R/DefaultCovariateSettings.R
In OHDSI/FeatureExtraction: Generating Features for a Cohort
Defines functions
createCovariateSettings
Documented in
createCovariateSettings
# Copyright 2024 Observational Health Data Sciences and Informatics
#
# This file is part of FeatureExtraction
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
# This file has been autogenerated. Do not change by hand.
#' Create covariate settings
#'
#' @details
#' creates an object specifying how covariates should be constructed from data in the CDM model.
#'
#' @param useDemographicsGender Gender of the subject. (analysis ID 1)
#' @param useDemographicsAge Age of the subject on the index date (in
#' years). (analysis ID 2)
#' @param useDemographicsAgeGroup Age of the subject on the index date (in
#' 5 year age groups) (analysis ID 3)
#' @param useDemographicsRace Race of the subject. (analysis ID 4)
#' @param useDemographicsEthnicity Ethnicity of the subject. (analysis ID
#' 5)
#' @param useDemographicsIndexYear Year of the index date. (analysis ID 6)
#' @param useDemographicsIndexMonth Month of the index date. (analysis ID 7)
#' @param useDemographicsPriorObservationTime Number of continuous days of observation
#' time preceding the index date. (analysis
#' ID 8)
#' @param useDemographicsPostObservationTime Number of continuous days of observation
#' time following the index date. (analysis
#' ID 9)
#' @param useDemographicsTimeInCohort Number of days of observation time
#' during cohort period. (analysis ID 10)
#' @param useDemographicsIndexYearMonth Both calendar year and month of the
#' index date in a single variable.
#' (analysis ID 11)
#' @param useCareSiteId Care site associated with the cohort
#' start, pulled from the visit_detail,
#' visit_occurrence, or person table, in
#' that order. (analysis ID 12)
#' @param useConditionOccurrenceAnyTimePrior One covariate per condition in the
#' condition_occurrence table starting any
#' time prior to index. (analysis ID 101)
#' @param useConditionOccurrenceLongTerm One covariate per condition in the
#' condition_occurrence table starting in
#' the long term window. (analysis ID 102)
#' @param useConditionOccurrenceMediumTerm One covariate per condition in the
#' condition_occurrence table starting in
#' the medium term window. (analysis ID
#' 103)
#' @param useConditionOccurrenceShortTerm One covariate per condition in the
#' condition_occurrence table starting in
#' the short term window. (analysis ID 104)
#' @param 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)
#' @param 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)
#' @param 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)
#' @param 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)
#' @param useConditionEraAnyTimePrior One covariate per condition in the
#' condition_era table overlapping with any
#' time prior to index. (analysis ID 201)
#' @param useConditionEraLongTerm One covariate per condition in the
#' condition_era table overlapping with any
#' part of the long term window. (analysis
#' ID 202)
#' @param useConditionEraMediumTerm One covariate per condition in the
#' condition_era table overlapping with any
#' part of the medium term window.
#' (analysis ID 203)
#' @param useConditionEraShortTerm One covariate per condition in the
#' condition_era table overlapping with any
#' part of the short term window. (analysis
#' ID 204)
#' @param useConditionEraOverlapping One covariate per condition in the
#' condition_era table overlapping with the
#' end of the risk window. (analysis ID
#' 205)
#' @param useConditionEraStartLongTerm One covariate per condition in the
#' condition_era table starting in the long
#' term window. (analysis ID 206)
#' @param useConditionEraStartMediumTerm One covariate per condition in the
#' condition_era table starting in the
#' medium term window. (analysis ID 207)
#' @param useConditionEraStartShortTerm One covariate per condition in the
#' condition_era table starting in the
#' short term window. (analysis ID 208)
#' @param 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)
#' @param 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)
#' @param 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)
#' @param 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)
#' @param 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)
#' @param useConditionGroupEraStartLongTerm One covariate per condition era rolled
#' up to groups in the condition_era table
#' starting in the long term window.
