTerm = TRUE,
useMeasurementAnyTimePrior = FALSE,
useMeasurementLongTerm = TRUE,
useMeasurementMediumTerm = FALSE,
useMeasurementShortTerm = TRUE,
useMeasurementValueAnyTimePrior = FALSE,
useMeasurementValueLongTerm = FALSE,
useMeasurementValueMediumTerm = FALSE,
useMeasurementValueShortTerm = FALSE,
useMeasurementRangeGroupAnyTimePrior = FALSE,
useMeasurementRangeGroupLongTerm = TRUE,
useMeasurementRangeGroupMediumTerm = FALSE,
useMeasurementRangeGroupShortTerm = TRUE,
useMeasurementValueAsConceptAnyTimePrior = FALSE,
useMeasurementValueAsConceptLongTerm = TRUE,
useMeasurementValueAsConceptMediumTerm = FALSE,
useMeasurementValueAsConceptShortTerm = TRUE,
useObservationAnyTimePrior = FALSE,
useObservationLongTerm = TRUE,
useObservationMediumTerm = FALSE,
useObservationShortTerm = TRUE,
useObservationValueAsConceptAnyTimePrior = FALSE,
useObservationValueAsConceptLongTerm = TRUE,
useObservationValueAsConceptMediumTerm = FALSE,
useObservationValueAsConceptShortTerm = TRUE,
useCharlsonIndex = TRUE,
useDcsi = TRUE,
useChads2 = TRUE,
useChads2Vasc = TRUE,
useHfrs = FALSE,
useDistinctConditionCountLongTerm = FALSE,
useDistinctConditionCountMediumTerm = FALSE,
useDistinctConditionCountShortTerm = FALSE,
useDistinctIngredientCountLongTerm = FALSE,
useDistinctIngredientCountMediumTerm = FALSE,
useDistinctIngredientCountShortTerm = FALSE,
useDistinctProcedureCountLongTerm = FALSE,
useDistinctProcedureCountMediumTerm = FALSE,
useDistinctProcedureCountShortTerm = FALSE,
useDistinctMeasurementCountLongTerm = FALSE,
useDistinctMeasurementCountMediumTerm = FALSE,
useDistinctMeasurementCountShortTerm = FALSE,
useDistinctObservationCountLongTerm = FALSE,
useDistinctObservationCountMediumTerm = FALSE,
useDistinctObservationCountShortTerm = FALSE,
useVisitCountLongTerm = FALSE,
useVisitCountMediumTerm = FALSE,
useVisitCountShortTerm = FALSE,
useVisitConceptCountLongTerm = FALSE,
useVisitConceptCountMediumTerm = FALSE,
useVisitConceptCountShortTerm = FALSE,
longTermStartDays = -365,
mediumTermStartDays = -180,
shortTermStartDays = -30,
endDays = 0,
includedCovariateConceptIds = c(),
addDescendantsToInclude = FALSE,
excludedCovariateConceptIds = c(),
addDescendantsToExclude = FALSE,
includedCovariateIds = c()
)
FeatureExtraction documentation built on Oct. 18, 2024, 9:06 a.m.
