R/CreateEvaluationCohort.R
In OHDSI/PheValuator: Rapid Phenotype Evaluation
Defines functions
createEvaluationCohort
Documented in
createEvaluationCohort
# 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 evaluation cohort
#'
#' @description
#' Create the evaluation cohort
#'
#' @details
#' Fits a diagnostic prediction model, and uses it to create an evaluation cohort with
#' probabilities for the health outcome of interest.
#'
#' @param connectionDetails connectionDetails created using the function
#' createConnectionDetails in the DatabaseConnector package.
#' @param oracleTempSchema DEPRECATED: use \code{tempEmulationSchema} instead.
#' @param tempEmulationSchema Some database platforms like Oracle and Impala do not truly support temp tables. To
#' emulate temp tables, provide a schema with write privileges where temp tables
#' can be created.
#' @param phenotype Name of the phenotype for analysis
#' @param analysisName Name of the analysis
#' @param runDateTime Starting date and time of the PheValuator run
#' @param databaseId Name of the database in the analysis
#' @param xSpecCohortId The number of the "extremely specific (xSpec)" cohort
#' definition id in the cohort table (for noisy positives).
#' @param daysFromxSpec Number of days allowed from xSpec condition until analyzed visit
#' @param xSensCohortId The number of the "extremely sensitive (xSens)" cohort
#' definition id in the cohort table (for noisy negatives).
#' @param prevalenceCohortId The number of the cohort definition id to determine the
#' disease prevalence.
#' @param caseCohortId The number of the cohort definition id to determine cases in the evaluation cohort
#' @param caseFirstOccurrenceOnly Set to true if only the first occurrence per subject in the case cohort is to be used
#' @param xSpecCohortSize The recommended xSpec sample size to use in model (default = 5000)
#' @param xSpecCohortSize The recommended xSpec sample size to use in model (default = NULL)
#' @param cdmDatabaseSchema The name of the database schema that contains the OMOP CDM
#' instance. Requires read permissions to this database. On SQL
#' Server, this should specifiy both the database and the
#' schema, so for example 'cdm_instance.dbo'.
#' @param cohortDatabaseSchema The name of the database schema that is the location where
#' the cohort data used to define the at risk cohort is
#' available. Requires read permissions to this database.
#' @param cohortTable The tablename that contains the at risk cohort. The
#' expectation is cohortTable has format of COHORT table:
#' cohort_concept_id, SUBJECT_ID, COHORT_START_DATE,
#' COHORT_END_DATE.
#' @param workDatabaseSchema The name of the database schema that is the location where
#' a table can be created and afterwards removed.
#' Requires write permissions to this database.
#' @param covariateSettings A covariateSettings object as generated using
#' createCovariateSettings().
#' @param modelPopulationCohortId The number of the cohort to be used as a base population for
#' the model. If set to 0, the entire database population will be
#' used.
#' @param modelPopulationCohortIdStartDay The number of days relative to the mainPopulationCohortId
#' cohort start date to begin including visits.
#' @param modelPopulationCohortIdEndDay The number of days relative to the mainPopulationCohortId
#' cohort start date to end including visits.
#' @param inclusionEvaluationCohortId The number of the cohort of the population to be used to designate which visits
#' are eligible to be in the evaluation cohort
#' @param inclusionEvaluationDaysFromStart The number of days from the cohort start date of the inclusionEvaluationCohortId
#' to start eligible included visits
#' @param inclusionEvaluationDaysFromEnd The number of days from the cohort start date of the inclusionEvaluationCohortId
#' to end eligible included visits
#' @param duringInclusionEvaluationOnly Only include visits that are within the cohort start and end dates
#' @param exclusionEvaluationCohortId The number of the cohort of the population to be used to designate which visits
#' are NOT eligible to be in the evaluation cohort
#' @param exclusionEvaluationDaysFromStart The number of days from the cohort start date of the exclusionEvaluationCohortId
#' to start ineligible included visits
#' @param exclusionEvaluationDaysFromEnd The number of days from the cohort start date of the exclusionEvaluationCohortId
#' to end ineligible included visits
#' @param priorModelToUse folder where a previously developed model to use in analysis will be found
#' @param minimumOffsetFromStart Minimum number of days to offset for the analysis visit from the start of the observation period
#' @param minimumOffsetFromEnd Minimum number of days to offset for the analysis visit from the end of the observation period
#' @param modelBaseSampleSize The number of non-xSpec subjects to include in the model
#' @param baseSampleSize The maximum number of subjects in the evaluation cohort.