#' (analysis ID 214)
#' @param useConditionGroupEraStartMediumTerm One covariate per condition era rolled
#' up to groups in the condition_era table
#' starting in the medium term window.
#' (analysis ID 215)
#' @param useConditionGroupEraStartShortTerm One covariate per condition era rolled
#' up to groups in the condition_era table
#' starting in the short term window.
#' (analysis ID 216)
#' @param useDrugExposureAnyTimePrior One covariate per drug in the
#' drug_exposure table starting any time
#' prior to index. (analysis ID 301)
#' @param useDrugExposureLongTerm One covariate per drug in the
#' drug_exposure table starting in the long
#' term window. (analysis ID 302)
#' @param useDrugExposureMediumTerm One covariate per drug in the
#' drug_exposure table starting in the
#' medium term window. (analysis ID 303)
#' @param useDrugExposureShortTerm One covariate per drug in the
#' drug_exposure table starting in the
#' short term window. (analysis ID 304)
#' @param useDrugEraAnyTimePrior One covariate per drug in the drug_era
#' table overlapping with any time prior to
#' index. (analysis ID 401)
#' @param useDrugEraLongTerm One covariate per drug in the drug_era
#' table overlapping with any part of the
#' long term window. (analysis ID 402)
#' @param useDrugEraMediumTerm One covariate per drug in the drug_era
#' table overlapping with any part of the
#' medium term window. (analysis ID 403)
#' @param useDrugEraShortTerm One covariate per drug in the drug_era
#' table overlapping with any part of the
#' short window. (analysis ID 404)
#' @param useDrugEraOverlapping One covariate per drug in the drug_era
#' table overlapping with the end of the
#' risk window. (analysis ID 405)
#' @param useDrugEraStartLongTerm One covariate per drug in the drug_era
#' table starting in the long term window.
#' (analysis ID 406)
#' @param useDrugEraStartMediumTerm One covariate per drug in the drug_era
#' table starting in the medium term
#' window. (analysis ID 407)
#' @param useDrugEraStartShortTerm One covariate per drug in the drug_era
#' table starting in the long short window.
#' (analysis ID 408)
#' @param 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)
#' @param 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)
#' @param 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)
#' @param 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)
#' @param 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)
#' @param useDrugGroupEraStartLongTerm One covariate per drug rolled up to ATC
#' groups in the drug_era table starting in
#' the long term window. (analysis ID 414)
#' @param useDrugGroupEraStartMediumTerm One covariate per drug rolled up to ATC
#' groups in the drug_era table starting in
#' the medium term window. (analysis ID
#' 415)
#' @param useDrugGroupEraStartShortTerm One covariate per drug rolled up to ATC
#' groups in the drug_era table starting in
#' the short term window. (analysis ID 416)
#' @param useProcedureOccurrenceAnyTimePrior One covariate per procedure in the
#' procedure_occurrence table any time
#' prior to index. (analysis ID 501)
#' @param useProcedureOccurrenceLongTerm One covariate per procedure in the
#' procedure_occurrence table in the long
#' term window. (analysis ID 502)
#' @param useProcedureOccurrenceMediumTerm One covariate per procedure in the
#' procedure_occurrence table in the medium
#' term window. (analysis ID 503)
#' @param useProcedureOccurrenceShortTerm One covariate per procedure in the
#' procedure_occurrence table in the short
#' term window. (analysis ID 504)
#' @param useDeviceExposureAnyTimePrior One covariate per device in the device
#' exposure table starting any time prior
#' to index. (analysis ID 601)
#' @param useDeviceExposureLongTerm One covariate per device in the device
#' exposure table starting in the long term
#' window. (analysis ID 602)
#' @param useDeviceExposureMediumTerm One covariate per device in the device
#' exposure table starting in the medium
#' term window. (analysis ID 603)
#' @param useDeviceExposureShortTerm One covariate per device in the device
#' exposure table starting in the short
