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# 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 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 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 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 useDrugEraGroupStart One covariate per drug rolled up to ATC groups in
#' the drug_era table starting in the time window.
#' (analysis ID 403)
#' @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 useObservation One covariate per observation in the observation
#' table in the time window. (analysis ID 801)
#' @param timePart The interval scale ('DAY', 'MONTH', 'YEAR')
#' @param timeInterval Fixed interval length for timeId using the 'timePart' scale. For example, a 'timePart' of DAY with
#' 'timeInterval' 30 has timeIds where timeId 1 is day 0 to day 29, timeId 2 is day 30 to day 59, etc.
#' @param sequenceEndDay What is the end day (relative to the
#' index date) of the data extraction?
#' @param sequenceStartDay What is the start day (relative to the
#' index date) of the data extraction?
#' @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 <- createTemporalSequenceCovariateSettings(
#' useDemographicsGender = TRUE,
#' useDemographicsAge = FALSE,
#' useDemographicsAgeGroup = TRUE,
#' useDemographicsRace = TRUE,
#' useDemographicsEthnicity = TRUE,
#' useDemographicsIndexYear = TRUE,
#' useDemographicsIndexMonth = TRUE,
#' useConditionOccurrence = FALSE,
#' useConditionOccurrencePrimaryInpatient = FALSE,
#' useConditionEraStart = FALSE,
#' useConditionEraGroupStart = FALSE,
#' useDrugExposure = FALSE,
#' useDrugEraStart = FALSE,
#' useDrugEraGroupStart = FALSE,
#' useProcedureOccurrence = TRUE,
#' useDeviceExposure = TRUE,
#' useMeasurement = TRUE,
#' useMeasurementValue = FALSE,
#' useObservation = TRUE,
#' timePart = "DAY",
#' timeInterval = 1,
#' sequenceEndDay = -1,
#' sequenceStartDay = -730,
#' includedCovariateConceptIds = c(),
#' addDescendantsToInclude = FALSE,
#' excludedCovariateConceptIds = c(),
#' addDescendantsToExclude = FALSE,
#' includedCovariateIds = c()
#' )
#'
#' @export
createTemporalSequenceCovariateSettings <- function(useDemographicsGender = FALSE,
useDemographicsAge = FALSE,
useDemographicsAgeGroup = FALSE,
useDemographicsRace = FALSE,
useDemographicsEthnicity = FALSE,
useDemographicsIndexYear = FALSE,
useDemographicsIndexMonth = FALSE,
useConditionOccurrence = FALSE,
useConditionOccurrencePrimaryInpatient = FALSE,
useConditionEraStart = FALSE,
useConditionEraGroupStart = FALSE,
useDrugExposure = FALSE,
useDrugEraStart = FALSE,
useDrugEraGroupStart = FALSE,
useProcedureOccurrence = FALSE,
useDeviceExposure = FALSE,
useMeasurement = FALSE,
useMeasurementValue = FALSE,
useObservation = FALSE,
timePart = "month",
timeInterval = 1,
sequenceEndDay = -1,
sequenceStartDay = -730,
includedCovariateConceptIds = c(),
addDescendantsToInclude = FALSE,
excludedCovariateConceptIds = c(),
addDescendantsToExclude = FALSE,
includedCovariateIds = c()) {
covariateSettings <- list(
temporal = FALSE,
temporalSequence = TRUE
)
formalNames <- names(formals(createTemporalSequenceCovariateSettings))
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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