tests/testthat/test-estimateSurvival-branches.R

In OdysseusSurvivalModule: Cohort-Based Single-Event Survival Utilities

test_that("singleEventSurvival supports cox model with and without covariates", {
  df <- data.frame(
    subject_id = 1:16,
    time = c(4, 6, 9, 11, 13, 16, 18, 21, 7, 8, 10, 14, 17, 19, 24, 28),
    status = c(1, 0, 1, 0, 1, 1, 0, 1, 1, 0, 1, 0, 1, 0, 1, 0),
    age_years = c(23, 31, 44, 56, 62, 36, 41, 70, 29, 33, 48, 53, 65, 39, 58, 72),
    score = c(1.2, 0.8, 1.5, 1.0, 1.1, 0.9, 1.6, 1.3, 0.7, 1.4, 1.2, 1.1, 1.5, 0.95, 1.05, 1.25)
  )

  out_base <- OdysseusSurvivalModule:::singleEventSurvival(
    survivalData = df,
    model = "cox",
    covariates = NULL,
    confType = "none"
  )
  expect_true("overall" %in% names(out_base))

  out_cov <- OdysseusSurvivalModule:::singleEventSurvival(
    survivalData = df,
    model = "cox",
    covariates = c("age_years", "score")
  )
  expect_true("overall" %in% names(out_cov))
  expect_true(all(c("data", "summary") %in% names(out_cov$overall)))
})


test_that("singleEventSurvival validates ageBreaks content", {
  df <- data.frame(
    subject_id = 1:8,
    time = c(3, 5, 8, 10, 14, 17, 19, 23),
    status = c(1, 0, 1, 0, 1, 0, 1, 0),
    age_years = c(19, 24, 37, 46, 52, 61, 69, 74)
  )

  expect_error(
    OdysseusSurvivalModule:::singleEventSurvival(
      survivalData = df,
      model = "km",
      strata = c("age_group"),
      ageBreaks = list(c(10, 20, 30))
    ),
    "length 2"
  )

  expect_error(
    OdysseusSurvivalModule:::singleEventSurvival(
      survivalData = df,
      model = "km",
      strata = c("age_group"),
      ageBreaks = list(c(Inf, 20))
    ),
    "min age"
  )
})


test_that("internal age helpers and logrank helper handle edge cases", {
  expect_error(
    OdysseusSurvivalModule:::.validate_age_groups(list(c(10, 20), c(20, 30))),
    "non-overlapping"
  )

  valid <- OdysseusSurvivalModule:::.validate_age_groups(list(c(0, 17), c(18, 44), c(45, Inf)))
  expect_equal(valid$lowers, c(0, 18, 45))

  labels <- OdysseusSurvivalModule:::.make_age_labels(valid$lowers, valid$uppers)
  expect_equal(labels, c("0-17", "18-44", "45+"))

  no_event_df <- data.frame(
    time_scaled = c(1, 2, 3, 4),
    status = c(0, 0, 0, 0),
    gender = c("Male", "Female", "Male", "Female")
  )
  expect_null(OdysseusSurvivalModule:::.logrank_from_df(no_event_df, "gender"))

  one_group_df <- data.frame(
    time_scaled = c(1, 2, 3, 4),
    status = c(1, 1, 0, 1),
    gender = c("Male", "Male", "Male", "Male")
  )
  expect_null(OdysseusSurvivalModule:::.logrank_from_df(one_group_df, "gender"))
})


test_that("singleEventSurvival parametric variants return overall entry", {
  df <- data.frame(
    subject_id = 1:14,
    time = c(3, 5, 7, 9, 11, 13, 16, 18, 21, 24, 27, 30, 34, 38),
    status = c(1, 0, 1, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1),
    age_years = c(21, 34, 29, 47, 53, 41, 38, 66, 58, 62, 49, 71, 55, 68)
  )

  for (dist in c("exponential", "lognormal", "loglogistic")) {
    out <- OdysseusSurvivalModule:::singleEventSurvival(
      survivalData = df,
      model = dist,
      covariates = c("age_years"),
      probs = c(0.8, 0.5, 0.2)
    )

    expect_true("overall" %in% names(out))
    expect_true(is.list(out$overall$summary))
  }
})