#' term window. (analysis ID 604)
#' @param useMeasurementAnyTimePrior One covariate per measurement in the
#' measurement table any time prior to
#' index. (analysis ID 701)
#' @param useMeasurementLongTerm One covariate per measurement in the
#' measurement table in the long term
#' window. (analysis ID 702)
#' @param useMeasurementMediumTerm One covariate per measurement in the
#' measurement table in the medium term
#' window. (analysis ID 703)
#' @param useMeasurementShortTerm One covariate per measurement in the
#' measurement table in the short term
#' window. (analysis ID 704)
#' @param useMeasurementValueAnyTimePrior One covariate containing the value per
#' measurement-unit combination any time
#' prior to index. (analysis ID 705)
#' @param useMeasurementValueLongTerm One covariate containing the value per
#' measurement-unit combination in the long
#' term window. (analysis ID 706)
#' @param useMeasurementValueMediumTerm One covariate containing the value per
#' measurement-unit combination in the
#' medium term window. (analysis ID 707)
#' @param useMeasurementValueShortTerm One covariate containing the value per
#' measurement-unit combination in the
#' short term window. (analysis ID 708)
#' @param useMeasurementRangeGroupAnyTimePrior Covariates indicating whether
#' measurements are below, within, or above
#' normal range any time prior to index.
#' (analysis ID 709)
#' @param useMeasurementRangeGroupLongTerm Covariates indicating whether
#' measurements are below, within, or above
#' normal range in the long term window.
#' (analysis ID 710)
#' @param useMeasurementRangeGroupMediumTerm Covariates indicating whether
#' measurements are below, within, or above
#' normal range in the medium term window.
#' (analysis ID 711)
#' @param useMeasurementRangeGroupShortTerm Covariates indicating whether
#' measurements are below, within, or above
#' normal range in the short term window.
#' (analysis ID 712)
#' @param useObservationAnyTimePrior One covariate per observation in the
#' observation table any time prior to
#' index. (analysis ID 801)
#' @param useObservationLongTerm One covariate per observation in the
#' observation table in the long term
#' window. (analysis ID 802)
#' @param useObservationMediumTerm One covariate per observation in the
#' observation table in the medium term
#' window. (analysis ID 803)
#' @param useObservationShortTerm One covariate per observation in the
#' observation table in the short term
#' window. (analysis ID 804)
#' @param useCharlsonIndex The Charlson comorbidity index (Romano
#' adaptation) using all conditions prior
#' to the window end. (analysis ID 901)
#' @param useDcsi The Diabetes Comorbidity Severity Index
#' (DCSI) using all conditions prior to the
#' window end. (analysis ID 902)
#' @param useChads2 The CHADS2 score using all conditions
#' prior to the window end. (analysis ID
#' 903)
#' @param useChads2Vasc The CHADS2VASc score using all
#' conditions prior to the window end.
#' (analysis ID 904)
#' @param useHfrs The Hospital Frailty Risk Score score
#' using all conditions prior to the window
#' end. (analysis ID 926)
#' @param useDistinctConditionCountLongTerm The number of distinct condition
#' concepts observed in the long term
#' window. (analysis ID 905)
#' @param useDistinctConditionCountMediumTerm The number of distinct condition
#' concepts observed in the medium term
#' window. (analysis ID 906)
#' @param useDistinctConditionCountShortTerm The number of distinct condition
#' concepts observed in the short term
#' window. (analysis ID 907)
#' @param useDistinctIngredientCountLongTerm The number of distinct ingredients
#' observed in the long term window.
#' (analysis ID 908)
#' @param useDistinctIngredientCountMediumTerm The number of distinct ingredients
#' observed in the medium term window.
#' (analysis ID 909)
#' @param useDistinctIngredientCountShortTerm The number of distinct ingredients
#' observed in the short term window.
#' (analysis ID 910)
#' @param useDistinctProcedureCountLongTerm The number of distinct procedures
#' observed in the long term window.
