skip_if_not_installed("survival")
skip_if_not_installed("lme4")
skip_if_not_installed("nlme")
skip_if_not_installed("bdsmatrix")
skip_if_not_installed("coxme")

lung <- survival::lung
Surv <- survival::Surv

set.seed(1234)
lung$inst2 <- sample(1:10, size = nrow(lung), replace = TRUE)
lung <- subset(lung, subset = ph.ecog %in% 0:2)
lung$ph.ecog <- factor(lung$ph.ecog, labels = c("good", "ok", "limited"))

d <<- lung

m1 <- coxme::coxme(Surv(time, status) ~ ph.ecog + age + (1 | inst), d)
m2 <- coxme::coxme(Surv(time, status) ~ ph.ecog + age + (1 | inst) + (1 | inst2), d)

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("ph.ecog", "age")))
  expect_identical(
    find_predictors(m1, effects = "random"),
    list(random = "inst")
  )
  expect_identical(find_predictors(m2), list(conditional = c("ph.ecog", "age")))
  expect_identical(find_predictors(m2, effects = "random"), list(random = c("inst", "inst2")))
})

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)
  expect_equal(link_inverse(m2)(0.2), plogis(0.2), tolerance = 1e-5)
})

test_that("get_data", {
  expect_equal(nrow(get_data(m1)), 225)
  expect_equal(
    colnames(get_data(m1)),
    c(
      "time",
      "status",
      "ph.ecog",
      "age",
      "inst"
    )
  )
  expect_equal(
    colnames(get_data(m2)),
    c(
      "time",
      "status",
      "ph.ecog",
      "age",
      "inst",
      "inst2"
    )
  )
})

test_that("find_formula", {
  expect_length(find_formula(m1), 2)
  expect_equal(
    find_formula(m1),
    list(
      conditional = as.formula("Surv(time, status) ~ ph.ecog + age"),
      random = as.formula("~1 | inst")
    ),
    ignore_attr = TRUE
  )

  expect_length(find_formula(m2), 2)
  expect_equal(
    find_formula(m2),
    list(
      conditional = as.formula("Surv(time, status) ~ ph.ecog + age"),
      random = list(as.formula("~1 | inst"), as.formula("~1 | inst2"))
    ),
    ignore_attr = TRUE
  )
})

test_that("find_terms", {
  expect_equal(
    find_terms(m1),
    list(
      response = "Surv(time, status)",
      conditional = c("ph.ecog", "age"),
      random = "inst"
    )
  )
  expect_equal(
    find_terms(m1, flatten = TRUE),
    c("Surv(time, status)", "ph.ecog", "age", "inst")
  )
  expect_equal(
    find_terms(m2),
    list(
      response = "Surv(time, status)",
      conditional = c("ph.ecog", "age"),
      random = c("inst", "inst2")
    )
  )
  expect_equal(
    find_terms(m2, flatten = TRUE),
    c("Surv(time, status)", "ph.ecog", "age", "inst", "inst2")
  )
})

test_that("find_variables", {
  expect_equal(
    find_variables(m1),
    list(
      response = c("time", "status"),
      conditional = c("ph.ecog", "age"),
      random = "inst"
    )
  )
  expect_equal(
    find_variables(m1, flatten = TRUE),
    c("time", "status", "ph.ecog", "age", "inst")
  )
  expect_equal(
    find_variables(m2),
    list(
      response = c("time", "status"),
      conditional = c("ph.ecog", "age"),
      random = c("inst", "inst2")
    )
  )
  expect_equal(
    find_variables(m2, flatten = TRUE),
    c("time", "status", "ph.ecog", "age", "inst", "inst2")
  )
})

test_that("n_obs", {
  expect_equal(n_obs(m1), 225)
  expect_equal(n_obs(m2), 225)
})

test_that("get_response", {
  expect_equal(colnames(get_response(m1)), c("time", "status"))
  expect_equal(nrow(get_response(m1)), 225)
  expect_equal(colnames(get_response(m1)), c("time", "status"))
  expect_equal(nrow(get_response(m2)), 225)
})

test_that("linkfun", {
  expect_false(is.null(link_function(m1)))
  expect_false(is.null(link_function(m2)))
})

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

test_that("find_parameters", {
  expect_equal(
    find_parameters(m1),
    list(
      conditional = c("ph.ecogok", "ph.ecoglimited", "age"),
      random = "inst"
    )
  )
  expect_equal(
    find_parameters(m2),
    list(
      conditional = c("ph.ecogok", "ph.ecoglimited", "age"),
      random = c("inst", "inst2")
    )
  )
  expect_equal(nrow(get_parameters(m1)), 3)
  expect_equal(
    get_parameters(m1)$Parameter,
    c("ph.ecogok", "ph.ecoglimited", "age")
  )

  expect_equal(nrow(get_parameters(m2)), 3)
  expect_equal(
    get_parameters(m2)$Parameter,
    c("ph.ecogok", "ph.ecoglimited", "age")
  )

  expect_length(get_parameters(m2, effects = "random"), 2)
})

test_that("find_statistic", {
  expect_identical(find_statistic(m1), "z-statistic")
  expect_identical(find_statistic(m2), "z-statistic")
})