tests/testthat/test-compare_smds.R

In TOSTER: Two One-Sided Tests (TOST) Equivalence Testing

#context("Run Examples for boot_t_TOST")

# need hush function to run print through examples

hush = function(code) {
  sink("NUL") # use /dev/null in UNIX
  tmp = code
  sink()
  return(tmp)
}

test_that("compare_smd", {

  # Errors ----

  expect_error(compare_smd())


  # One sample
  set.seed(7894021)
  datx1 = rnorm(20)
  datx2 = rnorm(45)

  one_boot1 = boot_compare_smd(x1 = datx1,
                               x2 = datx2)
  one_1 = compare_smd(smd1 = one_boot1$df_ci$estimate[2],
                      n1 = length(datx1),
                      smd2 = one_boot1$df_ci$estimate[3],
                      n2 = length(datx2),
                      paired = TRUE)
  expect_error(compare_smd(smd1 = one_boot1$df_ci$estimate[2],
                           n1 = length(datx1),
                           smd2 = one_boot1$df_ci$estimate[3],
                           n2 = c(1,1),
                           paired = TRUE))
  se1 = TOSTER:::se_dz(one_boot1$df_ci$estimate[2], length(datx1))
  se2 = TOSTER:::se_dz(one_boot1$df_ci$estimate[3], length(datx2))

  one_11 = compare_smd(smd1 = one_boot1$df_ci$estimate[2],
                      n1 = length(datx1),
                      se1 = se1,
                      smd2 = one_boot1$df_ci$estimate[3],
                      n2 = length(datx2),
                      se2 = se2,
                      paired = TRUE)

  expect_equal(unname(one_1$statistic),
               unname(one_boot1$statistic))

  # Paired sample -----
  daty1 = rnorm(20)
  daty2 = rnorm(45)

  one_boot2 = boot_compare_smd(x1 = datx1,
                               x2 = datx2,
                               y1 = daty1,
                               y2 = daty2,
                               paired = TRUE)
  one_2 = compare_smd(smd1 = one_boot2$df_ci$estimate[2],
                      n1 = length(datx1),
                      smd2 = one_boot2$df_ci$estimate[3],
                      n2 = length(datx2),
                      paired = TRUE)

  expect_equal(unname(one_2$statistic),
               unname(one_boot2$statistic))

  # Two sample -----

  one_boot3 = boot_compare_smd(x1 = datx1,
                               x2 = datx2,
                               y1 = daty1,
                               y2 = daty2,
                               paired = FALSE)
  one_3 = compare_smd(smd1 = one_boot3$df_ci$estimate[2],
                      n1 = c(length(datx1),length(daty1)),
                      smd2 = one_boot3$df_ci$estimate[3],
                      n2 = c(length(datx2),length(daty2)),
                      paired = FALSE)

  expect_error(compare_smd(smd1 = one_boot3$df_ci$estimate[2],
              n1 = c(length(datx1),length(daty1)),
              smd2 = one_boot3$df_ci$estimate[3],
              n2 = c(length(datx2),length(daty2),1),
              paired = FALSE))

  se1 = TOSTER:::se_dz(one_boot1$df_ci$estimate[2], c(length(datx1),length(daty1)))
  se2 = TOSTER:::se_dz(one_boot1$df_ci$estimate[3], c(length(datx2),length(daty2)))

  one_33 = compare_smd(smd1 = one_boot3$df_ci$estimate[2],
                      n1 = length(datx1),
                      se1 = se1,
                      smd2 = one_boot3$df_ci$estimate[3],
                      n2 = length(datx2),
                      se2 = se2,
                      paired = TRUE)

  expect_equal(unname(one_3$statistic),
               unname(one_boot3$statistic))

  one_3 = compare_smd(smd1 = one_boot3$df_ci$estimate[2],
                      n1 = c(length(datx1),length(daty1)),
                      smd2 = one_boot3$df_ci$estimate[3]+.32,
                      n2 = c(length(datx2),length(daty2)),
                      paired = FALSE,
                      TOST = TRUE,
                      null = .25)
  one_31 = compare_smd(smd1 = one_boot3$df_ci$estimate[2],
                      n1 = c(length(datx1),length(daty1)),
                      smd2 = one_boot3$df_ci$estimate[3]+.32,
                      n2 = c(length(datx2),length(daty2)),
                      paired = FALSE,
                      alternative = "e",
                      null = .25)

  expect_equal(one_3$p.value,
               one_31$p.value)

  one_4 = compare_smd(smd1 = one_boot3$df_ci$estimate[2],
                      n1 = c(length(datx1),length(daty1)),
                      smd2 = one_boot3$df_ci$estimate[3]+.32,
                      n2 = c(length(datx2),length(daty2)),
                      paired = FALSE,
                      alternative = "m",
                      null = .25)
  one_41 = compare_smd(smd1 = one_boot3$df_ci$estimate[2],
                       n1 = c(length(datx1),length(daty1)),
                       smd2 = one_boot3$df_ci$estimate[3]+.32,
                       n2 = c(length(datx2),length(daty2)),
                       paired = FALSE,
                       alternative = "m",
                       null = c(.25,-.25))

  expect_equal(one_4$p.value,
               one_41$p.value)

  one_5 = compare_smd(smd1 = one_boot3$df_ci$estimate[2],
                      n1 = c(length(datx1),length(daty1)),
                      smd2 = one_boot3$df_ci$estimate[3]+.32,
                      n2 = c(length(datx2),length(daty2)),
                      paired = FALSE,
                      alternative = "g",
                      null = .25)
  one_51 = compare_smd(smd1 = one_boot3$df_ci$estimate[2],
                       n1 = c(length(datx1),length(daty1)),
                       smd2 = one_boot3$df_ci$estimate[3]+.32,
                       n2 = c(length(datx2),length(daty2)),
                       paired = FALSE,
                       alternative = "l",
                       null = c(.25))

  expect_error(compare_smd(smd1 = one_boot3$df_ci$estimate[2],
                       n1 = c(length(datx1),length(daty1)),
                       smd2 = one_boot3$df_ci$estimate[3]+.32,
                       n2 = c(length(datx2),length(daty2)),
                       paired = FALSE,
                       alternative = "l",
                       null = c(.25,-.25)))

})

test_that("compare_cor",{
  # Compare the difference between two correlations based
  # on two independent groups:
  r1.jk <- .7  # Correlation between age and intelligence measured in group 1
  n1 <- 305    # Size of group 1

  r2.hm <- .6  # Correlation between age and intelligence measured in group 2
  n2 <- 210    # Size of group 2
  test_cor = compare_cor(r1 = r1.jk, r2 = r2.hm,
              df1 = n1-2, df2 = n2-2)

  expect_equal(unname(test_cor$statistic),
               1.93, tolerance = 0.0001)
  expect_equal(test_cor$p.value,
               0.0536, tolerance = 0.0001)

  test_cor2 = compare_cor(r1 = r1.jk, r2 = r2.hm,
                         df1 = n1-2, df2 = n2-2,
                         alternative = "l")
  test_cor3 = compare_cor(r1 = r1.jk, r2 = r2.hm,
                         df1 = n1-2, df2 = n2-2,
                         alternative = "g")

  test_cor4 = compare_cor(r1 = r1.jk, r2 = r2.hm,
                          df1 = n1-2, df2 = n2-2,
                          alternative = "l",
                          method = "k")
  test_cor5 = compare_cor(r1 = r1.jk, r2 = r2.hm,
                          df1 = n1-2, df2 = n2-2,
                          alternative = "g",
                          method = "k")

})