#' (analysis ID 911)
#' @param useDistinctProcedureCountMediumTerm The number of distinct procedures
#' observed in the medium term window.
#' (analysis ID 912)
#' @param useDistinctProcedureCountShortTerm The number of distinct procedures
#' observed in the short term window.
#' (analysis ID 913)
#' @param useDistinctMeasurementCountLongTerm The number of distinct measurements
#' observed in the long term window.
#' (analysis ID 914)
#' @param useDistinctMeasurementCountMediumTerm The number of distinct measurements
#' observed in the medium term window.
#' (analysis ID 915)
#' @param useDistinctMeasurementCountShortTerm The number of distinct measurements
#' observed in the short term window.
#' (analysis ID 916)
#' @param useDistinctObservationCountLongTerm The number of distinct observations
#' observed in the long term window.
#' (analysis ID 917)
#' @param useDistinctObservationCountMediumTerm The number of distinct observations
#' observed in the medium term window.
#' (analysis ID 918)
#' @param useDistinctObservationCountShortTerm The number of distinct observations
#' observed in the short term window.
#' (analysis ID 919)
#' @param useVisitCountLongTerm The number of visits observed in the
#' long term window. (analysis ID 920)
#' @param useVisitCountMediumTerm The number of visits observed in the
#' medium term window. (analysis ID 921)
#' @param useVisitCountShortTerm The number of visits observed in the
#' short term window. (analysis ID 922)
#' @param useVisitConceptCountLongTerm The number of visits observed in the
#' long term window, stratified by visit
#' concept ID. (analysis ID 923)
#' @param useVisitConceptCountMediumTerm The number of visits observed in the
#' medium term window, stratified by visit
#' concept ID. (analysis ID 924)
#' @param useVisitConceptCountShortTerm The number of visits observed in the
#' short term window, stratified by visit
#' concept ID. (analysis ID 925)
#' @param longTermStartDays What is the start day (relative to the
#' index date) of the long-term window?
#' @param mediumTermStartDays What is the start day (relative to the
#' index date) of the medium-term window?
#' @param shortTermStartDays What is the start day (relative to the
#' index date) of the short-term window?
#' @param endDays What is the end day (relative to the
#' index date) of the window?
#' @param includedCovariateConceptIds A list of concept IDs that should be
#' used to construct covariates.
#' @param addDescendantsToInclude Should descendant concept IDs be added
#' to the list of concepts to include?
#' @param excludedCovariateConceptIds A list of concept IDs that should NOT be
#' used to construct covariates.
#' @param addDescendantsToExclude Should descendant concept IDs be added
#' to the list of concepts to exclude?
#' @param includedCovariateIds A list of covariate IDs that should be
#' restricted to.
#'
#' @return
#' An object of type \code{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 = FALSE,
#' useObservationAnyTimePrior = FALSE,
#' useObservationLongTerm = TRUE,
#' useObservationMediumTerm = FALSE,
#' useObservationShortTerm = 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()
#' )
#'
#' @export
createCovariateSettings <- function(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,
useObservationAnyTimePrior = FALSE,
useObservationLongTerm = FALSE,
useObservationMediumTerm = FALSE,
useObservationShortTerm = 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()) {
covariateSettings <- list(
temporal = FALSE,
temporalSequence = FALSE
)
formalNames <- names(formals(createCovariateSettings))
anyUseTrue <- FALSE
for (name in formalNames) {
value <- get(name)
if (is.null(value)) {
value <- vector()
}
if (grepl("use.*", name)) {
if (value) {
covariateSettings[[sub("use", "", name)]] <- value
anyUseTrue <- TRUE
}
} else {
covariateSettings[[name]] <- value
}
}
if (!anyUseTrue) {
stop("No covariate analysis selected. Must select at least one")
}
attr(covariateSettings, "fun") <- "getDbDefaultCovariateData"
class(covariateSettings) <- "covariateSettings"
return(covariateSettings)
}
OHDSI/FeatureExtraction documentation built on May 2, 2024, 11:30 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions createCovariateSettings
Documented in createCovariateSettings
# Copyright 2024 Observational Health Data Sciences and Informatics
#
# This file is part of FeatureExtraction
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
# This file has been autogenerated. Do not change by hand.
#' Create covariate settings
#'
#' @details
#' creates an object specifying how covariates should be constructed from data in the CDM model.
