R/DefaultTemporalCovariateSettings.R
In OHDSI/FeatureExtraction: Generating Features for a Cohort
Defines functions
createTemporalCovariateSettings
Documented in
createTemporalCovariateSettings
# 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 days of observation time preceding the
#' index date. (analysis ID 8)
#' @param useDemographicsPostObservationTime Number of days of observation time preceding the
#' index date. (analysis ID 9)
#' @param useDemographicsTimeInCohort Number of days of observation time preceding the
#' index date. (analysis ID 10)
#' @param useDemographicsIndexYearMonth Calendar month of the index date. (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 useConditionOccurrence One covariate per condition in the
#' condition_occurrence table starting in the time
#' window. (analysis ID 101)
#' @param useConditionOccurrencePrimaryInpatient One covariate per condition observed as a primary
#' diagnosis in an inpatient setting in the
#' condition_occurrence table starting in the time
#' window. (analysis ID 102)
#' @param useConditionEraStart One covariate per condition in the condition_era
#' table starting in the time window. (analysis ID 201)
#' @param useConditionEraOverlap One covariate per condition in the condition_era
#' table overlapping with any part of the time window.
#' (analysis ID 202)
#' @param useConditionEraGroupStart One covariate per condition era rolled up to SNOMED
#' groups in the condition_era table starting in the
#' time window. (analysis ID 203)
#' @param useConditionEraGroupOverlap One covariate per condition era rolled up to SNOMED
#' groups in the condition_era table overlapping with
#' any part of the time window. (analysis ID 204)
#' @param useDrugExposure One covariate per drug in the drug_exposure table
#' starting in the time window. (analysis ID 301)
#' @param useDrugEraStart One covariate per drug in the drug_era table
#' starting in the time window. (analysis ID 401)
#' @param useDrugEraOverlap One covariate per drug in the drug_era table
#' overlapping with any part of the time window.
#' (analysis ID 402)
#' @param useDrugEraGroupStart One covariate per drug rolled up to ATC groups in
#' the drug_era table starting in the time window.
#' (analysis ID 403)
#' @param useDrugEraGroupOverlap One covariate per drug rolled up to ATC groups in
#' the drug_era table overlapping with any part of
#' the time window. (analysis ID 404)
#' @param useProcedureOccurrence One covariate per procedure in the
#' procedure_occurrence table in the time window.
#' (analysis ID 501)
#' @param useDeviceExposure One covariate per device in the device exposure
#' table starting in the timewindow. (analysis ID 601)
#' @param useMeasurement One covariate per measurement in the measurement
#' table in the time window. (analysis ID 701)
#' @param useMeasurementValue One covariate containing the value per
#' measurement-unit combination in the time window. If
#' multiple values are found, the last is taken.
#' (analysis ID 702)
#' @param useMeasurementRangeGroup Covariates indicating whether measurements are
#' below, within, or above normal range within the time
#' period. (analysis ID 703)
#' @param useObservation One covariate per observation in the observation
#' table in the time window. (analysis ID 801)
#' @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 useDistinctConditionCount The number of distinct condition concepts observed
#' in the time window. (analysis ID 905)
#' @param useDistinctIngredientCount The number of distinct ingredients observed in the
#' time window. (analysis ID 906)
#' @param useDistinctProcedureCount The number of distinct procedures observed in the
#' time window. (analysis ID 907)
#' @param useDistinctMeasurementCount The number of distinct measurements observed in the
#' time window. (analysis ID 908)
#' @param useDistinctObservationCount The number of distinct observations in the time
#' window. (analysis ID 909)
#' @param useVisitCount The number of visits observed in the time window.
#' (analysis ID 910)
#' @param useVisitConceptCount The number of visits observed in the time window,
#' stratified by visit concept ID. (analysis ID 911)
#' @param temporalStartDays A list of integers representing the start of a time
#' period, relative to the index date. 0 indicates the
#' index date, -1 indicates the day before the index
#' date, etc. The start day is included in the time
#' period.