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View source: R/DefaultCovariateSettings.R
| createCovariateSettings | R Documentation |
Create covariate settings
Description
Create covariate settings
Usage
createCovariateSettings(
useDemographicsGender = FALSE,
useDemographicsAge = FALSE,
useDemographicsAgeGroup = FALSE,
useDemographicsRace = FALSE,
useDemographicsEthnicity = FALSE,
useDemographicsIndexYear = FALSE,
useDemographicsIndexMonth = FALSE,
useDemographicsPriorObservationTime = FALSE,
useDemographicsPostObservationTime = FALSE,
useDemographicsTimeInCohort = FALSE,
useDemographicsIndexYearMonth = FALSE,
useCareSiteId = FALSE,
useConditionOccurrenceAnyTimePrior = FALSE,
useConditionOccurrenceLongTerm = FALSE,
useConditionOccurrenceMediumTerm = FALSE,
useConditionOccurrenceShortTerm = FALSE,
useConditionOccurrencePrimaryInpatientAnyTimePrior = FALSE,
useConditionOccurrencePrimaryInpatientLongTerm = FALSE,
useConditionOccurrencePrimaryInpatientMediumTerm = FALSE,
useConditionOccurrencePrimaryInpatientShortTerm = FALSE,
useConditionEraAnyTimePrior = FALSE,
useConditionEraLongTerm = FALSE,
useConditionEraMediumTerm = FALSE,
useConditionEraShortTerm = FALSE,
useConditionEraOverlapping = FALSE,
useConditionEraStartLongTerm = FALSE,
useConditionEraStartMediumTerm = FALSE,
useConditionEraStartShortTerm = FALSE,
useConditionGroupEraAnyTimePrior = FALSE,
useConditionGroupEraLongTerm = FALSE,
useConditionGroupEraMediumTerm = FALSE,
useConditionGroupEraShortTerm = FALSE,
useConditionGroupEraOverlapping = FALSE,
useConditionGroupEraStartLongTerm = FALSE,
useConditionGroupEraStartMediumTerm = FALSE,
useConditionGroupEraStartShortTerm = FALSE,
useDrugExposureAnyTimePrior = FALSE,
useDrugExposureLongTerm = FALSE,
useDrugExposureMediumTerm = FALSE,
useDrugExposureShortTerm = FALSE,
useDrugEraAnyTimePrior = FALSE,
useDrugEraLongTerm = FALSE,
useDrugEraMediumTerm = FALSE,
useDrugEraShortTerm = FALSE,
useDrugEraOverlapping = FALSE,
useDrugEraStartLongTerm = FALSE,
useDrugEraStartMediumTerm = FALSE,
useDrugEraStartShortTerm = FALSE,
useDrugGroupEraAnyTimePrior = FALSE,
useDrugGroupEraLongTerm = FALSE,
useDrugGroupEraMediumTerm = FALSE,
useDrugGroupEraShortTerm = FALSE,
useDrugGroupEraOverlapping = FALSE,
useDrugGroupEraStartLongTerm = FALSE,
useDrugGroupEraStartMediumTerm = FALSE,
useDrugGroupEraStartShortTerm = FALSE,
useProcedureOccurrenceAnyTimePrior = FALSE,
useProcedureOccurrenceLongTerm = FALSE,
useProcedureOccurrenceMediumTerm = FALSE,
useProcedureOccurrenceShortTerm = FALSE,
useDeviceExposureAnyTimePrior = FALSE,
useDeviceExposureLongTerm = FALSE,
useDeviceExposureMediumTerm = FALSE,
useDeviceExposureShortTerm = FALSE,
useMeasurementAnyTimePrior = FALSE,
useMeasurementLongTerm = FALSE,
useMeasurementMediumTerm = FALSE,
useMeasurementShortTerm = FALSE,
useMeasurementValueAnyTimePrior = FALSE,
useMeasurementValueLongTerm = FALSE,
useMeasurementValueMediumTerm = FALSE,
useMeasurementValueShortTerm = FALSE,
useMeasurementRangeGroupAnyTimePrior = FALSE,
useMeasurementRangeGroupLongTerm = FALSE,
useMeasurementRangeGroupMediumTerm = FALSE,
useMeasurementRangeGroupShortTerm = FALSE,
useMeasurementValueAsConceptAnyTimePrior = FALSE,
useMeasurementValueAsConceptLongTerm = FALSE,
useMeasurementValueAsConceptMediumTerm = FALSE,
useMeasurementValueAsConceptShortTerm = FALSE,
useObservationAnyTimePrior = FALSE,
useObservationLongTerm = FALSE,
useObservationMediumTerm = FALSE,
useObservationShortTerm = FALSE,
useObservationValueAsConceptAnyTimePrior = FALSE,
useObservationValueAsConceptLongTerm = FALSE,
useObservationValueAsConceptMediumTerm = FALSE,
useObservationValueAsConceptShortTerm = FALSE,
useCharlsonIndex = FALSE,
useDcsi = FALSE,
useChads2 = FALSE,
useChads2Vasc = FALSE,
useHfrs = FALSE,
useDistinctConditionCountLongTerm = FALSE,
useDistinctConditionCountMediumTerm = FALSE,
useDistinctConditionCountShortTerm = FALSE,
useDistinctIngredientCountLongTerm = FALSE,
useDistinctIngredientCountMediumTerm = FALSE,
useDistinctIngredientCountShortTerm = FALSE,
useDistinctProcedureCountLongTerm = FALSE,
useDistinctProcedureCountMediumTerm = FALSE,