#'
#' @param useDemographicsGender Gender of the subject. (analysis ID 1)
#' @param useDemographicsAge Age of the subject on the index date (in
#' years). (analysis ID 2)
#' @param useDemographicsAgeGroup Age of the subject on the index date (in
#' 5 year age groups) (analysis ID 3)
#' @param useDemographicsRace Race of the subject. (analysis ID 4)
#' @param useDemographicsEthnicity Ethnicity of the subject. (analysis ID
#' 5)
#' @param useDemographicsIndexYear Year of the index date. (analysis ID 6)
#' @param useDemographicsIndexMonth Month of the index date. (analysis ID 7)
#' @param useDemographicsPriorObservationTime Number of continuous days of observation
#' time preceding the index date. (analysis
#' ID 8)
#' @param useDemographicsPostObservationTime Number of continuous days of observation
#' time following the index date. (analysis
#' ID 9)
#' @param useDemographicsTimeInCohort Number of days of observation time
#' during cohort period. (analysis ID 10)
#' @param useDemographicsIndexYearMonth Both calendar year and month of the
#' index date in a single variable.
#' (analysis ID 11)
#' @param useCareSiteId Care site associated with the cohort
#' start, pulled from the visit_detail,
#' visit_occurrence, or person table, in
#' that order. (analysis ID 12)
#' @param useConditionOccurrenceAnyTimePrior One covariate per condition in the
#' condition_occurrence table starting any
#' time prior to index. (analysis ID 101)
#' @param useConditionOccurrenceLongTerm One covariate per condition in the
#' condition_occurrence table starting in
#' the long term window. (analysis ID 102)
#' @param useConditionOccurrenceMediumTerm One covariate per condition in the
#' condition_occurrence table starting in
#' the medium term window. (analysis ID
#' 103)
#' @param useConditionOccurrenceShortTerm One covariate per condition in the
#' condition_occurrence table starting in
#' the short term window. (analysis ID 104)
#' @param 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)
#' @param 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)
#' @param 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)
#' @param 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)
#' @param useConditionEraAnyTimePrior One covariate per condition in the
#' condition_era table overlapping with any
#' time prior to index. (analysis ID 201)
#' @param useConditionEraLongTerm One covariate per condition in the
#' condition_era table overlapping with any
#' part of the long term window. (analysis
#' ID 202)
#' @param useConditionEraMediumTerm One covariate per condition in the
#' condition_era table overlapping with any
#' part of the medium term window.
#' (analysis ID 203)
#' @param useConditionEraShortTerm One covariate per condition in the
#' condition_era table overlapping with any
#' part of the short term window. (analysis
#' ID 204)
#' @param useConditionEraOverlapping One covariate per condition in the
#' condition_era table overlapping with the
#' end of the risk window. (analysis ID
#' 205)
#' @param useConditionEraStartLongTerm One covariate per condition in the
#' condition_era table starting in the long
#' term window. (analysis ID 206)
#' @param useConditionEraStartMediumTerm One covariate per condition in the
#' condition_era table starting in the
#' medium term window. (analysis ID 207)
#' @param useConditionEraStartShortTerm One covariate per condition in the
#' condition_era table starting in the
#' short term window. (analysis ID 208)
#' @param 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)
#' @param 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)
#' @param 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)
#' @param 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)
#' @param 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)
#' @param useConditionGroupEraStartLongTerm One covariate per condition era rolled
#' up to groups in the condition_era table
#' starting in the long term window.