#' @param lowerAgeLimit The lower age for subjects in the model.
#' @param upperAgeLimit The upper age for subjects in the model.
#' @param visitLength The minimum length of index visit for acute outcomes.
#' @param visitType The concept_id for the visit type.
#' @param gender The gender(s) to be included.
#' @param race The race(s) to be included.
#' @param ethnicity The ethnicity(s) to be included.
#' @param startDate The starting date for including subjects in the model.
#' @param endDate The ending date for including subjects in the model.
#' @param falsePositiveNegativeSubjects Number of subjects to include for evaluating false positives and negatives
#' @param cdmVersion The CDM version of the database.
#' @param outFolder The folder where the output files will be written.
#' @param exportFolder The folder where the csv output files will be written.
#' @param modelId A string used to generate the file names for this model.
#' @param evaluationCohortId A string used to generate the file names for this evaluation cohort.
#' @param excludeModelFromEvaluation Should subjects used in the model be excluded from the evaluation cohort?
#' @param randomVisitTable Table stored in work directory with pre-selected random visits in format of visit_occurrence table
#' @param removeSubjectsWithFutureDates For buggy data with data in the future: ignore subjects with
#' dates in the future?
#' @param saveEvaluationCohortPlpData Should the large PLP file for the evaluation cohort be saved? To be
#' used for debugging purposes.
#'
#' @export
createEvaluationCohort <- function(connectionDetails,
oracleTempSchema = NULL,
tempEmulationSchema = getOption("sqlRenderTempEmulationSchema"),
phenotype,
analysisName,
runDateTime,
databaseId,
xSpecCohortId,
daysFromxSpec = 0,
xSensCohortId,
prevalenceCohortId,
caseCohortId,
caseFirstOccurrenceOnly,
xSpecCohortSize = 5000,
cdmDatabaseSchema,
cohortDatabaseSchema,
cohortTable,
workDatabaseSchema,
covariateSettings = createDefaultCovariateSettings(
excludedCovariateConceptIds = c(),
addDescendantsToExclude = TRUE
),
modelPopulationCohortId = 0,
modelPopulationCohortIdStartDay = 0,
modelPopulationCohortIdEndDay = 0,
inclusionEvaluationCohortId = 0,
inclusionEvaluationDaysFromStart = 0,
inclusionEvaluationDaysFromEnd = 0,
duringInclusionEvaluationOnly = FALSE,
exclusionEvaluationCohortId = 0,
exclusionEvaluationDaysFromStart = 0,
exclusionEvaluationDaysFromEnd = 0,
priorModelToUse = NULL,
minimumOffsetFromStart = 365,
minimumOffsetFromEnd = 365,
modelBaseSampleSize = 25000,
baseSampleSize = 2e+06,
lowerAgeLimit = 0,
upperAgeLimit = 120,
visitLength = 0,
visitType = c(9201, 9202, 9203, 262, 581477),
gender = c(8507, 8532),
race = 0,
ethnicity = 0,
startDate = "19001010",
endDate = "21000101",
falsePositiveNegativeSubjects = 10,
cdmVersion = "5",
outFolder = getwd(),
exportFolder,
modelId = "main",
evaluationCohortId = "main",
excludeModelFromEvaluation = FALSE,
randomVisitTable = "",
removeSubjectsWithFutureDates = TRUE,
saveEvaluationCohortPlpData = FALSE) {
if (length(connectionDetails) == 0) {
stop("Must supply a connection string")
}
if (xSpecCohortId == "") {
stop("Must have an xSpec cohort id (e.g., 1234)")
}
if (xSensCohortId == "") {
stop("Must have an xSens cohort id (e.g., 1235)")
}
if (prevalenceCohortId == "") {
stop("Must have an prevalence cohort (prevCohort) (e.g., 1235)")
}
if (cdmDatabaseSchema == "") {
stop(".Must have a defined CDM schema (e.g., \"YourCDM.YourCDMSchema\")")
}
if (cohortDatabaseSchema == "") {
stop(".Must have a defined Cohort schema ((e.g., \"YourCDM.YourCohortSchema\")")
}
if (cohortTable == "") {
stop(".Must have a defined Cohort table (e.g., \"cohort\")")
}
if (workDatabaseSchema == "") {
stop(".Must have a defined Out Database schema (e.g., \"scratch.dbo\")")
}
if (!is.null(oracleTempSchema) && oracleTempSchema != "") {
warning("The 'oracleTempSchema' argument is deprecated. Use 'tempEmulationSchema' instead.")
