tests/testthat/test-build_spec_coveff.R

In BayesERtools: Bayesian Exposure-Response Analysis Tools

if (.if_run_ex_coveff()) {
  data(d_sim_binom_cov_hgly2)

  set.seed(1234)

  ermod_bin <- suppressWarnings(dev_ermod_bin(
    data = d_sim_binom_cov_hgly2, var_resp = "AEFLAG",
    var_exposure = "AUCss_1000", var_cov = c("BGLUC", "RACE"),
    verbosity_level = 0,
    # Below option to make the example run fast
    chains = 2, iter = 1000
  ))


  spec_coveff <- build_spec_coveff(ermod_bin)

  spec_new_bgluc <- build_spec_coveff_one_variable(
    "BGLUC", seq(4, 8, by = 0.1),
    qi_width_cov = 0.8, show_ref_value = TRUE
  )
  spec_var_race <- build_spec_coveff_one_variable(
    "RACE", c("Black", "Black", "Asian", "White"),
    show_ref_value = TRUE
  )

  spec_coveff_new <- replace_spec_coveff(
    spec_coveff,
    dplyr::bind_rows(spec_var_race, spec_new_bgluc)
  )
  spec_coveff_no_keep_ref <-
    replace_spec_coveff(spec_coveff, spec_new_bgluc, replace_ref_value = TRUE)
  spec_coveff_no_keep_ref_race <-
    replace_spec_coveff(spec_coveff, spec_var_race, replace_ref_value = TRUE)

  coveffsim1 <- sim_coveff(ermod_bin, spec_coveff = spec_coveff_new)
  coveffsim2 <- sim_coveff(ermod_bin, spec_coveff = spec_coveff_no_keep_ref)
  coveffsim3 <-
    sim_coveff(ermod_bin, spec_coveff = spec_coveff_no_keep_ref_race)


  # Tests ---------------------------------------------------------------------
  test_that("input col & row error", {
    expect_error(replace_spec_coveff(
      spec_coveff, spec_new_bgluc |> dplyr::select(-value_cont)
    ), "At least one of value_cont or value_cat columns must be present.")

    expect_error(replace_spec_coveff(
      spec_coveff, spec_new_bgluc |> dplyr::mutate(test = "a")
    ), "`spec_new` expected to have the")
    expect_error(replace_spec_coveff(
      spec_coveff, spec_new_bgluc |> dplyr::select(-is_ref_value)
    ), "`spec_new` expected to have the")

    expect_error(replace_spec_coveff(
      spec_coveff, spec_new_bgluc |> dplyr::mutate(var_name = "TEST")
    ), "Following var_name in spec_new do not")
  })


  test_that("sim with modified spec", {
    expect_equal(coveffsim1$.odds_ratio,
      c(
        0.5362096, 1, 4.1778986, 1, 0.2176921, 0.9138167, 3.8359728, 1,
        1.0926579, 1.8544957, 1
      ),
      tolerance = 1e-6
    )
    expect_equal(coveffsim2$.odds_ratio,
      c(
        0.5362096, 1, 4.1778986, 0.2382229, 1, 4.1977486, 1, 1.8544957,
        1.0926579
      ),
      tolerance = 1e-6
    )
    expect_equal(coveffsim3$.odds_ratio,
      c(
        0.5362096, 1, 4.1778986, 0.2242438, 1, 3.8026690, 1, 1.7090927,
        0.9151996
      ),
      tolerance = 1e-6
    )
  })
}