tests/testthat/test-ch6.R

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

context("Chapter 6")

test_that("Chapter 6 functions basically work", {
  n_short <- floor(lydersen_2012a / 2)
  expect_output(
    object = print(Brant_test_2xc(lydersen_2012a)),
    regexp = "P = 0.434217, T = 1.668 \\(df = 2\\)"
  )
  expect_output(
    object = print(Cumulative_models_for_2xc(lydersen_2012a)),
    regexp = "Wald \\(Z-statistic\\):          P =  0.14097, Z = -1.472"
  )
  expect_output(
    object = print(Cumulative_models_for_2xc(fontanella_2008, "probit")),
    regexp = "  Pearson .+ P =  0.06041, X2 =  5.613 \\(df=2\\)"
  )
  expect_output(
    object = print(Cumulative_models_for_2xc(fontanella_2008, "logit")),
    regexp = "Wald \\(OR\\)       0.318     0.228 to  0.444"
  )
  expect_error(Cumulative_models_for_2xc(tea), "must have at least 3 columms")
  expect_error(Cumulative_models_for_rxc(n_short[, 1, drop = FALSE]), "must have at least 3")
  expect_error(Cumulative_models_for_rxc(n_short[, 1:2]), "must have at least 3")
  expect_output(
    object = print(Exact_cond_midP_linear_rank_tests_2xc(n_short)),
    regexp = "Exact cond. linear rank test: P = 0.23854"
  )
  expect_output(
    object = print(
      Exact_cond_midP_linear_rank_tests_2xc(matrix(c(1, 200, 300, 0, 5, 6), 2))
    ),
    "Exact cond. linear rank test: P = 0.00000"
  )
  dir <- "decreasing"
  expect_output(
    object = print(Exact_cond_midP_unspecific_ordering_rx2(t(n_short), dir)),
    regexp = "Exact conditional test\\s*:\\s*P =\\s*0.23094"
  )
  stat <- "PearsonCumOR"
  expect_output(
    object = print(Exact_cond_midP_unspecific_ordering_rx2(t(n_short), dir, stat)),
    regexp = "Exact conditional test\\s*:\\s*P =\\s*0.08012"
  )
  expect_error(
    Exact_cond_midP_unspecific_ordering_rx2(matrix(1:4, 2), "increasing"),
    "n must have either 4 or 5 rows. Consider transposing it."
  )
  expect_output(
    object = print(MantelHaenszel_test_2xc(lydersen_2012a)),
    regexp = "test of association: P = 0.1442, T = 2.132 \\(df=1\\)"
  )
  expect_output(
    object = print(Pearson_LR_tests_cum_OR_2xc(lydersen_2012a)),
    regexp = "Pearson chi-squared test: T =  3.813,  P = 0.07223"
  )
  expect_output(
    object = print(Pearson_LR_tests_cum_OR_2xc(t(lydersen_2012a), "increasing")),
    regexp = "Pearson chi-squared test: T =  2.708,  P = 0.04993"
  )
  alphahat0 <- c(-0.1923633, 0.5588396, 1.271953)
  expect_output(
    object = print(
        Score_test_for_effect_in_the_probit_model_2xc(
        lydersen_2012a, alphahat0
      )
    ),
    regexp = "Score test for effect: P = 0.1431, T = 2.145 \\(df=1\\)"
  )
  expect_output(
    object = print(the_2xc_table(n_short, direction = "decreasing")),
    regexp = "Wald \\(OR\\)       2.420     0.598 to  9.788"
  )
})