tempEmulationSchema <- oracleTempSchema
}
if (!file.exists(outFolder)) {
dir.create(outFolder, recursive = TRUE)
}
start <- Sys.time()
.createPhenotypeModel(
connectionDetails = connectionDetails,
phenotype = phenotype,
analysisName = analysisName,
runDateTime = runDateTime,
databaseId = databaseId,
cdmDatabaseSchema = cdmDatabaseSchema,
cohortDatabaseSchema = cohortDatabaseSchema,
cohortTable = cohortTable,
workDatabaseSchema = workDatabaseSchema,
tempEmulationSchema = tempEmulationSchema,
xSpecCohortId = xSpecCohortId,
daysFromxSpec = daysFromxSpec,
xSensCohortId = xSensCohortId,
prevalenceCohortId = prevalenceCohortId,
xSpecCohortSize = xSpecCohortSize,
covariateSettings = covariateSettings,
modelPopulationCohortId = modelPopulationCohortId,
modelPopulationCohortIdStartDay = modelPopulationCohortIdStartDay,
modelPopulationCohortIdEndDay = modelPopulationCohortIdEndDay,
priorModelToUse = priorModelToUse,
modelBaseSampleSize = modelBaseSampleSize,
minimumOffsetFromStart = minimumOffsetFromStart,
minimumOffsetFromEnd = minimumOffsetFromEnd,
lowerAgeLimit = lowerAgeLimit,
upperAgeLimit = upperAgeLimit,
visitLength = visitLength,
visitType = c(visitType),
gender = gender,
race = race,
ethnicity = ethnicity,
startDate = startDate,
endDate = endDate,
removeSubjectsWithFutureDates = removeSubjectsWithFutureDates,
cdmVersion = cdmVersion,
outFolder = outFolder,
exportFolder = exportFolder,
randomVisitTable = randomVisitTable,
modelId = modelId
)
.createEvaluationCohort(
connectionDetails = connectionDetails,
phenotype = phenotype,
analysisName = analysisName,
runDateTime = runDateTime,
databaseId = databaseId,
xSpecCohortId = xSpecCohortId,
xSensCohortId = xSensCohortId,
prevalenceCohortId = prevalenceCohortId,
caseCohortId = caseCohortId,
caseFirstOccurrenceOnly = caseFirstOccurrenceOnly,
cdmDatabaseSchema = cdmDatabaseSchema,
cohortDatabaseSchema = cohortDatabaseSchema,
cohortTable = cohortTable,
workDatabaseSchema = workDatabaseSchema,
tempEmulationSchema = tempEmulationSchema,
covariateSettings = covariateSettings,
inclusionEvaluationCohortId = inclusionEvaluationCohortId,
inclusionEvaluationDaysFromStart = inclusionEvaluationDaysFromStart,
inclusionEvaluationDaysFromEnd = inclusionEvaluationDaysFromEnd,
duringInclusionEvaluationOnly = duringInclusionEvaluationOnly,
exclusionEvaluationCohortId = exclusionEvaluationCohortId,
exclusionEvaluationDaysFromStart = exclusionEvaluationDaysFromStart,
exclusionEvaluationDaysFromEnd = exclusionEvaluationDaysFromEnd,
minimumOffsetFromStart = minimumOffsetFromStart,
minimumOffsetFromEnd = minimumOffsetFromEnd,
baseSampleSize = baseSampleSize,
lowerAgeLimit = lowerAgeLimit,
upperAgeLimit = upperAgeLimit,
visitLength = visitLength,
visitType = c(visitType),
gender = gender,
race = race,
ethnicity = ethnicity,
startDate = startDate,
endDate = endDate,
falsePositiveNegativeSubjects = falsePositiveNegativeSubjects,
cdmVersion = cdmVersion,
outFolder = outFolder,
exportFolder = exportFolder,
modelId = modelId,
evaluationCohortId = evaluationCohortId,
excludeModelFromEvaluation = excludeModelFromEvaluation,
randomVisitTable = randomVisitTable,
savePlpData = saveEvaluationCohortPlpData
)
delta <- Sys.time() - start
ParallelLogger::logInfo("Creating evaluation cohort took ", signif(delta, 3), " ", attr(delta, "units"))
}
OHDSI/PheValuator documentation built on Jan. 28, 2024, 4:05 a.m.
