tests/testthat/test-GetCovariatesTemporalSequence.R

In OHDSI/FeatureExtraction: Generating Features for a Cohort

# 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,
    useMeasurement = T,
    useMeasurementValue = 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_on_cran()
  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"))
})