tests/testthat/test-SMD.R

In minter: Effect Sizes for Meta-Analysis of Interactions from Factorial Experiments

data(testing_data)

test_that("Pooled sampling variance is computed correctly", {
  test_S1 <- 8.276473   # Manually calculated
  res_S1 <- .pooled_sd(
    Ctrl_sd = 5,
    Ctrl_n = 5,
    A_sd = 10,
    A_n = 5,
    B_sd = 10,
    B_n = 5,
    AB_sd = 7,
    AB_n = 5
  )

  test_S2 <- 5.0249  # Page 227 from The Handbook of Meta Analysis (Borensetin et al. 2009)
  res_S2 <- .pooled_sd(
    Ctrl_sd = 4.5,
    Ctrl_n = 50,
    A_sd = 5.5,
    A_n = 50
  )

  expect_equal(res_S1, test_S1, tolerance = 1e-6)
  expect_equal(res_S2, test_S2, tolerance = 1e-4)

})


test_that(".j_correction is working fine", {
  test_j <- 0.9923  # From page 227 of The Handbook of Meta Analysis (Borenstein et al. 2009)
  res_j <- .j_correction(50 + 50 - 2)

  expect_equal(res_j, test_j, tolerance = 1e-4)
})


test_that("Simple SMD (Cohen's d) is working fine", {
  Ctrl_mean <- 2.5
  Ctrl_sd <- 1.5
  Ctrl_n <- 10
  A_mean <- 4
  A_sd <- 4.3
  A_n <- 10

  # Computed with metafor::escalc
  test_SMD <- 0.4658026
  test_SMDv <- 0.2054243

  res <- .simple_SMD(
    Ctrl_mean = Ctrl_mean,
    Ctrl_sd = Ctrl_sd,
    Ctrl_n = Ctrl_n,
    A_mean = A_mean,
    A_sd = A_sd,
    A_n = A_n,
    hedges_correction = FALSE
  )

  expect_equal(res$simple_SMD, test_SMD, tolerance = 1e-6)
  expect_equal(res$simple_SMDv, test_SMDv, tolerance = 1e-6)
})


test_that("Simple SMD (Hedges' g) is working fine", {
  Ctrl_mean <- 2.5
  Ctrl_sd <- 1.5
  Ctrl_n <- 10
  A_mean <- 4
  A_sd <- 4.3
  A_n <- 10

  # Computed with metafor::escalc
  test_SMD <- 0.44601
  test_SMDv <- 0.20497

  res <- .simple_SMD(
    Ctrl_mean = Ctrl_mean,
    Ctrl_sd = Ctrl_sd,
    Ctrl_n = Ctrl_n,
    A_mean = A_mean,
    A_sd = A_sd,
    A_n = A_n,
    hedges_correction = TRUE
  )

  expect_equal(res$simple_SMD, test_SMD, tolerance = 1e-3)
  expect_equal(res$simple_SMDv, test_SMDv, tolerance = 1e-3)
})


test_that("Main SMD (Cohen's d) is correctly computed", {
  # This computes the main SMD for Factor A
  res_A <- with(testing_data, .main_SMD(
    Ctrl_mean = C_mean,
    Ctrl_sd = C_sd,
    Ctrl_n = C_n,
    A_mean = A_mean,
    A_sd = A_sd,
    A_n = A_n,
    B_mean = B_mean,
    B_sd = B_sd,
    B_n = B_n,
    AB_mean = AB_mean,
    AB_sd = AB_sd,
    AB_n = AB_n,
    hedges_correction = FALSE
  ))

  expect_equal(res_A$main_SMD, testing_data$A_main_SMD, tolerance = 1e-6)
  expect_equal(res_A$main_SMDv, testing_data$A_main_SMDv, tolerance = 1e-6)
})



test_that("The interaction SMD (Cohen's d) is correctly computed", {
  # This computes the main SMD for Factor A
  res <- with(testing_data, .interaction_SMD(
    Ctrl_mean = C_mean,
    Ctrl_sd = C_sd,
    Ctrl_n = C_n,
    A_mean = A_mean,
    A_sd = A_sd,
    A_n = A_n,
    B_mean = B_mean,
    B_sd = B_sd,
    B_n = B_n,
    AB_mean = AB_mean,
    AB_sd = AB_sd,
    AB_n = AB_n,
    hedges_correction = FALSE
  ))

  expect_equal(res$inter_SMD, testing_data$AB_main_SMD, tolerance = 1e-6)
  expect_equal(res$inter_SMDv, testing_data$AB_main_SMDv, tolerance = 1e-6)
})