useDistinctProcedureCountShortTerm = FALSE,
useDistinctMeasurementCountLongTerm = FALSE,
useDistinctMeasurementCountMediumTerm = FALSE,
useDistinctMeasurementCountShortTerm = FALSE,
useDistinctObservationCountLongTerm = FALSE,
useDistinctObservationCountMediumTerm = FALSE,
useDistinctObservationCountShortTerm = FALSE,
useVisitCountLongTerm = FALSE,
useVisitCountMediumTerm = FALSE,
useVisitCountShortTerm = FALSE,
useVisitConceptCountLongTerm = FALSE,
useVisitConceptCountMediumTerm = FALSE,
useVisitConceptCountShortTerm = FALSE,
longTermStartDays = -365,
mediumTermStartDays = -180,
shortTermStartDays = -30,
endDays = 0,
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) |
useDemographicsPriorObservationTime |
Number of continuous days of observation time preceding the index date. (analysis ID 8) |
useDemographicsPostObservationTime |
Number of continuous days of observation time following the index date. (analysis ID 9) |
useDemographicsTimeInCohort |
Number of days of observation time during cohort period. (analysis ID 10) |
useDemographicsIndexYearMonth |
Both calendar year and month of the index date in a single variable. (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) |
useConditionOccurrenceAnyTimePrior |
One covariate per condition in the condition_occurrence table starting any time prior to index. (analysis ID 101) |
useConditionOccurrenceLongTerm |
One covariate per condition in the condition_occurrence table starting in the long term window. (analysis ID 102) |
useConditionOccurrenceMediumTerm |
One covariate per condition in the condition_occurrence table starting in the medium term window. (analysis ID 103) |
useConditionOccurrenceShortTerm |
One covariate per condition in the condition_occurrence table starting in the short term window. (analysis ID 104) |
useConditionOccurrencePrimaryInpatientAnyTimePrior |
One covariate per condition observed as a primary diagnosis in an inpatient setting in the condition_occurrence table starting any time prior to index. (analysis ID 105) |
useConditionOccurrencePrimaryInpatientLongTerm |
One covariate per condition observed as a primary diagnosis in an inpatient setting in the condition_occurrence table starting in the long term window. (analysis ID 106) |
useConditionOccurrencePrimaryInpatientMediumTerm |
One covariate per condition observed as a primary diagnosis in an inpatient setting in the condition_occurrence table starting in the medium term window. (analysis ID 107) |
useConditionOccurrencePrimaryInpatientShortTerm |
One covariate per condition observed as a primary diagnosis in an inpatient setting in the condition_occurrence table starting in the short term window. (analysis ID 108) |
useConditionEraAnyTimePrior |
One covariate per condition in the condition_era table overlapping with any time prior to index. (analysis ID 201) |
useConditionEraLongTerm |
One covariate per condition in the condition_era table overlapping with any part of the long term window. (analysis ID 202) |
useConditionEraMediumTerm |
One covariate per condition in the condition_era table overlapping with any part of the medium term window. (analysis ID 203) |
useConditionEraShortTerm |
One covariate per condition in the condition_era table overlapping with any part of the short term window. (analysis ID 204) |
useConditionEraOverlapping |
One covariate per condition in the condition_era table overlapping with the end of the risk window. (analysis ID 205) |
useConditionEraStartLongTerm |
One covariate per condition in the condition_era table starting in the long term window. (analysis ID 206) |
useConditionEraStartMediumTerm |
One covariate per condition in the condition_era table starting in the medium term window. (analysis ID 207) |
useConditionEraStartShortTerm |
One covariate per condition in the condition_era table starting in the short term window. (analysis ID 208) |
useConditionGroupEraAnyTimePrior |
One covariate per condition era rolled up to groups in the condition_era table overlapping with any time prior to index. (analysis ID 209) |
useConditionGroupEraLongTerm |
