tests/testthat/test-ch10.R

In ocbe-uio/contingencytables: Statistical Analysis of Contingency Tables

context("Chapter 10")

test_that("Chapter 10 functions basically work", {
  expect_error(
    object = BreslowDay_homogeneity_test_stratified_2x2(hine_1989[, , 1]),
    regexp = "n must have 3 dimensions"
  )
  expect_output(
    object = print(BreslowDay_homogeneity_test_stratified_2x2(doll_hill_1950)),
    regexp = "The Breslow-Day test: P = 0.022919, T0 = 5.175 \\(df = 1\\)"
  )
  expect_output(
    object = print(MantelHaenszel_estimate_stratified_2x2(doll_hill_1950)),
    regexp = "The Mantel-Haenszel estimate =  4.5239"
  )
  expect_output(
    object = print(CochranMantelHaenszel_test_stratified_2x2(doll_hill_1950)),
    regexp = "Cochran-Mantel-Haenszel test: P = 0.000001, T0 = 24.920 \\(df = 1"
  )
  expect_output(
    object = print(InverseVariance_estimate_stratified_2x2(doll_hill_1950)),
    regexp = "The inverse variance estimate =  3.5563"
  )
  expect_output(
    object = print(Cochran_Q_test_stratified_2x2(doll_hill_1950)),
    regexp = "The Cochran Q test \\(MH\\): P = 0.010251, Q = 6.591 \\(df = 1\\)"
  )
  expect_output(
    object = print(ML_estimates_and_CIs_stratified_2x2(doll_hill_1950)),
    regexp = "gammahat_2 =  0.2122 \\(95% CI 0.0276 to 0.3967\\)"
  )
  expect_output(
    object = print(Pearson_LR_homogeneity_test_stratified_2x2(doll_hill_1950)),
    regexp = "Pearson chi-squared test: P = 0.02471, T0 = 5.044 \\(df = 1\\)"
  )
  expect_output(
    object = print(Pearson_LR_test_common_effect_stratified_2x2(doll_hill_1950)),
    regexp = "Pearson chi-squared test: P = 0.00000, T0 = 25.101 \\(df = 1\\)"
  )
  expect_output(
    object = print(Peto_homogeneity_test_stratified_2x2(doll_hill_1950)),
    regexp = "The Peto test: P = 0.09297, T0 = 2.822 \\(df = 1\\)"
  )
  expect_output(
    object = print(Peto_OR_estimate_stratified_2x2(doll_hill_1950)),
    regexp = "The Peto OR estimate =  3.7120"
  )
  expect_output(
    object = print(RBG_test_and_CI_stratified_2x2(doll_hill_1950)),
    regexp = "The RBG CI: thetahatMH = 4.5239 \\(95% CI 2.3556 to 8.6880\\)"
  )
  expect_output(
    object = print(Wald_test_and_CI_common_diff_stratified_2x2(doll_hill_1950)),
    regexp = "Wald CI \\(MH\\): deltahat = 0.3294 \\(95% CI 0.2281 to 0.4307\\)"
  )
  expect_output(
    object = print(Wald_test_and_CI_common_ratio_stratified_2x2(doll_hill_1950)),
    regexp = "Wald CI \\(MH\\): phihat = 2.4751 \\(95% CI 1.5831 to 3.8698\\)"
  )
  expect_output(
    object = print(Woolf_test_and_CI_stratified_2x2(doll_hill_1950)),
    regexp = "The Woolf CI: thetahatIV = 3.5563 \\(95% CI 1.8365 to 6.8866\\)"
  )
  expect_output(
    object = print(stratified_2x2_tables(doll_hill_1950)),
    regexp = "Woolf \\(IV\\)           3.5563     1.8365 to  6.8866"
  )
  expect_output(
    object = stratified_2x2_tables(doll_hill_1950),
    regexp = "Maximum likelihood   4.2549     2.3478 to  7.7112"
  )
})