#' @param temporalEndDays A list of integers representing the end of a time
#' period, relative to the index date. 0 indicates the
#' index date, -1 indicates the day before the index
#' date, etc. The end day is included in the time
#' period.
#' @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 <- createTemporalCovariateSettings(
#' useDemographicsGender = TRUE,
#' useDemographicsAge = FALSE,
#' useDemographicsAgeGroup = TRUE,
#' useDemographicsRace = TRUE,
#' useDemographicsEthnicity = TRUE,
#' useDemographicsIndexYear = TRUE,
#' useDemographicsIndexMonth = TRUE,
#' useDemographicsPriorObservationTime = FALSE,
#' useDemographicsPostObservationTime = FALSE,
#' useDemographicsTimeInCohort = FALSE,
#' useDemographicsIndexYearMonth = FALSE,
#' useCareSiteId = FALSE,
#' useConditionOccurrence = FALSE,
#' useConditionOccurrencePrimaryInpatient = FALSE,
#' useConditionEraStart = FALSE,
#' useConditionEraOverlap = FALSE,
#' useConditionEraGroupStart = FALSE,
#' useConditionEraGroupOverlap = TRUE,
#' useDrugExposure = FALSE,
#' useDrugEraStart = FALSE,
#' useDrugEraOverlap = FALSE,
#' useDrugEraGroupStart = FALSE,
#' useDrugEraGroupOverlap = TRUE,
#' useProcedureOccurrence = TRUE,
#' useDeviceExposure = TRUE,
#' useMeasurement = TRUE,
#' useMeasurementValue = FALSE,
#' useMeasurementRangeGroup = TRUE,
#' useObservation = TRUE,
#' useCharlsonIndex = TRUE,
#' useDcsi = TRUE,
#' useChads2 = TRUE,
#' useChads2Vasc = TRUE,
#' useHfrs = FALSE,
#' useDistinctConditionCount = FALSE,
#' useDistinctIngredientCount = FALSE,
#' useDistinctProcedureCount = FALSE,
#' useDistinctMeasurementCount = FALSE,
#' useDistinctObservationCount = FALSE,
#' useVisitCount = FALSE,
#' useVisitConceptCount = FALSE,
#' temporalStartDays = -365:-1,
#' temporalEndDays = -365:-1,
#' includedCovariateConceptIds = c(),
#' addDescendantsToInclude = FALSE,
#' excludedCovariateConceptIds = c(),
#' addDescendantsToExclude = FALSE,
#' includedCovariateIds = c()
#' )
#'
#' @export
createTemporalCovariateSettings <- 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,
useConditionOccurrence = FALSE,
useConditionOccurrencePrimaryInpatient = FALSE,
useConditionEraStart = FALSE,
useConditionEraOverlap = FALSE,
useConditionEraGroupStart = FALSE,
useConditionEraGroupOverlap = FALSE,
useDrugExposure = FALSE,
useDrugEraStart = FALSE,
useDrugEraOverlap = FALSE,
useDrugEraGroupStart = FALSE,
useDrugEraGroupOverlap = FALSE,
useProcedureOccurrence = FALSE,
useDeviceExposure = FALSE,
useMeasurement = FALSE,
useMeasurementValue = FALSE,
useMeasurementRangeGroup = FALSE,
useObservation = FALSE,
useCharlsonIndex = FALSE,
useDcsi = FALSE,
useChads2 = FALSE,
useChads2Vasc = FALSE,
useHfrs = FALSE,
useDistinctConditionCount = FALSE,
useDistinctIngredientCount = FALSE,
useDistinctProcedureCount = FALSE,
useDistinctMeasurementCount = FALSE,
useDistinctObservationCount = FALSE,
useVisitCount = FALSE,
useVisitConceptCount = FALSE,
temporalStartDays = -365:-1,
temporalEndDays = -365:-1,
includedCovariateConceptIds = c(),
addDescendantsToInclude = FALSE,
excludedCovariateConceptIds = c(),
addDescendantsToExclude = FALSE,
includedCovariateIds = c()) {
covariateSettings <- list(
temporal = TRUE,
temporalSequence = FALSE
)
formalNames <- names(formals(createTemporalCovariateSettings))
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 April 22, 2024, 10:24 p.m.