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Defines functions createEvaluationCohort
Documented in createEvaluationCohort
# 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 evaluation cohort
#'
#' @description
#' Create the evaluation cohort
#'
#' @details
#' Fits a diagnostic prediction model, and uses it to create an evaluation cohort with
#' probabilities for the health outcome of interest.
#'
#' @param connectionDetails connectionDetails created using the function
#' createConnectionDetails in the DatabaseConnector package.
#' @param oracleTempSchema DEPRECATED: use \code{tempEmulationSchema} instead.
#' @param tempEmulationSchema Some database platforms like Oracle and Impala do not truly support temp tables. To
#' emulate temp tables, provide a schema with write privileges where temp tables
#' can be created.
#' @param phenotype Name of the phenotype for analysis
#' @param analysisName Name of the analysis
#' @param runDateTime Starting date and time of the PheValuator run
#' @param databaseId Name of the database in the analysis
#' @param xSpecCohortId The number of the "extremely specific (xSpec)" cohort
#' definition id in the cohort table (for noisy positives).
#' @param daysFromxSpec Number of days allowed from xSpec condition until analyzed visit
#' @param xSensCohortId The number of the "extremely sensitive (xSens)" cohort
#' definition id in the cohort table (for noisy negatives).
#' @param prevalenceCohortId The number of the cohort definition id to determine the
#' disease prevalence.
#' @param caseCohortId The number of the cohort definition id to determine cases in the evaluation cohort
#' @param caseFirstOccurrenceOnly Set to true if only the first occurrence per subject in the case cohort is to be used
#' @param xSpecCohortSize The recommended xSpec sample size to use in model (default = 5000)
#' @param xSpecCohortSize The recommended xSpec sample size to use in model (default = NULL)
#' @param cdmDatabaseSchema The name of the database schema that contains the OMOP CDM
#' instance. Requires read permissions to this database. On SQL
#' Server, this should specifiy both the database and the
#' schema, so for example 'cdm_instance.dbo'.
#' @param cohortDatabaseSchema The name of the database schema that is the location where
#' the cohort data used to define the at risk cohort is
#' available. Requires read permissions to this database.
#' @param cohortTable The tablename that contains the at risk cohort. The
#' expectation is cohortTable has format of COHORT table:
#' cohort_concept_id, SUBJECT_ID, COHORT_START_DATE,
#' COHORT_END_DATE.
#' @param workDatabaseSchema The name of the database schema that is the location where
#' a table can be created and afterwards removed.
#' Requires write permissions to this database.
#' @param covariateSettings A covariateSettings object as generated using
#' createCovariateSettings().
#' @param modelPopulationCohortId The number of the cohort to be used as a base population for
#' the model. If set to 0, the entire database population will be
#' used.
#' @param modelPopulationCohortIdStartDay The number of days relative to the mainPopulationCohortId
#' cohort start date to begin including visits.
#' @param modelPopulationCohortIdEndDay The number of days relative to the mainPopulationCohortId
#' cohort start date to end including visits.
#' @param inclusionEvaluationCohortId The number of the cohort of the population to be used to designate which visits
#' are eligible to be in the evaluation cohort
#' @param inclusionEvaluationDaysFromStart The number of days from the cohort start date of the inclusionEvaluationCohortId
#' to start eligible included visits
#' @param inclusionEvaluationDaysFromEnd The number of days from the cohort start date of the inclusionEvaluationCohortId
#' to end eligible included visits
#' @param duringInclusionEvaluationOnly Only include visits that are within the cohort start and end dates
#' @param exclusionEvaluationCohortId The number of the cohort of the population to be used to designate which visits
#' are NOT eligible to be in the evaluation cohort
#' @param exclusionEvaluationDaysFromStart The number of days from the cohort start date of the exclusionEvaluationCohortId
#' to start ineligible included visits
#' @param exclusionEvaluationDaysFromEnd The number of days from the cohort start date of the exclusionEvaluationCohortId
#' to end ineligible included visits
#' @param priorModelToUse folder where a previously developed model to use in analysis will be found
#' @param minimumOffsetFromStart Minimum number of days to offset for the analysis visit from the start of the observation period
#' @param minimumOffsetFromEnd Minimum number of days to offset for the analysis visit from the end of the observation period
#' @param modelBaseSampleSize The number of non-xSpec subjects to include in the model
#' @param baseSampleSize The maximum number of subjects in the evaluation cohort.