#' (analysis ID 214)
#' @param useConditionGroupEraStartMediumTerm One covariate per condition era rolled
#' up to groups in the condition_era table
#' starting in the medium term window.
#' (analysis ID 215)
#' @param useConditionGroupEraStartShortTerm One covariate per condition era rolled
#' up to groups in the condition_era table
#' starting in the short term window.
#' (analysis ID 216)
#' @param useDrugExposureAnyTimePrior One covariate per drug in the
#' drug_exposure table starting any time
#' prior to index. (analysis ID 301)
#' @param useDrugExposureLongTerm One covariate per drug in the
#' drug_exposure table starting in the long
#' term window. (analysis ID 302)
#' @param useDrugExposureMediumTerm One covariate per drug in the
#' drug_exposure table starting in the
#' medium term window. (analysis ID 303)
#' @param useDrugExposureShortTerm One covariate per drug in the
#' drug_exposure table starting in the
#' short term window. (analysis ID 304)
#' @param useDrugEraAnyTimePrior One covariate per drug in the drug_era
#' table overlapping with any time prior to
#' index. (analysis ID 401)
#' @param useDrugEraLongTerm One covariate per drug in the drug_era
#' table overlapping with any part of the
#' long term window. (analysis ID 402)
#' @param useDrugEraMediumTerm One covariate per drug in the drug_era
#' table overlapping with any part of the
#' medium term window. (analysis ID 403)
#' @param useDrugEraShortTerm One covariate per drug in the drug_era
#' table overlapping with any part of the
#' short window. (analysis ID 404)
#' @param useDrugEraOverlapping One covariate per drug in the drug_era
#' table overlapping with the end of the
#' risk window. (analysis ID 405)
#' @param useDrugEraStartLongTerm One covariate per drug in the drug_era
#' table starting in the long term window.
#' (analysis ID 406)
#' @param useDrugEraStartMediumTerm One covariate per drug in the drug_era
#' table starting in the medium term
#' window. (analysis ID 407)
#' @param useDrugEraStartShortTerm One covariate per drug in the drug_era
#' table starting in the long short window.
#' (analysis ID 408)
#' @param 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)
#' @param 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)
#' @param 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)
#' @param 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)
#' @param 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)
#' @param useDrugGroupEraStartLongTerm One covariate per drug rolled up to ATC
#' groups in the drug_era table starting in
#' the long term window. (analysis ID 414)
#' @param useDrugGroupEraStartMediumTerm One covariate per drug rolled up to ATC
#' groups in the drug_era table starting in
#' the medium term window. (analysis ID
#' 415)
#' @param useDrugGroupEraStartShortTerm One covariate per drug rolled up to ATC
#' groups in the drug_era table starting in
#' the short term window. (analysis ID 416)
#' @param useProcedureOccurrenceAnyTimePrior One covariate per procedure in the
#' procedure_occurrence table any time
#' prior to index. (analysis ID 501)
#' @param useProcedureOccurrenceLongTerm One covariate per procedure in the
#' procedure_occurrence table in the long
#' term window. (analysis ID 502)
#' @param useProcedureOccurrenceMediumTerm One covariate per procedure in the
#' procedure_occurrence table in the medium
#' term window. (analysis ID 503)
#' @param useProcedureOccurrenceShortTerm One covariate per procedure in the
#' procedure_occurrence table in the short
#' term window. (analysis ID 504)
#' @param useDeviceExposureAnyTimePrior One covariate per device in the device
#' exposure table starting any time prior
#' to index. (analysis ID 601)
#' @param useDeviceExposureLongTerm One covariate per device in the device
#' exposure table starting in the long term
#' window. (analysis ID 602)
#' @param useDeviceExposureMediumTerm One covariate per device in the device
#' exposure table starting in the medium
#' term window. (analysis ID 603)
#' @param useDeviceExposureShortTerm One covariate per device in the device
#' exposure table starting in the short
