tests/testthat/test_imd_anova_paired.R

In pmartR/pmartR: Panomics Marketplace - Quality Control and Statistical Analysis for Panomics Data

context('IMD-ANOVA paired tests')

test_that('all paired tests conform to the decrees of the God of Stats', {
  # Load IMD-ANOVA filter objects ----------------------------------------------
  testthat::skip_on_cran()
  load(system.file('testdata',
    'standards_filter_paired.RData',
    package = 'pmartR'
  ))

  # Load IMD-ANOVA standards ---------------------------------------------------

  load(system.file('testdata',
    'standards_imd_anova_paired.RData',
    package = 'pmartR'
  ))

  # Compare IMD-ANOVAly --------------------------------------------------------

  afruit_0_0_3 <- imd_anova(afilta_0_0_3,
    test_method = "anova",
    parallel = FALSE
  )

  afruit_1_0_3 <- imd_anova(afilta_1_0_3,
    test_method = "anova"
  )
  gfruit_1_0_3 <- imd_anova(gfilta_1_0_3,
    test_method = "gtest"
  )
  cfruit_1_0_3 <- imd_anova(cfilta_1_0_3,
    test_method = "combined"
  )

  afruit_1_1_3 <- imd_anova(afilta_1_1_3,
    test_method = "anova"
  )
  gfruit_1_1_3 <- imd_anova(gfilta_1_1_3,
    test_method = "gtest",
    parallel = FALSE
  )
  cfruit_1_1_3 <- imd_anova(cfilta_1_1_3,
    test_method = "combined"
  )

  # Holy IMD-ANOVA unit tests, Statman! ----------------------------------------

  # ANOVA: Unadjusted p-values ---------------

  expect_equal(afruit_0_0_3, astan_0_0_3)
  expect_equal(afruit_1_0_3, astan_1_0_3)
  expect_equal(afruit_1_1_3, astan_1_1_3)

  # G-Test: Unadjusted p-values ---------------

  expect_error(
    imd_anova(gfilta_0_0_3,
      test_method = "gtest"
    ),
    "If there are no main effects test_method cannot be gtest or combined."
  )
  expect_equal(gfruit_1_0_3, gstan_1_0_3)
  expect_equal(gfruit_1_1_3, gstan_1_1_3)

  # Combined: Unadjusted p-values ---------------

  expect_error(
    imd_anova(cfilta_0_0_3,
      test_method = "gtest"
    ),
    "If there are no main effects test_method cannot be gtest or combined."
  )
  expect_equal(cfruit_1_0_3, cstan_1_0_3)
  expect_equal(cfruit_1_1_3, cstan_1_1_3)

  # Test argument checks -------------------------------------------------------

  # Maybe add later (depending on the position of the planets and stars).
})