revdep/checks.noindex/insight/new/insight.Rcheck/tests/testthat/test-vgam.R

In gbm-developers/gbm: Generalized Boosted Regression Models

.runThisTest <- Sys.getenv("RunAllinsightTests") == "yes"

if (.runThisTest && Sys.getenv("USER") != "travis") {
  if (require("testthat") && require("insight") && require("VGAM")) {
    context("insight, model_info")

    data("hunua")
    m1 <- download_model("vgam_1")
    m2 <- download_model("vgam_2")

    test_that("model_info", {
      expect_true(model_info(m1)$is_binomial)
      expect_true(model_info(m2)$is_binomial)
      expect_false(model_info(m1)$is_bayesian)
      expect_false(model_info(m2)$is_bayesian)
    })

    test_that("find_predictors", {
      expect_identical(find_predictors(m1), list(conditional = c("vitluc", "altitude")))
      expect_identical(
        find_predictors(m1, flatten = TRUE),
        c("vitluc", "altitude")
      )
      expect_null(find_predictors(m1, effects = "random"))
      expect_identical(find_predictors(m2), list(conditional = c("vitluc", "altitude")))
      expect_identical(
        find_predictors(m2, flatten = TRUE),
        c("vitluc", "altitude")
      )
      expect_null(find_predictors(m2, effects = "random"))
    })

    test_that("find_random", {
      expect_null(find_random(m1))
      expect_null(find_random(m2))
    })

    test_that("get_random", {
      expect_warning(get_random(m1))
      expect_warning(get_random(m2))
    })

    test_that("find_response", {
      expect_identical(find_response(m1), "agaaus")
      expect_identical(find_response(m2), "cbind(agaaus, kniexc)")
      expect_identical(find_response(m2, combine = FALSE), c("agaaus", "kniexc"))
    })

    test_that("get_response", {
      expect_equal(get_response(m1), hunua$agaaus)
      expect_equal(
        get_response(m2),
        data.frame(agaaus = hunua$agaaus, kniexc = hunua$kniexc)
      )
    })

    test_that("get_predictors", {
      expect_equal(colnames(get_predictors(m1)), c("vitluc", "altitude"))
      expect_equal(colnames(get_predictors(m2)), c("vitluc", "altitude"))
    })

    test_that("link_inverse", {
      expect_equal(link_inverse(m1)(.2), plogis(.2), tolerance = 1e-5)
      expect_equal(link_inverse(m2)(.2), plogis(.2), tolerance = 1e-5)
    })

    test_that("get_data", {
      expect_equal(nrow(get_data(m1)), 392)
      expect_equal(nrow(get_data(m2)), 392)
      expect_equal(colnames(get_data(m1)), c("agaaus", "vitluc", "altitude"))
      expect_equal(
        colnames(get_data(m2)),
        c("agaaus", "kniexc", "vitluc", "altitude")
      )
    })

    test_that("find_formula", {
      expect_length(find_formula(m1), 1)
      expect_equal(
        find_formula(m1),
        list(conditional = as.formula("agaaus ~ vitluc + s(altitude, df = 2)"))
      )
      expect_length(find_formula(m2), 1)
      expect_equal(
        find_formula(m2),
        list(
          conditional = as.formula("cbind(agaaus, kniexc) ~ vitluc + s(altitude, df = c(2, 3))")
        )
      )
    })

    test_that("find_terms", {
      expect_equal(
        find_terms(m1),
        list(
          response = "agaaus",
          conditional = c("vitluc", "s(altitude, df = 2)")
        )
      )
      expect_equal(
        find_terms(m1, flatten = TRUE),
        c("agaaus", "vitluc", "s(altitude, df = 2)")
      )
      expect_equal(
        find_terms(m2),
        list(
          response = "cbind(agaaus, kniexc)",
          conditional = c("vitluc", "s(altitude, df = c(2, 3))")
        )
      )
      expect_equal(
        find_terms(m2, flatten = TRUE),
        c(
          "cbind(agaaus, kniexc)",
          "vitluc",
          "s(altitude, df = c(2, 3))"
        )
      )
    })

    test_that("find_variables", {
      expect_equal(
        find_variables(m1),
        list(
          response = "agaaus",
          conditional = c("vitluc", "altitude")
        )
      )
      expect_equal(
        find_variables(m1, flatten = TRUE),
        c("agaaus", "vitluc", "altitude")
      )
      expect_equal(find_variables(m2), list(
        response = c("agaaus", "kniexc"),
        conditional = c("vitluc", "altitude")
      ))
      expect_equal(
        find_variables(m2, flatten = TRUE),
        c("agaaus", "kniexc", "vitluc", "altitude")
      )
    })

    test_that("n_obs", {
      expect_equal(n_obs(m1), 392)
      expect_equal(n_obs(m2), 392)
    })

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

    test_that("find_parameters", {
      expect_equal(
        find_parameters(m1),
        list(
          conditional = c("(Intercept)", "vitluc"),
          smooth_terms = "s(altitude, df = 2)"
        )
      )
      expect_equal(nrow(get_parameters(m1)), 3)
      expect_equal(
        get_parameters(m1)$Parameter,
        c("(Intercept)", "vitluc", "s(altitude, df = 2)")
      )

      expect_equal(
        find_parameters(m2),
        list(
          conditional = c(
            "(Intercept):1",
            "(Intercept):2",
            "vitluc:1",
            "vitluc:2"
          ),
          smooth_terms = c("s(altitude, df = c(2, 3)):1", "s(altitude, df = c(2, 3)):2")
        )
      )
      expect_equal(nrow(get_parameters(m2)), 6)
      expect_equal(
        get_parameters(m2)$Parameter,
        c(
          "(Intercept):1",
          "(Intercept):2",
          "vitluc:1",
          "vitluc:2",
          "s(altitude, df = c(2, 3)):1",
          "s(altitude, df = c(2, 3)):2"
        )
      )
    })

    test_that("is_multivariate", {
      expect_false(is_multivariate(m1))
      expect_false(is_multivariate(m2))
    })

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