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

In gbm-developers/gbm: Generalized Boosted Regression Models

if (require("testthat") &&
  require("insight") &&
  require("stats")) {
  context("insight, lm")

  data(iris)
  data(mtcars)

  m1 <- lm(Sepal.Length ~ Petal.Width + Species, data = iris)
  m2 <-
    lm(log(mpg) ~ log(hp) + cyl + I(cyl^2) + poly(wt, degree = 2, raw = TRUE),
      data = mtcars
    )

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

  test_that("find_predictors", {
    expect_identical(find_predictors(m1), list(conditional = c("Petal.Width", "Species")))
    expect_identical(
      find_predictors(m1, flatten = TRUE),
      c("Petal.Width", "Species")
    )
    expect_null(find_predictors(m1, effects = "random"))

    expect_identical(find_predictors(m2), list(conditional = c("hp", "cyl", "wt")))
    expect_identical(find_predictors(m2, flatten = TRUE), c("hp", "cyl", "wt"))
    expect_null(find_predictors(m2, effects = "random"))
  })

  test_that("find_response", {
    expect_identical(find_response(m1), "Sepal.Length")
    expect_identical(find_response(m2), "mpg")
  })

  test_that("link_inverse", {
    expect_identical(link_inverse(m1)(.2), .2)
    expect_identical(link_inverse(m2)(.2), .2)
  })

  test_that("get_data", {
    expect_equal(nrow(get_data(m1)), 150)
    expect_equal(
      colnames(get_data(m1)),
      c("Sepal.Length", "Petal.Width", "Species")
    )
    expect_equal(nrow(get_data(m2)), 32)
    expect_equal(colnames(get_data(m2)), c("mpg", "hp", "cyl", "wt"))
  })

  test_that("find_formula", {
    expect_length(find_formula(m1), 1)
    expect_equal(
      find_formula(m1),
      list(conditional = as.formula("Sepal.Length ~ Petal.Width + Species"))
    )

    expect_length(find_formula(m2), 1)
    expect_equal(
      find_formula(m2),
      list(
        conditional = as.formula(
          "log(mpg) ~ log(hp) + cyl + I(cyl^2) + poly(wt, degree = 2, raw = TRUE)"
        )
      )
    )
  })

  test_that("find_terms", {
    expect_equal(
      find_terms(m1),
      list(
        response = "Sepal.Length",
        conditional = c("Petal.Width", "Species")
      )
    )
    expect_equal(
      find_terms(m2),
      list(
        response = "log(mpg)",
        conditional = c(
          "log(hp)",
          "cyl",
          "I(cyl^2)",
          "poly(wt, degree = 2, raw = TRUE)"
        )
      )
    )
    expect_equal(
      find_terms(m1, flatten = TRUE),
      c("Sepal.Length", "Petal.Width", "Species")
    )
    expect_equal(
      find_terms(m2, flatten = TRUE),
      c(
        "log(mpg)",
        "log(hp)",
        "cyl",
        "I(cyl^2)",
        "poly(wt, degree = 2, raw = TRUE)"
      )
    )
  })

  test_that("find_variables", {
    expect_equal(
      find_variables(m1),
      list(
        response = "Sepal.Length",
        conditional = c("Petal.Width", "Species")
      )
    )
    expect_equal(find_variables(m2), list(
      response = "mpg",
      conditional = c("hp", "cyl", "wt")
    ))
    expect_equal(
      find_variables(m1, flatten = TRUE),
      c("Sepal.Length", "Petal.Width", "Species")
    )
    expect_equal(
      find_variables(m2, flatten = TRUE),
      c("mpg", "hp", "cyl", "wt")
    )
  })

  test_that("find_parameters", {
    expect_equal(
      find_parameters(m1),
      list(
        conditional = c(
          "(Intercept)",
          "Petal.Width",
          "Speciesversicolor",
          "Speciesvirginica"
        )
      )
    )
    expect_equal(nrow(get_parameters(m1)), 4)
    expect_equal(
      get_parameters(m1)$Parameter,
      c(
        "(Intercept)",
        "Petal.Width",
        "Speciesversicolor",
        "Speciesvirginica"
      )
    )
  })

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

  test_that("find_algorithm", {
    expect_equal(find_algorithm(m1), list(algorithm = "OLS"))
  })

  test_that("get_variance", {
    expect_warning(expect_null(get_variance(m1)))
    expect_warning(expect_null(get_variance_dispersion(m1)))
    expect_warning(expect_null(get_variance_distribution(m1)))
    expect_warning(expect_null(get_variance_fixed(m1)))
    expect_warning(expect_null(get_variance_intercept(m1)))
    expect_warning(expect_null(get_variance_random(m1)))
    expect_warning(expect_null(get_variance_residual(m1)))
  })

  test_that("is_model", {
    expect_true(is_model(m1))
  })

  test_that("all_models_equal", {
    expect_true(all_models_equal(m1, m2))
  })

  test_that("get_varcov", {
    expect_equal(diag(get_varcov(m1)), diag(vcov(m1)))
  })

  test_that("get_statistic", {
    expect_equal(get_statistic(m1)$Statistic, c(57.5427, 4.7298, -0.2615, -0.1398), tolerance = 1e-3)
  })

  test_that("find_statistic", {
    expect_equal(find_statistic(m1), "t-statistic")
  })


  data("DNase")
  DNase1 <- subset(DNase, Run == 1)
  m3 <-
    stats::nls(
      density ~ stats::SSlogis(log(conc), Asym, xmid, scal),
      DNase1,
      start = list(
        Asym = 1,
        xmid = 1,
        scal = 1
      )
    )

  ## Dobson (1990) Page 93: Randomized Controlled Trial :
  counts <- c(18, 17, 15, 20, 10, 20, 25, 13, 12)
  outcome <- gl(3, 1, 9)
  treatment <- gl(3, 3)
  m4 <- glm(counts ~ outcome + treatment, family = poisson())

  test_that("is_model", {
    expect_true(is_model(m3))
  })

  test_that("is_model", {
    expect_false(is_model_supported(m3))
  })

  test_that("all_models_equal", {
    expect_false(all_models_equal(m1, m2, m3))
    expect_false(all_models_equal(m1, m2, m4))
  })

  test_that("find_statistic", {
    expect_identical(find_statistic(m1), "t-statistic")
    expect_identical(find_statistic(m2), "t-statistic")
    expect_identical(find_statistic(m3), "t-statistic")
    expect_identical(find_statistic(m4), "z-statistic")
  })
}