One covariate per condition era rolled up to groups in the condition_era table overlapping with any part of the long term window. (analysis ID 210) |
useConditionGroupEraMediumTerm |
One covariate per condition era rolled up to groups in the condition_era table overlapping with any part of the medium term window. (analysis ID 211) |
useConditionGroupEraShortTerm |
One covariate per condition era rolled up to groups in the condition_era table overlapping with any part of the short term window. (analysis ID 212) |
useConditionGroupEraOverlapping |
One covariate per condition era rolled up to groups in the condition_era table overlapping with the end of the risk window. (analysis ID 213) |
useConditionGroupEraStartLongTerm |
One covariate per condition era rolled up to groups in the condition_era table starting in the long term window. (analysis ID 214) |
useConditionGroupEraStartMediumTerm |
One covariate per condition era rolled up to groups in the condition_era table starting in the medium term window. (analysis ID 215) |
useConditionGroupEraStartShortTerm |
One covariate per condition era rolled up to groups in the condition_era table starting in the short term window. (analysis ID 216) |
useDrugExposureAnyTimePrior |
One covariate per drug in the drug_exposure table starting any time prior to index. (analysis ID 301) |
useDrugExposureLongTerm |
One covariate per drug in the drug_exposure table starting in the long term window. (analysis ID 302) |
useDrugExposureMediumTerm |
One covariate per drug in the drug_exposure table starting in the medium term window. (analysis ID 303) |
useDrugExposureShortTerm |
One covariate per drug in the drug_exposure table starting in the short term window. (analysis ID 304) |
useDrugEraAnyTimePrior |
One covariate per drug in the drug_era table overlapping with any time prior to index. (analysis ID 401) |
useDrugEraLongTerm |
One covariate per drug in the drug_era table overlapping with any part of the long term window. (analysis ID 402) |
useDrugEraMediumTerm |
One covariate per drug in the drug_era table overlapping with any part of the medium term window. (analysis ID 403) |
useDrugEraShortTerm |
One covariate per drug in the drug_era table overlapping with any part of the short term window. (analysis ID 404) |
useDrugEraOverlapping |
One covariate per drug in the drug_era table overlapping with the end of the risk window. (analysis ID 405) |
useDrugEraStartLongTerm |
One covariate per drug in the drug_era table starting in the long term window. (analysis ID 406) |
useDrugEraStartMediumTerm |
One covariate per drug in the drug_era table starting in the medium term window. (analysis ID 407) |
useDrugEraStartShortTerm |
One covariate per drug in the drug_era table starting in the short term window. (analysis ID 408) |
useDrugGroupEraAnyTimePrior |
One covariate per drug rolled up to ATC groups in the drug_era table overlapping with any time prior to index. (analysis ID 409) |
useDrugGroupEraLongTerm |
One covariate per drug rolled up to ATC groups in the drug_era table overlapping with any part of the long term window. (analysis ID 410) |
useDrugGroupEraMediumTerm |
One covariate per drug rolled up to ATC groups in the drug_era table overlapping with any part of the medium term window. (analysis ID 411) |
useDrugGroupEraShortTerm |
One covariate per drug rolled up to ATC groups in the drug_era table overlapping with any part of the short term window. (analysis ID 412) |
useDrugGroupEraOverlapping |
One covariate per drug rolled up to ATC groups in the drug_era table overlapping with the end of the risk window. (analysis ID 413) |
useDrugGroupEraStartLongTerm |
One covariate per drug rolled up to ATC groups in the drug_era table starting in the long term window. (analysis ID 414) |
useDrugGroupEraStartMediumTerm |
One covariate per drug rolled up to ATC groups in the drug_era table starting in the medium term window. (analysis ID 415) |
useDrugGroupEraStartShortTerm |
One covariate per drug rolled up to ATC groups in the drug_era table starting in the short term window. (analysis ID 416) |
useProcedureOccurrenceAnyTimePrior |
