revdep/checks.noindex/insight/old/insight.Rcheck/tests/testthat/test-coxph.R

In gbm-developers/gbm: Generalized Boosted Regression Models

if (require("testthat") &&
  require("insight") &&
  require("survival")) {
  context("insight, coxph")

  data("lung")
  lung <- subset(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"))

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

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

  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)(.2), plogis(.2), tolerance = 1e-5)
  })

  test_that("get_data", {
    expect_equal(nrow(get_data(m1)), 226)
    expect_equal(
      colnames(get_data(m1)),
      c(
        "time",
        "status",
        "Surv(time, status)",
        "sex",
        "age",
        "ph.ecog"
      )
    )
  })

  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"
      ))
    )
  })

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

  test_that("n_obs", {
    expect_equal(n_obs(m1), 226)
  })

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

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

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

  test_that("find_terms", {
    expect_equal(
      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")
  })
}