tests/testthat/test-coxph.R

In insight: Easy Access to Model Information for Various Model Objects

skip_if_not_installed("survival")
skip_if_not_installed("insight")
skip_if_not_installed("JM")
skip_if_not_installed("withr")

lung <- subset(survival::lung, subset = ph.ecog %in% 0:2)
lung$sex <- factor(lung$sex, labels = c("male", "female"))
lung$ph.ecog <- factor(lung$ph.ecog, labels = c("good", "ok", "limited"))

Surv <- survival::Surv
strata <- survival::strata
bladder <- survival::bladder

m1 <- survival::coxph(Surv(time, status) ~ sex + age + ph.ecog, data = lung)


test_that("model_info", {
  expect_true(model_info(m1)$is_logit)
  expect_false(model_info(m1)$is_linear)
})

test_that("find_predictors", {
  expect_identical(find_predictors(m1), list(conditional = c("sex", "age", "ph.ecog")))
  expect_null(find_predictors(m1, effects = "random"))
})

test_that("find_response", {
  expect_identical(find_response(m1), "Surv(time, status)")
  expect_identical(find_response(m1, combine = FALSE), c("time", "status"))
})

test_that("link_inverse", {
  expect_equal(link_inverse(m1)(0.2), plogis(0.2), tolerance = 1e-5)
})

test_that("get_data", {
  ## NOTE check back every now and then and see if tests still work
  skip("works interactively")
  expect_s3_class(get_data(m1), "data.frame")
  expect_identical(dim(get_data(m1)), c(166L, 10L))
})


withr::with_environment(
  new.env(),
  test_that("get_data: regression test for previous bug", {
    dat_regression_test <- data.frame(
      time = c(4, 3, 1, 1, 2, 2, 3),
      status = c(1, 1, 1, 0, 1, 1, 0),
      x = c(0, 2, 1, 1, 1, 0, 0),
      sex = c(0, 0, 0, 0, 1, 1, 1)
    )
    mod <- survival::coxph(Surv(time, status) ~ x + strata(sex),
      data = dat_regression_test,
      ties = "breslow"
    )
    expect_equal(get_data(mod), dat_regression_test, ignore_attr = TRUE)
  })
)


withr::with_environment(
  new.env(),
  test_that("get_data: regression test for data stored as list", {
    dat_regression_test <- list(
      time = c(4, 3, 1, 1, 2, 2, 3),
      status = c(1, 1, 1, 0, 1, 1, 0),
      x = c(0, 2, 1, 1, 1, 0, 0),
      sex = c(0, 0, 0, 0, 1, 1, 1)
    )
    mod <- survival::coxph(Surv(time, status) ~ x + strata(sex),
      data = dat_regression_test,
      ties = "breslow"
    )
    expect_equal(get_data(mod), as.data.frame(dat_regression_test), ignore_attr = TRUE)
  })
)


test_that("find_formula", {
  expect_length(find_formula(m1), 1)
  expect_equal(
    find_formula(m1),
    list(conditional = as.formula(
      "Surv(time, status) ~ sex + age + ph.ecog"
    )),
    ignore_attr = TRUE
  )
})

test_that("find_variables", {
  expect_identical(find_variables(m1), list(
    response = c("time", "status"),
    conditional = c("sex", "age", "ph.ecog")
  ))
  expect_identical(
    find_variables(m1, flatten = TRUE),
    c("time", "status", "sex", "age", "ph.ecog")
  )
})

test_that("n_obs", {
  expect_identical(n_obs(m1), 226L)
})

test_that("linkfun", {
  expect_false(is.null(link_function(m1)))
})

test_that("is_multivariate", {
  expect_false(is_multivariate(m1))
})

test_that("find_parameters", {
  expect_identical(
    find_parameters(m1),
    list(
      conditional = c("sexfemale", "age", "ph.ecogok", "ph.ecoglimited")
    )
  )
  expect_identical(nrow(get_parameters(m1)), 4L)
  expect_identical(
    get_parameters(m1)$Parameter,
    c("sexfemale", "age", "ph.ecogok", "ph.ecoglimited")
  )
})

test_that("find_terms", {
  expect_identical(
    find_terms(m1),
    list(
      response = "Surv(time, status)",
      conditional = c("sex", "age", "ph.ecog")
    )
  )
})

test_that("find_statistic", {
  expect_identical(find_statistic(m1), "z-statistic")
})

test_that("JM", {
  data("aids", package = "JM")
  m <- survival::coxph(Surv(start, stop, event) ~ CD4, data = aids)
  d <- get_data(m)
  expect_identical(dim(d), c(1405L, 4L))
  expect_named(d, c("start", "stop", "event", "CD4"))
  expect_identical(find_variables(m), list(response = c("start", "stop", "event"), conditional = "CD4"))
})

test_that("get_statistic", {
  skip_if_not_installed("survival")
  bladder1 <- bladder[bladder$enum < 5, ]
  mod <- survival::coxph(
    Surv(stop, event) ~ (rx + size + number) * strata(enum),
    cluster = id, bladder1, robust = TRUE
  )
  z1 <- get_statistic(mod)$Statistic
  z2 <- coef(summary(mod))[, "z"]
  expect_equal(z1, z2, ignore_attr = TRUE)

  lung <- survival::lung
  mod <- survival::coxph(
    formula = Surv(time, status) ~ age + sex + survival::frailty(inst),
    data = lung
  )
  z1 <- get_statistic(mod)$Statistic
  z2 <- coef(summary(mod))[, "Chisq"]
  expect_equal(z1, z2, ignore_attr = TRUE)
})