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Defines functions createTemporalCovariateSettings
Documented in createTemporalCovariateSettings
# 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 days of observation time preceding the
#' index date. (analysis ID 8)
#' @param useDemographicsPostObservationTime Number of days of observation time preceding the
#' index date. (analysis ID 9)
#' @param useDemographicsTimeInCohort Number of days of observation time preceding the
#' index date. (analysis ID 10)
#' @param useDemographicsIndexYearMonth Calendar month of the index date. (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 useConditionOccurrence One covariate per condition in the
#' condition_occurrence table starting in the time
#' window. (analysis ID 101)
#' @param useConditionOccurrencePrimaryInpatient One covariate per condition observed as a primary
#' diagnosis in an inpatient setting in the
#' condition_occurrence table starting in the time
#' window. (analysis ID 102)
#' @param useConditionEraStart One covariate per condition in the condition_era
#' table starting in the time window. (analysis ID 201)
#' @param useConditionEraOverlap One covariate per condition in the condition_era
#' table overlapping with any part of the time window.
#' (analysis ID 202)
#' @param useConditionEraGroupStart One covariate per condition era rolled up to SNOMED
#' groups in the condition_era table starting in the
#' time window. (analysis ID 203)
#' @param useConditionEraGroupOverlap One covariate per condition era rolled up to SNOMED
#' groups in the condition_era table overlapping with
#' any part of the time window. (analysis ID 204)
#' @param useDrugExposure One covariate per drug in the drug_exposure table
#' starting in the time window. (analysis ID 301)
#' @param useDrugEraStart One covariate per drug in the drug_era table
#' starting in the time window. (analysis ID 401)
#' @param useDrugEraOverlap One covariate per drug in the drug_era table
#' overlapping with any part of the time window.
#' (analysis ID 402)
#' @param useDrugEraGroupStart One covariate per drug rolled up to ATC groups in
#' the drug_era table starting in the time window.
#' (analysis ID 403)
#' @param useDrugEraGroupOverlap One covariate per drug rolled up to ATC groups in
#' the drug_era table overlapping with any part of
#' the time window. (analysis ID 404)
#' @param useProcedureOccurrence One covariate per procedure in the
#' procedure_occurrence table in the time window.
#' (analysis ID 501)
#' @param useDeviceExposure One covariate per device in the device exposure
#' table starting in the timewindow. (analysis ID 601)
#' @param useMeasurement One covariate per measurement in the measurement
#' table in the time window. (analysis ID 701)
#' @param useMeasurementValue One covariate containing the value per
#' measurement-unit combination in the time window. If
#' multiple values are found, the last is taken.
#' (analysis ID 702)
#' @param useMeasurementRangeGroup Covariates indicating whether measurements are
#' below, within, or above normal range within the time
#' period. (analysis ID 703)
#' @param useObservation One covariate per observation in the observation
#' table in the time window. (analysis ID 801)
#' @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 useDistinctConditionCount The number of distinct condition concepts observed
#' in the time window. (analysis ID 905)
#' @param useDistinctIngredientCount The number of distinct ingredients observed in the
#' time window. (analysis ID 906)
#' @param useDistinctProcedureCount The number of distinct procedures observed in the
#' time window. (analysis ID 907)
#' @param useDistinctMeasurementCount The number of distinct measurements observed in the
#' time window. (analysis ID 908)
#' @param useDistinctObservationCount The number of distinct observations in the time
#' window. (analysis ID 909)
#' @param useVisitCount The number of visits observed in the time window.
#' (analysis ID 910)
#' @param useVisitConceptCount The number of visits observed in the time window,
#' stratified by visit concept ID. (analysis ID 911)
#' @param temporalStartDays A list of integers representing the start of a time
#' period, relative to the index date. 0 indicates the
#' index date, -1 indicates the day before the index
#' date, etc. The start day is included in the time
#' period.
#' @param temporalEndDays A list of integers representing the end of a time
#' period, relative to the index date. 0 indicates the
#' index date, -1 indicates the day before the index
#' date, etc. The end day is included in the time
#' period.
