tests/testthat/test-mcnemar.R

In inferr: Inferential Statistics

context("mcnemar-test")

test_that("output from infer_mcnemar_test matches the expected result", {
  k <- infer_mcnemar_test(matrix(c(172, 7, 6, 15), nrow = 2))
  expect_equal(k$statistic, 0.0769)
  expect_equal(k$df, 1.000)
  expect_equal(k$pvalue, 0.7815)
  expect_equal(k$exactp, 1.0000)
  expect_equal(k$kappa, 0.6613)
  expect_equal(k$std_err, 0.0873)
  expect_equal(k$kappa_cil, 0.4901)
  expect_equal(k$kappa_ciu, 0.8324)
  expect_equal(k$cases, 0.8900)
  expect_equal(k$controls, 0.8950)
  expect_equal(k$ratio, 0.9944)
  expect_equal(k$odratio, 0.8571)
})


test_that("output from infer_mcnemar_test matches the expected result", {
  k <- infer_mcnemar_test(table(hsb$female, hsb$schtyp))
  expect_equal(k$statistic, 56.4667)
  expect_equal(k$df, 1)
  expect_equal(k$pvalue, 0)
  expect_equal(k$exactp, 0)
  expect_equal(k$kappa, 0.0106)
  expect_equal(unname(k$std_err), 0.0485)
  expect_equal(unname(k$kappa_cil), -0.0846)
  expect_equal(unname(k$kappa_ciu), 0.1057)
  expect_equal(unname(k$cases), 0.455)
  expect_equal(unname(k$controls), 0.84)
  expect_equal(unname(k$ratio), 0.5417)
  expect_equal(k$odratio, 0.1538)
})




test_that("output from mcnemar test is as expected", {
  x <- cat("           Controls
---------------------------------
Cases       0       1       Total
---------------------------------
  0        135      21        156
  1         18      26         44
---------------------------------
Total      153      47        200
---------------------------------

       McNemar's Test
----------------------------
McNemar's chi2        0.2308
DF                         1
Pr > chi2              0.631
Exact Pr >= chi2      0.7493
----------------------------

       Kappa Coefficient
--------------------------------
Kappa                     0.4454
ASE                        0.075
95% Lower Conf Limit      0.2984
95% Upper Conf Limit      0.5923
--------------------------------

Proportion With Factor
----------------------
cases             0.78
controls         0.765
ratio           1.0196
odds ratio      1.1667
----------------------")

  himath <- ifelse(hsb$math > 60, 1, 0)
  hiread <- ifelse(hsb$read > 60, 1, 0)
  expect_equivalent(print(infer_mcnemar_test(table(himath, hiread))), x)
})