R/DefaultCovariateSettings.R

In OHDSI/PheValuator: Rapid Phenotype Evaluation

# Copyright 2022 Observational Health Data Sciences and Informatics
#
# This file is part of PheValuator
#
# 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.

#' Create the default covariate settings
#'
#' @description
#' Create the default covariate settings for acute or chronic diseases
#'
#' @details
#' Function to create the default covariate settings for acute or chronic diseases
#'
#' @param excludedCovariateConceptIds   A list of conceptIds to exclude from featureExtraction.  These
#'                                      should include all concept_ids that were used to define the
#'                                      xSpec model (default=NULL)
#' @param includedCovariateIds          A list of covariate IDs that should be restricted to.
#' @param includedCovariateConceptIds   A list of covariate concept IDs that should be restricted to.
#' @param addDescendantsToExclude       Should descendants of excluded concepts also be excluded?
#'                                      (default=FALSE)
#' @param startDayWindow1              The day to start time window 1 for feature extraction
#' @param endDayWindow1                The day to end time window 1 for feature extraction
#' @param startDayWindow2              The day to start time window 2 for feature extraction
#' @param endDayWindow2                The day to end time window 2 for feature extraction
#' @param startDayWindow3              The day to start time window 3 for feature extraction
#' @param endDayWindow3                The day to end time window 3 for feature extraction #'
#'
#' @export
createDefaultCovariateSettings <- function(excludedCovariateConceptIds = c(),
                                           includedCovariateIds = c(),
                                           includedCovariateConceptIds = c(),
                                           addDescendantsToExclude = FALSE,
                                           startDayWindow1 = 0,
                                           endDayWindow1 = 9999,
                                           startDayWindow2 = NULL,
                                           endDayWindow2 = NULL,
                                           startDayWindow3 = NULL,
                                           endDayWindow3 = NULL) {
  covariateSettings1 <- FeatureExtraction::createCovariateSettings(
    useDemographicsGender = TRUE,
    useDemographicsAgeGroup = TRUE,
    useDemographicsRace = TRUE,
    useDemographicsEthnicity = TRUE,
    useConditionGroupEraLongTerm = TRUE,
    useDrugGroupEraLongTerm = TRUE,
    useProcedureOccurrenceLongTerm = TRUE,
    useDeviceExposureLongTerm = TRUE,
    useMeasurementLongTerm = TRUE,
    useMeasurementValueLongTerm = TRUE,
    useMeasurementRangeGroupLongTerm = TRUE,
    useObservationLongTerm = TRUE,
    useDistinctConditionCountLongTerm = TRUE,
    useDistinctIngredientCountLongTerm = TRUE,
    useDistinctProcedureCountLongTerm = TRUE,
    useDistinctMeasurementCountLongTerm = TRUE,
    useVisitCountLongTerm = TRUE,
    useVisitConceptCountLongTerm = TRUE,
    longTermStartDays = startDayWindow1,
    shortTermStartDays = startDayWindow1,
    mediumTermStartDays = startDayWindow1,
    endDays = endDayWindow1,
    includedCovariateConceptIds = c(includedCovariateConceptIds),
    addDescendantsToInclude = addDescendantsToExclude,
    excludedCovariateConceptIds = excludedCovariateConceptIds,
    addDescendantsToExclude = addDescendantsToExclude,
    includedCovariateIds = c(includedCovariateIds)
  )

  if (!(is.null(startDayWindow2))) {
    covariateSettings2 <- FeatureExtraction::createCovariateSettings(
      useConditionGroupEraShortTerm = TRUE,
      useDrugGroupEraShortTerm = TRUE,
      useProcedureOccurrenceShortTerm = TRUE,
      useDeviceExposureShortTerm = TRUE,
      useMeasurementShortTerm = TRUE,
      useMeasurementValueShortTerm = TRUE,
      useMeasurementRangeGroupShortTerm = TRUE,
      useObservationShortTerm = TRUE,
      useDistinctConditionCountShortTerm = TRUE,
      useDistinctIngredientCountShortTerm = TRUE,
      useDistinctProcedureCountShortTerm = TRUE,
      useDistinctMeasurementCountShortTerm = TRUE,
      useVisitCountShortTerm = TRUE,
      useVisitConceptCountShortTerm = TRUE,
      longTermStartDays = startDayWindow2,
      shortTermStartDays = startDayWindow2,
      mediumTermStartDays = startDayWindow2,
      endDays = endDayWindow2,
      includedCovariateConceptIds = c(includedCovariateConceptIds),
      addDescendantsToInclude = addDescendantsToExclude,
      excludedCovariateConceptIds = excludedCovariateConceptIds,
      addDescendantsToExclude = addDescendantsToExclude,
      includedCovariateIds = c(includedCovariateIds)
    )
  }

  if (!(is.null(startDayWindow3))) {
    covariateSettings3 <- FeatureExtraction::createCovariateSettings(
      useConditionGroupEraMediumTerm = TRUE,
      useDrugGroupEraMediumTerm = TRUE,
      useProcedureOccurrenceMediumTerm = TRUE,
      useDeviceExposureMediumTerm = TRUE,
      useMeasurementMediumTerm = TRUE,
      useMeasurementValueMediumTerm = TRUE,
      useMeasurementRangeGroupMediumTerm = TRUE,
      useObservationMediumTerm = TRUE,
      useDistinctConditionCountMediumTerm = TRUE,
      useDistinctIngredientCountMediumTerm = TRUE,
      useDistinctProcedureCountMediumTerm = TRUE,
      useDistinctMeasurementCountMediumTerm = TRUE,
      useVisitCountMediumTerm = TRUE,
      useVisitConceptCountMediumTerm = TRUE,
      longTermStartDays = startDayWindow3,
      shortTermStartDays = startDayWindow3,
      mediumTermStartDays = startDayWindow3, endDays = endDayWindow3,
      includedCovariateConceptIds = c(includedCovariateConceptIds),
      addDescendantsToInclude = addDescendantsToExclude,
      excludedCovariateConceptIds = excludedCovariateConceptIds,
      addDescendantsToExclude = addDescendantsToExclude,
      includedCovariateIds = c(includedCovariateIds)
    )
  }

  if (is.null(startDayWindow1)) {
    stop("The first time window must not be null")
  } else if (is.null(startDayWindow2) & is.null(startDayWindow3)) {
    covariateSettings <- list(covariateSettings1)
  } else if (!(is.null(startDayWindow2)) & is.null(startDayWindow3)) {
    covariateSettings <- list(covariateSettings1, covariateSettings2)
  } else if (!(is.null(startDayWindow3)) & is.null(startDayWindow2)) {
    covariateSettings <- list(covariateSettings1, covariateSettings3)
  } else {
    covariateSettings <- list(covariateSettings1, covariateSettings2, covariateSettings3)
  }

  return(covariateSettings)
}