#' @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 <- createTemporalCovariateSettings(
#' useDemographicsGender = TRUE,
#' useDemographicsAge = FALSE,
#' useDemographicsAgeGroup = TRUE,
#' useDemographicsRace = TRUE,
#' useDemographicsEthnicity = TRUE,
#' useDemographicsIndexYear = TRUE,
#' useDemographicsIndexMonth = TRUE,
#' useDemographicsPriorObservationTime = FALSE,
#' useDemographicsPostObservationTime = FALSE,
#' useDemographicsTimeInCohort = FALSE,
#' useDemographicsIndexYearMonth = FALSE,
#' useCareSiteId = FALSE,
#' useConditionOccurrence = FALSE,
#' useConditionOccurrencePrimaryInpatient = FALSE,
#' useConditionEraStart = FALSE,
#' useConditionEraOverlap = FALSE,
#' useConditionEraGroupStart = FALSE,
#' useConditionEraGroupOverlap = TRUE,
#' useDrugExposure = FALSE,
#' useDrugEraStart = FALSE,
#' useDrugEraOverlap = FALSE,
#' useDrugEraGroupStart = FALSE,
#' useDrugEraGroupOverlap = TRUE,
#' useProcedureOccurrence = TRUE,
#' useDeviceExposure = TRUE,
#' useMeasurement = TRUE,
#' useMeasurementValue = FALSE,
#' useMeasurementRangeGroup = TRUE,
#' useObservation = TRUE,
#' useCharlsonIndex = TRUE,
#' useDcsi = TRUE,
#' useChads2 = TRUE,
#' useChads2Vasc = TRUE,
#' useHfrs = FALSE,
#' useDistinctConditionCount = FALSE,
#' useDistinctIngredientCount = FALSE,
#' useDistinctProcedureCount = FALSE,
#' useDistinctMeasurementCount = FALSE,
#' useDistinctObservationCount = FALSE,
#' useVisitCount = FALSE,
#' useVisitConceptCount = FALSE,
#' temporalStartDays = -365:-1,
#' temporalEndDays = -365:-1,
#' includedCovariateConceptIds = c(),
#' addDescendantsToInclude = FALSE,
#' excludedCovariateConceptIds = c(),
#' addDescendantsToExclude = FALSE,
#' includedCovariateIds = c()
#' )
#'
#' @export
createTemporalCovariateSettings <- 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,
useConditionOccurrence = FALSE,
useConditionOccurrencePrimaryInpatient = FALSE,
useConditionEraStart = FALSE,
useConditionEraOverlap = FALSE,
useConditionEraGroupStart = FALSE,
useConditionEraGroupOverlap = FALSE,
useDrugExposure = FALSE,
useDrugEraStart = FALSE,
useDrugEraOverlap = FALSE,
useDrugEraGroupStart = FALSE,
useDrugEraGroupOverlap = FALSE,
useProcedureOccurrence = FALSE,
useDeviceExposure = FALSE,
useMeasurement = FALSE,
useMeasurementValue = FALSE,
useMeasurementRangeGroup = FALSE,
useObservation = FALSE,
useCharlsonIndex = FALSE,
useDcsi = FALSE,
useChads2 = FALSE,
useChads2Vasc = FALSE,
useHfrs = FALSE,
useDistinctConditionCount = FALSE,
useDistinctIngredientCount = FALSE,
useDistinctProcedureCount = FALSE,
useDistinctMeasurementCount = FALSE,
useDistinctObservationCount = FALSE,
useVisitCount = FALSE,
useVisitConceptCount = FALSE,
temporalStartDays = -365:-1,
temporalEndDays = -365:-1,
includedCovariateConceptIds = c(),
addDescendantsToInclude = FALSE,
excludedCovariateConceptIds = c(),
addDescendantsToExclude = FALSE,
includedCovariateIds = c()) {
covariateSettings <- list(
temporal = TRUE,
temporalSequence = FALSE
)
formalNames <- names(formals(createTemporalCovariateSettings))
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)
}
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