#' term window. (analysis ID 604)
#' @param useMeasurementAnyTimePrior One covariate per measurement in the
#' measurement table any time prior to
#' index. (analysis ID 701)
#' @param useMeasurementLongTerm One covariate per measurement in the
#' measurement table in the long term
#' window. (analysis ID 702)
#' @param useMeasurementMediumTerm One covariate per measurement in the
#' measurement table in the medium term
#' window. (analysis ID 703)
#' @param useMeasurementShortTerm One covariate per measurement in the
#' measurement table in the short term
#' window. (analysis ID 704)
#' @param useMeasurementValueAnyTimePrior One covariate containing the value per
#' measurement-unit combination any time
#' prior to index. (analysis ID 705)
#' @param useMeasurementValueLongTerm One covariate containing the value per
#' measurement-unit combination in the long
#' term window. (analysis ID 706)
#' @param useMeasurementValueMediumTerm One covariate containing the value per
#' measurement-unit combination in the
#' medium term window. (analysis ID 707)
#' @param useMeasurementValueShortTerm One covariate containing the value per
#' measurement-unit combination in the
#' short term window. (analysis ID 708)
#' @param useMeasurementRangeGroupAnyTimePrior Covariates indicating whether
#' measurements are below, within, or above
#' normal range any time prior to index.
#' (analysis ID 709)
#' @param useMeasurementRangeGroupLongTerm Covariates indicating whether
#' measurements are below, within, or above
#' normal range in the long term window.
#' (analysis ID 710)
#' @param useMeasurementRangeGroupMediumTerm Covariates indicating whether
#' measurements are below, within, or above
#' normal range in the medium term window.
#' (analysis ID 711)
#' @param useMeasurementRangeGroupShortTerm Covariates indicating whether
#' measurements are below, within, or above
#' normal range in the short term window.
#' (analysis ID 712)
#' @param useObservationAnyTimePrior One covariate per observation in the
#' observation table any time prior to
#' index. (analysis ID 801)
#' @param useObservationLongTerm One covariate per observation in the
#' observation table in the long term
#' window. (analysis ID 802)
#' @param useObservationMediumTerm One covariate per observation in the
#' observation table in the medium term
#' window. (analysis ID 803)
#' @param useObservationShortTerm One covariate per observation in the
#' observation table in the short term
#' window. (analysis ID 804)
#' @param useCharlsonIndex The Charlson comorbidity index (Romano
#' adaptation) using all conditions prior
#' to the window end. (analysis ID 901)
#' @param useDcsi The Diabetes Comorbidity Severity Index
#' (DCSI) using all conditions prior to the
#' window end. (analysis ID 902)
#' @param useChads2 The CHADS2 score using all conditions
#' prior to the window end. (analysis ID
#' 903)
#' @param useChads2Vasc The CHADS2VASc score using all
#' conditions prior to the window end.
#' (analysis ID 904)
#' @param useHfrs The Hospital Frailty Risk Score score
#' using all conditions prior to the window
#' end. (analysis ID 926)
#' @param useDistinctConditionCountLongTerm The number of distinct condition
#' concepts observed in the long term
#' window. (analysis ID 905)
#' @param useDistinctConditionCountMediumTerm The number of distinct condition
#' concepts observed in the medium term
#' window. (analysis ID 906)
#' @param useDistinctConditionCountShortTerm The number of distinct condition
#' concepts observed in the short term
#' window. (analysis ID 907)
#' @param useDistinctIngredientCountLongTerm The number of distinct ingredients
#' observed in the long term window.
#' (analysis ID 908)
#' @param useDistinctIngredientCountMediumTerm The number of distinct ingredients
#' observed in the medium term window.
#' (analysis ID 909)
#' @param useDistinctIngredientCountShortTerm The number of distinct ingredients
#' observed in the short term window.
#' (analysis ID 910)
#' @param useDistinctProcedureCountLongTerm The number of distinct procedures
#' observed in the long term window.
