skip_on_covr()
skip_if_not_installed("logistf")

data(sex2, package = "logistf")
m1 <- logistf::logistf(case ~ age + oc + vic + vicl + vis + dia, data = sex2)

test_that("model_info", {
  expect_true(model_info(m1)$is_binomial)
  expect_true(model_info(m1)$is_bernoulli)
  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(
    "age", "oc", "vic", "vicl", "vis", "dia"
  )))
  expect_identical(
    find_predictors(m1, flatten = TRUE),
    c("age", "oc", "vic", "vicl", "vis", "dia")
  )
  expect_null(find_predictors(m1, effects = "random"))
})

test_that("find_random", {
  expect_null(find_random(m1))
})

test_that("get_random", {
  expect_warning(get_random(m1))
})

test_that("find_response", {
  expect_identical(find_response(m1), "case")
})

test_that("get_response", {
  expect_equal(get_response(m1), sex2$case, ignore_attr = TRUE)
})

test_that("get_predictors", {
  expect_named(
    get_predictors(m1),
    c("age", "oc", "vic", "vicl", "vis", "dia")
  )
})

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

test_that("get_data", {
  expect_identical(nrow(get_data(m1)), 239L)
  expect_identical(
    colnames(get_data(m1)),
    c("case", "age", "oc", "vic", "vicl", "vis", "dia")
  )
})

test_that("find_formula", {
  expect_length(find_formula(m1), 1)
  expect_equal(
    find_formula(m1),
    list(conditional = as.formula("case ~ age + oc + vic + vicl + vis + dia")),
    ignore_attr = TRUE
  )
})

test_that("find_terms", {
  expect_identical(find_terms(m1), list(
    response = "case",
    conditional = c("age", "oc", "vic", "vicl", "vis", "dia")
  ))
  expect_identical(
    find_terms(m1, flatten = TRUE),
    c("case", "age", "oc", "vic", "vicl", "vis", "dia")
  )
})

test_that("n_obs", {
  expect_identical(n_obs(m1), 239)
})

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

test_that("linkinverse", {
  expect_false(is.null(link_inverse(m1)))
})

test_that("find_parameters", {
  expect_identical(
    find_parameters(m1),
    list(
      conditional = c("(Intercept)", "age", "oc", "vic", "vicl", "vis", "dia")
    )
  )
  expect_identical(nrow(get_parameters(m1)), 7L)
  expect_identical(
    get_parameters(m1)$Parameter,
    c("(Intercept)", "age", "oc", "vic", "vicl", "vis", "dia")
  )
})

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

test_that("find_algorithm", {
  expect_identical(find_algorithm(m1), list(algorithm = "Penalized ML"))
})

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

unloadNamespace("logistf")