One covariate per procedure in the procedure_occurrence table any time prior to index. (analysis ID 501) |
useProcedureOccurrenceLongTerm |
One covariate per procedure in the procedure_occurrence table in the long term window. (analysis ID 502) |
useProcedureOccurrenceMediumTerm |
One covariate per procedure in the procedure_occurrence table in the medium term window. (analysis ID 503) |
useProcedureOccurrenceShortTerm |
One covariate per procedure in the procedure_occurrence table in the short term window. (analysis ID 504) |
useDeviceExposureAnyTimePrior |
One covariate per device in the device exposure table starting any time prior to index. (analysis ID 601) |
useDeviceExposureLongTerm |
One covariate per device in the device exposure table starting in the long term window. (analysis ID 602) |
useDeviceExposureMediumTerm |
One covariate per device in the device exposure table starting in the medium term window. (analysis ID 603) |
useDeviceExposureShortTerm |
One covariate per device in the device exposure table starting in the short term window. (analysis ID 604) |
useMeasurementAnyTimePrior |
One covariate per measurement in the measurement table any time prior to index. (analysis ID 701) |
useMeasurementLongTerm |
One covariate per measurement in the measurement table in the long term window. (analysis ID 702) |
useMeasurementMediumTerm |
One covariate per measurement in the measurement table in the medium term window. (analysis ID 703) |
useMeasurementShortTerm |
One covariate per measurement in the measurement table in the short term window. (analysis ID 704) |
useMeasurementValueAnyTimePrior |
One covariate containing the value per measurement-unit combination any time prior to index. (analysis ID 705) |
useMeasurementValueLongTerm |
One covariate containing the value per measurement-unit combination in the long term window. (analysis ID 706) |
useMeasurementValueMediumTerm |
One covariate containing the value per measurement-unit combination in the medium term window. (analysis ID 707) |
useMeasurementValueShortTerm |
One covariate containing the value per measurement-unit combination in the short term window. (analysis ID 708) |
useMeasurementRangeGroupAnyTimePrior |
Covariates indicating whether measurements are below, within, or above normal range any time prior to index. (analysis ID 709) |
useMeasurementRangeGroupLongTerm |
Covariates indicating whether measurements are below, within, or above normal range in the long term window. (analysis ID 710) |
useMeasurementRangeGroupMediumTerm |
Covariates indicating whether measurements are below, within, or above normal range in the medium term window. (analysis ID 711) |
useMeasurementRangeGroupShortTerm |
Covariates indicating whether measurements are below, within, or above normal range in the short term window. (analysis ID 712) |
useMeasurementValueAsConceptAnyTimePrior |
One covariate per measurement-value concept combination any time prior to index. (analysis ID 713) |
useMeasurementValueAsConceptLongTerm |
One covariate per measurement-value concept combination in the long term window. (analysis ID 714) |
useMeasurementValueAsConceptMediumTerm |
One covariate per measurement-value concept combination in the medium term window. (analysis ID 715) |
useMeasurementValueAsConceptShortTerm |
One covariate per measurement-value concept combination in the short term window. (analysis ID 716) |
useObservationAnyTimePrior |
One covariate per observation in the observation table any time prior to index. (analysis ID 801) |
useObservationLongTerm |
One covariate per observation in the observation table in the long term window. (analysis ID 802) |
useObservationMediumTerm |
One covariate per observation in the observation table in the medium term window. (analysis ID 803) |
useObservationShortTerm |
One covariate per observation in the observation table in the short term window. (analysis ID 804) |
useObservationValueAsConceptAnyTimePrior |
One covariate per observation-value concept combination any time prior to index. (analysis ID 805) |
useObservationValueAsConceptLongTerm |