#' @param lowerAgeLimit The lower age for subjects in the model.
#' @param upperAgeLimit The upper age for subjects in the model.
#' @param visitLength The minimum length of index visit for acute outcomes.
#' @param visitType The concept_id for the visit type.
#' @param gender The gender(s) to be included.
#' @param race The race(s) to be included.
#' @param ethnicity The ethnicity(s) to be included.
#' @param startDate The starting date for including subjects in the model.
#' @param endDate The ending date for including subjects in the model.
#' @param falsePositiveNegativeSubjects Number of subjects to include for evaluating false positives and negatives
#' @param cdmVersion The CDM version of the database.
#' @param outFolder The folder where the output files will be written.
#' @param exportFolder The folder where the csv output files will be written.
#' @param modelId A string used to generate the file names for this model.
#' @param evaluationCohortId A string used to generate the file names for this evaluation cohort.
#' @param excludeModelFromEvaluation Should subjects used in the model be excluded from the evaluation cohort?
#' @param randomVisitTable Table stored in work directory with pre-selected random visits in format of visit_occurrence table
#' @param removeSubjectsWithFutureDates For buggy data with data in the future: ignore subjects with
#' dates in the future?
#' @param saveEvaluationCohortPlpData Should the large PLP file for the evaluation cohort be saved? To be
#' used for debugging purposes.
#'
#' @export
createEvaluationCohort <- function(connectionDetails,
oracleTempSchema = NULL,
tempEmulationSchema = getOption("sqlRenderTempEmulationSchema"),
phenotype,
analysisName,
runDateTime,
databaseId,
xSpecCohortId,
daysFromxSpec = 0,
xSensCohortId,
prevalenceCohortId,
caseCohortId,
caseFirstOccurrenceOnly,
xSpecCohortSize = 5000,
cdmDatabaseSchema,
cohortDatabaseSchema,
cohortTable,
workDatabaseSchema,
covariateSettings = createDefaultCovariateSettings(
excludedCovariateConceptIds = c(),
addDescendantsToExclude = TRUE
),
modelPopulationCohortId = 0,
modelPopulationCohortIdStartDay = 0,
modelPopulationCohortIdEndDay = 0,
inclusionEvaluationCohortId = 0,
inclusionEvaluationDaysFromStart = 0,
inclusionEvaluationDaysFromEnd = 0,
duringInclusionEvaluationOnly = FALSE,
exclusionEvaluationCohortId = 0,
exclusionEvaluationDaysFromStart = 0,
exclusionEvaluationDaysFromEnd = 0,
priorModelToUse = NULL,
minimumOffsetFromStart = 365,
minimumOffsetFromEnd = 365,
modelBaseSampleSize = 25000,
baseSampleSize = 2e+06,
lowerAgeLimit = 0,
upperAgeLimit = 120,
visitLength = 0,
visitType = c(9201, 9202, 9203, 262, 581477),
gender = c(8507, 8532),
race = 0,
ethnicity = 0,
startDate = "19001010",
endDate = "21000101",
falsePositiveNegativeSubjects = 10,
cdmVersion = "5",
outFolder = getwd(),
exportFolder,
modelId = "main",
evaluationCohortId = "main",
excludeModelFromEvaluation = FALSE,
randomVisitTable = "",
removeSubjectsWithFutureDates = TRUE,
saveEvaluationCohortPlpData = FALSE) {
if (length(connectionDetails) == 0) {
stop("Must supply a connection string")
}
if (xSpecCohortId == "") {
stop("Must have an xSpec cohort id (e.g., 1234)")
}
if (xSensCohortId == "") {
stop("Must have an xSens cohort id (e.g., 1235)")
}
if (prevalenceCohortId == "") {
stop("Must have an prevalence cohort (prevCohort) (e.g., 1235)")
}
if (cdmDatabaseSchema == "") {
stop(".Must have a defined CDM schema (e.g., \"YourCDM.YourCDMSchema\")")
}
if (cohortDatabaseSchema == "") {
stop(".Must have a defined Cohort schema ((e.g., \"YourCDM.YourCohortSchema\")")
}
if (cohortTable == "") {
stop(".Must have a defined Cohort table (e.g., \"cohort\")")
}
if (workDatabaseSchema == "") {
stop(".Must have a defined Out Database schema (e.g., \"scratch.dbo\")")
}
if (!is.null(oracleTempSchema) && oracleTempSchema != "") {
warning("The 'oracleTempSchema' argument is deprecated. Use 'tempEmulationSchema' instead.")