#' (analysis ID 911)
#' @param useDistinctProcedureCountMediumTerm The number of distinct procedures
#' observed in the medium term window.
#' (analysis ID 912)
#' @param useDistinctProcedureCountShortTerm The number of distinct procedures
#' observed in the short term window.
#' (analysis ID 913)
#' @param useDistinctMeasurementCountLongTerm The number of distinct measurements
#' observed in the long term window.
#' (analysis ID 914)
#' @param useDistinctMeasurementCountMediumTerm The number of distinct measurements
#' observed in the medium term window.
#' (analysis ID 915)
#' @param useDistinctMeasurementCountShortTerm The number of distinct measurements
#' observed in the short term window.
#' (analysis ID 916)
#' @param useDistinctObservationCountLongTerm The number of distinct observations
#' observed in the long term window.
#' (analysis ID 917)
#' @param useDistinctObservationCountMediumTerm The number of distinct observations
#' observed in the medium term window.
#' (analysis ID 918)
#' @param useDistinctObservationCountShortTerm The number of distinct observations
#' observed in the short term window.
#' (analysis ID 919)
#' @param useVisitCountLongTerm The number of visits observed in the
#' long term window. (analysis ID 920)
#' @param useVisitCountMediumTerm The number of visits observed in the
#' medium term window. (analysis ID 921)
#' @param useVisitCountShortTerm The number of visits observed in the
#' short term window. (analysis ID 922)
#' @param useVisitConceptCountLongTerm The number of visits observed in the
#' long term window, stratified by visit
#' concept ID. (analysis ID 923)
#' @param useVisitConceptCountMediumTerm The number of visits observed in the
#' medium term window, stratified by visit
#' concept ID. (analysis ID 924)
#' @param useVisitConceptCountShortTerm The number of visits observed in the
#' short term window, stratified by visit
#' concept ID. (analysis ID 925)
#' @param longTermStartDays What is the start day (relative to the
#' index date) of the long-term window?
#' @param mediumTermStartDays What is the start day (relative to the
#' index date) of the medium-term window?
#' @param shortTermStartDays What is the start day (relative to the
#' index date) of the short-term window?
#' @param endDays What is the end day (relative to the
#' index date) of the window?
#' @param includedCovariateConceptIds A list of concept IDs that should be
#' used to construct covariates.
#' @param addDescendantsToInclude Should descendant concept IDs be added
#' to the list of concepts to include?
#' @param excludedCovariateConceptIds A list of concept IDs that should NOT be
#' used to construct covariates.
#' @param addDescendantsToExclude Should descendant concept IDs be added
#' to the list of concepts to exclude?
#' @param includedCovariateIds A list of covariate IDs that should be
#' restricted to.
#'
#' @return
#' An object of type \code{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 = FALSE,
#' useObservationAnyTimePrior = FALSE,
#' useObservationLongTerm = TRUE,
#' useObservationMediumTerm = FALSE,
#' useObservationShortTerm = 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()
#' )
#'
#' @export
createCovariateSettings <- function(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,
useObservationAnyTimePrior = FALSE,
useObservationLongTerm = FALSE,
useObservationMediumTerm = FALSE,
useObservationShortTerm = 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()) {
covariateSettings <- list(
temporal = FALSE,
temporalSequence = FALSE
)
formalNames <- names(formals(createCovariateSettings))
anyUseTrue <- FALSE
for (name in formalNames) {
value <- get(name)
if (is.null(value)) {
value <- vector()
}
if (grepl("use.*", name)) {
if (value) {
covariateSettings[[sub("use", "", name)]] <- value
anyUseTrue <- TRUE
}
} else {
covariateSettings[[name]] <- value
}
}
if (!anyUseTrue) {
stop("No covariate analysis selected. Must select at least one")
}
attr(covariateSettings, "fun") <- "getDbDefaultCovariateData"
class(covariateSettings) <- "covariateSettings"
return(covariateSettings)
}
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.