One covariate per observation-value concept combination in the long term window. (analysis ID 806) |
useObservationValueAsConceptMediumTerm |
One covariate per observation-value concept combination in the medium term window. (analysis ID 807) |
useObservationValueAsConceptShortTerm |
One covariate per observation-value concept combination in the short term window. (analysis ID 808) |
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) |
useDistinctConditionCountLongTerm |
The number of distinct condition concepts observed in the long term window. (analysis ID 905) |
useDistinctConditionCountMediumTerm |
The number of distinct condition concepts observed in the medium term window. (analysis ID 906) |
useDistinctConditionCountShortTerm |
The number of distinct condition concepts observed in the short term window. (analysis ID 907) |
useDistinctIngredientCountLongTerm |
The number of distinct ingredients observed in the long term window. (analysis ID 908) |
useDistinctIngredientCountMediumTerm |
The number of distinct ingredients observed in the medium term window. (analysis ID 909) |
useDistinctIngredientCountShortTerm |
The number of distinct ingredients observed in the short term window. (analysis ID 910) |
useDistinctProcedureCountLongTerm |
The number of distinct procedures observed in the long term window. (analysis ID 911) |
useDistinctProcedureCountMediumTerm |
The number of distinct procedures observed in the medium term window. (analysis ID 912) |
useDistinctProcedureCountShortTerm |
The number of distinct procedures observed in the short term window. (analysis ID 913) |
useDistinctMeasurementCountLongTerm |
The number of distinct measurements observed in the long term window. (analysis ID 914) |
useDistinctMeasurementCountMediumTerm |
The number of distinct measurements observed in the medium term window. (analysis ID 915) |
useDistinctMeasurementCountShortTerm |
The number of distinct measurements observed in the short term window. (analysis ID 916) |
useDistinctObservationCountLongTerm |
The number of distinct observations observed in the long term window. (analysis ID 917) |
useDistinctObservationCountMediumTerm |
The number of distinct observations observed in the medium term window. (analysis ID 918) |
useDistinctObservationCountShortTerm |
The number of distinct observations observed in the short term window. (analysis ID 919) |
useVisitCountLongTerm |
The number of visits observed in the long term window. (analysis ID 920) |
useVisitCountMediumTerm |
The number of visits observed in the medium term window. (analysis ID 921) |
useVisitCountShortTerm |
The number of visits observed in the short term window. (analysis ID 922) |
useVisitConceptCountLongTerm |
The number of visits observed in the long term window, stratified by visit concept ID. (analysis ID 923) |
useVisitConceptCountMediumTerm |
The number of visits observed in the medium term window, stratified by visit concept ID. (analysis ID 924) |
useVisitConceptCountShortTerm |
The number of visits observed in the short term window, stratified by visit concept ID. (analysis ID 925) |
longTermStartDays |
What is the start day (relative to the index date) of the long-term window? |
mediumTermStartDays |
What is the start day (relative to the index date) of the medium-term window? |
shortTermStartDays |
What is the start day (relative to the index date) of the short-term window? |
endDays |
What is the end day (relative to the index date) of the window? |
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 <- createCovariateSettings(
useDemographicsGender = TRUE,
useDemographicsAge = FALSE,
useDemographicsAgeGroup = TRUE,
useDemographicsRace = TRUE,
useDemographicsEthnicity = TRUE,
useDemographicsIndexYear = TRUE,
useDemographicsIndexMonth = TRUE,
useDemographicsPriorObservationTime = FALSE,
useDemographicsPostObservationTime = FALSE,
useDemographicsTimeInCohort = FALSE,
useDemographicsIndexYearMonth = FALSE,
useCareSiteId = FALSE,
useConditionOccurrenceAnyTimePrior = FALSE,
useConditionOccurrenceLongTerm = FALSE,
useConditionOccurrenceMediumTerm = FALSE,
useConditionOccurrenceShortTerm = FALSE,
