Nothing
# View coverage for this file using
# library(testthat); library(FeatureExtraction)
# covr::file_report(covr::file_coverage("R/DefaultTemporalSequenceCovariateSettings.R", "tests/testthat/test-GetCovariatesTemporalSequence.R"))
test_that("createTemporalSequenceCovariateSettings correctly sets list", {
settings <- createTemporalSequenceCovariateSettings(
useDemographicsGender = T,
useConditionEraGroupStart = T,
useDrugEraStart = T,
timePart = "month",
timeInterval = 1,
sequenceEndDay = -1,
sequenceStartDay = -365 * 5
)
testthat::expect_equal(settings$temporalSequence, T)
testthat::expect_equal(settings$temporal, F)
testthat::expect_equal(sum(c("DemographicsGender", "ConditionEraGroupStart", "DrugEraStart") %in% names(settings)), 3)
testthat::expect_equal(sum(c("DemographicsAge", "ConditionEraStart", "DrugEraGroupStart") %in% names(settings)), 0)
testthat::expect_equal(settings$timePart, "month")
testthat::expect_equal(settings$timeInterval, 1)
testthat::expect_equal(settings$sequenceEndDay, -1)
testthat::expect_equal(settings$sequenceStartDay, -365 * 5)
testthat::expect_equal(class(settings), "covariateSettings")
})
test_that("createTemporalSequenceCovariateSettings correctly sets function", {
settings <- createTemporalSequenceCovariateSettings(
useDemographicsGender = T,
useConditionEraGroupStart = T,
useDrugEraStart = T,
timePart = "month",
timeInterval = 1,
sequenceEndDay = -1,
sequenceStartDay = -365 * 5
)
testthat::expect_equal(attr(settings, "fun"), "getDbDefaultCovariateData")
})
# check extraction
test_that("getDbCovariateData works with createTemporalSequenceCovariateSettings", {
skip_if_not(dbms == "sqlite" && exists("eunomiaConnection"))
covSet <- createTemporalSequenceCovariateSettings(
useDemographicsGender = T,
useDemographicsAge = T,
useDemographicsRace = T,
useDemographicsEthnicity = T,
useDemographicsAgeGroup = T,
useConditionEraGroupStart = T,
useDrugEraStart = T,
timePart = "month",
timeInterval = 1,
sequenceEndDay = -1,
sequenceStartDay = -365 * 5
)
result <- getDbCovariateData(
connection = eunomiaConnection,
cdmDatabaseSchema = "main",
cohortTable = "cohort",
cohortIds = c(1),
covariateSettings = covSet
)
expect_true(is(result, "CovariateData"))
# check timeId is 59 or less
expect_true(max(as.data.frame(result$covariates)$timeId, na.rm = T) <= 60)
})
# Check backwards compatibility
test_that("Temporal Covariate Settings are backwards compatible", {
skip_if_not(dbms == "sqlite" && exists("eunomiaConnection"))
# Temporal covariate settings created previously will not have
# the temporalSequence property
covSet <- FeatureExtraction::createDefaultTemporalCovariateSettings()
covSet$temporalSequence <- NULL
result <- getDbCovariateData(
connection = eunomiaConnection,
cdmDatabaseSchema = "main",
cohortTable = "cohort",
cohortIds = c(1),
covariateSettings = covSet
)
expect_true(is(result, "CovariateData"))
})
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