tempEmulationSchema <- oracleTempSchema
}
if (!file.exists(outFolder)) {
dir.create(outFolder, recursive = TRUE)
}
start <- Sys.time()
.createPhenotypeModel(
connectionDetails = connectionDetails,
phenotype = phenotype,
analysisName = analysisName,
runDateTime = runDateTime,
databaseId = databaseId,
cdmDatabaseSchema = cdmDatabaseSchema,
cohortDatabaseSchema = cohortDatabaseSchema,
cohortTable = cohortTable,
workDatabaseSchema = workDatabaseSchema,
tempEmulationSchema = tempEmulationSchema,
xSpecCohortId = xSpecCohortId,
daysFromxSpec = daysFromxSpec,
xSensCohortId = xSensCohortId,
prevalenceCohortId = prevalenceCohortId,
xSpecCohortSize = xSpecCohortSize,
covariateSettings = covariateSettings,
modelPopulationCohortId = modelPopulationCohortId,
modelPopulationCohortIdStartDay = modelPopulationCohortIdStartDay,
modelPopulationCohortIdEndDay = modelPopulationCohortIdEndDay,
priorModelToUse = priorModelToUse,
modelBaseSampleSize = modelBaseSampleSize,
minimumOffsetFromStart = minimumOffsetFromStart,
minimumOffsetFromEnd = minimumOffsetFromEnd,
lowerAgeLimit = lowerAgeLimit,
upperAgeLimit = upperAgeLimit,
visitLength = visitLength,
visitType = c(visitType),
gender = gender,
race = race,
ethnicity = ethnicity,
startDate = startDate,
endDate = endDate,
removeSubjectsWithFutureDates = removeSubjectsWithFutureDates,
cdmVersion = cdmVersion,
outFolder = outFolder,
exportFolder = exportFolder,
randomVisitTable = randomVisitTable,
modelId = modelId
)
.createEvaluationCohort(
connectionDetails = connectionDetails,
phenotype = phenotype,
analysisName = analysisName,
runDateTime = runDateTime,
databaseId = databaseId,
xSpecCohortId = xSpecCohortId,
xSensCohortId = xSensCohortId,
prevalenceCohortId = prevalenceCohortId,
caseCohortId = caseCohortId,
caseFirstOccurrenceOnly = caseFirstOccurrenceOnly,
cdmDatabaseSchema = cdmDatabaseSchema,
cohortDatabaseSchema = cohortDatabaseSchema,
cohortTable = cohortTable,
workDatabaseSchema = workDatabaseSchema,
tempEmulationSchema = tempEmulationSchema,
covariateSettings = covariateSettings,
inclusionEvaluationCohortId = inclusionEvaluationCohortId,
inclusionEvaluationDaysFromStart = inclusionEvaluationDaysFromStart,
inclusionEvaluationDaysFromEnd = inclusionEvaluationDaysFromEnd,
duringInclusionEvaluationOnly = duringInclusionEvaluationOnly,
exclusionEvaluationCohortId = exclusionEvaluationCohortId,
exclusionEvaluationDaysFromStart = exclusionEvaluationDaysFromStart,
exclusionEvaluationDaysFromEnd = exclusionEvaluationDaysFromEnd,
minimumOffsetFromStart = minimumOffsetFromStart,
minimumOffsetFromEnd = minimumOffsetFromEnd,
baseSampleSize = baseSampleSize,
lowerAgeLimit = lowerAgeLimit,
upperAgeLimit = upperAgeLimit,
visitLength = visitLength,
visitType = c(visitType),
gender = gender,
race = race,
ethnicity = ethnicity,
startDate = startDate,
endDate = endDate,
falsePositiveNegativeSubjects = falsePositiveNegativeSubjects,
cdmVersion = cdmVersion,
outFolder = outFolder,
exportFolder = exportFolder,
modelId = modelId,
evaluationCohortId = evaluationCohortId,
excludeModelFromEvaluation = excludeModelFromEvaluation,
randomVisitTable = randomVisitTable,
savePlpData = saveEvaluationCohortPlpData
)
delta <- Sys.time() - start
ParallelLogger::logInfo("Creating evaluation cohort took ", signif(delta, 3), " ", attr(delta, "units"))
}
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