tests/testthat/test-test_normality.R

In GegznaV/BioStat: Routines for Basic (Bio)Statistics

context("Function `test_normality()`")

# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
test_that("`test_normality()` produces object with correct classes", {
  data(CO2, package = "datasets")
  rez <- test_normality(uptake ~ Type, data = CO2)

  expect_is(rez, c("data.frame"))
  expect_is(rez, c("test_normality"))
})

# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
test_that("`test_normality()` produces correct attributes", {
  data(CO2, package = "datasets")
  rez <- test_normality(uptake ~ Type, data = CO2, p_adjust_method = "holm")

  expect_equal(attr(rez, "test"), "Shapiro-Wilk normality test")
  expect_equal(attr(rez, "p_adjust_method"), "holm")
})
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
test_that("`test_normality()` works with one-sided formula `~var`", {
  data(CO2, package = "datasets")
  rez <- test_normality(~uptake, data = CO2)

  expect_is(rez, c("data.frame"))
  expect_is(rez, c("test_normality"))
  expect_equal(nrow(rez), 1)
})
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
test_that("`test_normality()` produces object with correct classes", {
  data(CO2, package = "datasets")
  rez <- test_normality(uptake ~ Type, data = CO2)

  expect_is(rez, c("data.frame"))
  expect_is(rez, c("test_normality"))
})

# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
test_that("parameter test = 'chi-squared' for `test_normality()` is recognized correctly", {
  data(CO2, package = "datasets")

  rez1 <- test_normality(uptake ~ Type, data = CO2, test = "chi-squared")
  rez2 <- test_normality(uptake ~ Type, data = CO2, test = "chi")
  rez3 <- test_normality(uptake ~ Type, data = CO2, test = "Pearson")
  rez4 <- test_normality(uptake ~ Type, data = CO2, test = "pearson")

  expect_true(unique(rez1$method) == "Pearson chi-square normality test")
  expect_true(unique(rez2$method) == "Pearson chi-square normality test")
  expect_true(unique(rez3$method) == "Pearson chi-square normality test")
  expect_true(unique(rez4$method) == "Pearson chi-square normality test")
})
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
test_that("parameter test = 'Shapiro-Wilk' for `test_normality()` is recognized correctly", {
  data(CO2, package = "datasets")

  rez1 <- test_normality(uptake ~ Type, data = CO2)
  rez2 <- test_normality(uptake ~ Type, data = CO2, test = "Shapiro-Wilk")
  rez3 <- test_normality(uptake ~ Type, data = CO2, test = "sW")
  rez4 <- test_normality(uptake ~ Type, data = CO2, test = "SW")

  expect_true(unique(rez1$method) == "Shapiro-Wilk normality test")
  expect_true(unique(rez2$method) == "Shapiro-Wilk normality test")
  expect_true(unique(rez3$method) == "Shapiro-Wilk normality test")
  expect_true(unique(rez4$method) == "Shapiro-Wilk normality test")
})
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
test_that("parameter test = 'lilliefors' for `test_normality()` is recognized correctly", {
  data(CO2, package = "datasets")

  rez1 <- test_normality(uptake ~ Type, data = CO2, test = "lillie")
  rez2 <- test_normality(uptake ~ Type, data = CO2, test = "Lilliefors")

  expect_true(unique(rez1$method) == "Lilliefors (Kolmogorov-Smirnov) normality test")
  expect_true(unique(rez2$method) == "Lilliefors (Kolmogorov-Smirnov) normality test")
})
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
test_that("`test_normality()` produces correct p-values for each group", {
  data(CO2, package = "datasets")

  rez <- test_normality(uptake ~ Type, data = CO2)
  filter <- dplyr::filter

  expect_equal(
    filter(rez, Type == "Quebec")$p.value,
    shapiro.test(filter(CO2, Type == "Quebec")$uptake)$p.value
  )

  expect_equal(
    filter(rez, Type == "Mississippi")$p.value,
    shapiro.test(filter(CO2, Type == "Mississippi")$uptake)$p.value
  )
})
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
test_that("`print()` method for 'test_normality' object works", {
  data(CO2, package = "datasets")

  rez <- test_normality(uptake ~ Type, data = CO2)

  expect_output(print(rez), "normality test")
  expect_output(print(rez), "statistic")
  expect_output(print(rez), "p.value")
})

# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
test_that("`pander()` method for 'test_normality' object works", {
  data(CO2, package = "datasets")

  rez <- test_normality(uptake ~ Type, data = CO2)


  # Expect specific structure
  expect_output(pander(rez), "statistic")
  expect_output(pander(rez), "p.value")
  expect_output(pander(rez), "-------------")
  expect_output(pander(rez), "Table: ")
  expect_output(pander(rez), "The results of")
  expect_output(pander(rez), "normality test")

  # Expect specific caption
  expect_output(pander(rez, caption = "LA LA LA"), "Table: LA LA LA")

  # Output must not contain "Table: ", when `caption = NULL`
  output <- capture.output(pander(rez, caption = NULL))
  expect_true(all(!(grepl("Table: ", output))))
})