useConditionOccurrencePrimaryInpatientAnyTimePrior = FALSE,
useConditionOccurrencePrimaryInpatientLongTerm = FALSE,
useConditionOccurrencePrimaryInpatientMediumTerm = FALSE,
useConditionOccurrencePrimaryInpatientShortTerm = FALSE,
useConditionEraAnyTimePrior = FALSE,
useConditionEraLongTerm = FALSE,
useConditionEraMediumTerm = FALSE,
useConditionEraShortTerm = FALSE,
useConditionEraOverlapping = FALSE,
useConditionEraStartLongTerm = FALSE,
useConditionEraStartMediumTerm = FALSE,
useConditionEraStartShortTerm = FALSE,
useConditionGroupEraAnyTimePrior = FALSE,
useConditionGroupEraLongTerm = TRUE,
useConditionGroupEraMediumTerm = FALSE,
useConditionGroupEraShortTerm = TRUE,
useConditionGroupEraOverlapping = FALSE,
useConditionGroupEraStartLongTerm = FALSE,
useConditionGroupEraStartMediumTerm = FALSE,
useConditionGroupEraStartShortTerm = FALSE,
useDrugExposureAnyTimePrior = FALSE,
useDrugExposureLongTerm = FALSE,
useDrugExposureMediumTerm = FALSE,
useDrugExposureShortTerm = FALSE,
useDrugEraAnyTimePrior = FALSE,
useDrugEraLongTerm = FALSE,
useDrugEraMediumTerm = FALSE,
useDrugEraShortTerm = FALSE,
useDrugEraOverlapping = FALSE,
useDrugEraStartLongTerm = FALSE,
useDrugEraStartMediumTerm = FALSE,
useDrugEraStartShortTerm = FALSE,
useDrugGroupEraAnyTimePrior = FALSE,
useDrugGroupEraLongTerm = TRUE,
useDrugGroupEraMediumTerm = FALSE,
useDrugGroupEraShortTerm = TRUE,
useDrugGroupEraOverlapping = TRUE,
useDrugGroupEraStartLongTerm = FALSE,
useDrugGroupEraStartMediumTerm = FALSE,
useDrugGroupEraStartShortTerm = FALSE,
useProcedureOccurrenceAnyTimePrior = FALSE,
useProcedureOccurrenceLongTerm = TRUE,
useProcedureOccurrenceMediumTerm = FALSE,
useProcedureOccurrenceShortTerm = TRUE,
useDeviceExposureAnyTimePrior = FALSE,
useDeviceExposureLongTerm = TRUE,
useDeviceExposureMediumTerm = FALSE,
useDeviceExposureShortTerm = TRUE,
useMeasurementAnyTimePrior = FALSE,
useMeasurementLongTerm = TRUE,
useMeasurementMediumTerm = FALSE,
useMeasurementShortTerm = TRUE,
useMeasurementValueAnyTimePrior = FALSE,
useMeasurementValueLongTerm = FALSE,
useMeasurementValueMediumTerm = FALSE,
useMeasurementValueShortTerm = FALSE,
useMeasurementRangeGroupAnyTimePrior = FALSE,
useMeasurementRangeGroupLongTerm = TRUE,
useMeasurementRangeGroupMediumTerm = FALSE,
useMeasurementRangeGroupShortTerm = TRUE,
useMeasurementValueAsConceptAnyTimePrior = FALSE,
useMeasurementValueAsConceptLongTerm = TRUE,
useMeasurementValueAsConceptMediumTerm = FALSE,
useMeasurementValueAsConceptShortTerm = TRUE,
useObservationAnyTimePrior = FALSE,
useObservationLongTerm = TRUE,
useObservationMediumTerm = FALSE,
useObservationShortTerm = TRUE,
useObservationValueAsConceptAnyTimePrior = FALSE,
useObservationValueAsConceptLongTerm = TRUE,
useObservationValueAsConceptMediumTerm = FALSE,
useObservationValueAsConceptShortTerm = TRUE,
useCharlsonIndex = TRUE,
useDcsi = TRUE,
useChads2 = TRUE,
useChads2Vasc = TRUE,
useHfrs = FALSE,
useDistinctConditionCountLongTerm = FALSE,
useDistinctConditionCountMediumTerm = FALSE,
useDistinctConditionCountShortTerm = FALSE,
useDistinctIngredientCountLongTerm = FALSE,
useDistinctIngredientCountMediumTerm = FALSE,
useDistinctIngredientCountShortTerm = FALSE,
useDistinctProcedureCountLongTerm = FALSE,
useDistinctProcedureCountMediumTerm = FALSE,
useDistinctProcedureCountShortTerm = FALSE,
useDistinctMeasurementCountLongTerm = FALSE,
useDistinctMeasurementCountMediumTerm = FALSE,
useDistinctMeasurementCountShortTerm = FALSE,
useDistinctObservationCountLongTerm = FALSE,
useDistinctObservationCountMediumTerm = FALSE,
useDistinctObservationCountShortTerm = FALSE,
useVisitCountLongTerm = FALSE,
useVisitCountMediumTerm = FALSE,
useVisitCountShortTerm = FALSE,
useVisitConceptCountLongTerm = FALSE,
useVisitConceptCountMediumTerm = FALSE,
useVisitConceptCountShortTerm = FALSE,
longTermStartDays = -365,
mediumTermStartDays = -180,
shortTermStartDays = -30,
endDays = 0,
includedCovariateConceptIds = c(),
addDescendantsToInclude = FALSE,
excludedCovariateConceptIds = c(),
addDescendantsToExclude = FALSE,
includedCovariateIds = c()
)
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