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

In gbm-developers/gbm: Generalized Boosted Regression Models

if (require("testthat") &&
  require("insight") &&
  require("rms")) {
  context("insight, rms")

  n <- 400
  set.seed(1)
  age <- rnorm(n, 50, 12)
  sex <- factor(sample(c("Female", "Male"), n, TRUE))
  # Population hazard function:
  h <- .02 * exp(.06 * (age - 50) + .8 * (sex == "Female"))
  d.time <- -log(runif(n)) / h
  cens <- 15 * runif(n)
  death <- ifelse(d.time <= cens, 1, 0)
  d.time <- pmin(d.time, cens)

  dat <-
    data.frame(d.time, death, sex, age, stringsAsFactors = FALSE)

  m1 <-
    psm(Surv(d.time, death) ~ sex * pol(age, 2),
      dist = "lognormal",
      data = dat
    )

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

  test_that("find_predictors", {
    expect_identical(find_predictors(m1), list(conditional = c("sex", "age")))
    expect_identical(find_predictors(m1, flatten = TRUE), c("sex", "age"))
    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), "Surv(d.time, death)")
    expect_identical(find_response(m1, combine = FALSE), c("d.time", "death"))
  })

  test_that("get_response", {
    expect_equal(get_response(m1), dat[, c("d.time", "death")])
  })

  test_that("get_predictors", {
    expect_equal(colnames(get_predictors(m1)), c("sex", "age"))
  })

  test_that("link_inverse", {
    expect_equal(link_inverse(m1)(.2), exp(.2), tolerance = 1e-5)
  })

  test_that("get_data", {
    expect_equal(nrow(get_data(m1)), 400)
    expect_equal(colnames(get_data(m1)), c("d.time", "death", "sex", "age"))
  })

  test_that("find_formula", {
    expect_length(find_formula(m1), 1)
    expect_equal(
      find_formula(m1),
      list(conditional = as.formula(
        "Surv(d.time, death) ~ sex * pol(age, 2)"
      ))
    )
  })

  test_that("find_terms", {
    expect_length(find_terms(m1), 2)
    expect_equal(
      find_terms(m1),
      list(
        response = "Surv(d.time, death)",
        conditional = c("sex", "pol(age, 2)")
      )
    )
  })

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

  test_that("n_obs", {
    expect_equal(n_obs(m1), 400)
  })

  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_equal(
      find_parameters(m1),
      list(
        conditional = c(
          "(Intercept)",
          "sex=Male",
          "age",
          "age^2",
          "sex=Male * age",
          "sex=Male * age^2"
        )
      )
    )
    expect_equal(nrow(get_parameters(m1)), 6)
    expect_equal(
      get_parameters(m1)$Parameter,
      c(
        "(Intercept)",
        "sex=Male",
        "age",
        "age^2",
        "sex=Male * age",
        "sex=Male * age^2"
      )
    )
  })

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

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

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