tests/testthat/test_BFcortest.R

In BFpack: Flexible Bayes Factor Testing of Scientific Expectations

# exploratory testing correlations in multivariate normal model
set.seed(123)
cor1 <- cor_test(mtcars[,4:6])
BF1 <- BF(cor1)
PHPexplo <- matrix(
  c(0.1,  0.9,  0.0,
    0.0,  0.0,  1.0,
    0.0,  1.0,  0.0),nrow=3,byrow=T)
test_that("BF.cor_test exploratory hypotheses on correlations correctly evaluated", {
  expect_equivalent(
    BF1$PHP_exploratory,PHPexplo, tolerance = .1
  )})
# confirmatory hypothesis test on the correlations
BF2 <- BF(cor1,hypothesis="wt_with_drat<drat_with_hp<wt_with_hp;
   wt_with_drat=drat_with_hp<0<wt_with_hp")
BFtable <- matrix(c(   0,    1,  5.66,
                      -1,    0,  4.6,
                    -5.66, -4.6,    0),byrow=TRUE,nrow=3)
test_that("BF.cor_test confirmatory hypotheses on correlations correctly evaluated", {
  expect_equivalent(
    log(BF2$BFmatrix_confirmatory),BFtable, tolerance = .5
  )})

# test a single correlation
set.seed(123)
cor2 <- cor_test(mtcars[,1:2])
BF2 <- BF(cor2,hypothesis="cyl_with_mpg= -.9")
logBFexplo <- matrix(
  c(-19.75,  .7,  -23.4),nrow=1,byrow=T)
# exploratory hypothesis test on the correlation
test_that("BF.cor_test exploratory hypotheses on correlations correctly evaluated", {
  expect_equivalent(
    log(BF2$BFtu_exploratory),logBFexplo, tolerance = .3
  )})
# confirmatory hypothesis test on the correlation
test_that("BF.cor_test confirmatory hypotheses on correlations correctly evaluated", {
  expect_equivalent(
    log(BF2$BFmatrix_confirmatory[1,2]),.9, tolerance = .2
  )})

# estimate correlations for unequal groups
set.seed(123)
cor2b <- cor_test(mtcars[1:10,2:4],mtcars[11:32,2:4])
estimates_check <- c(.7,.63,.62,.85,.74,.68)
test_that("check estimate of polychoric correlation", {
  expect_equivalent(
    cor2b$correstimates[,1],estimates_check, tolerance = .1
  )})

# test a single correlation in multiple groups
test_that("BF.cor_test exploratory hypotheses on correlations correctly evaluated", {
  skip_on_cran()
  set.seed(123)
  cor3 <- cor_test(mtcars[,3:4],mtcars[,5:6])
  BF3 <- BF(cor3,hypothesis="hp_with_disp_in_g1= -wt_with_drat_in_g2")
  expect_equivalent(
    BF3$PHP_confirmatory,c(.78,.22), tolerance = .1
  )})

# # test a single correlation on categorical outcomes
# set.seed(123)
# mtcars_test <- mtcars[,8:9]
# mtcars_test[,2] <- as.factor(mtcars_test[,2])
# mtcars_test[,1] <- as.factor(mtcars_test[,1])
# cor2 <- cor_test(mtcars_test)
# test_that("check estimate of polychoric correlation", {
#   expect_equivalent(
#     cor2$correstimates[1,1],.24, tolerance = .1
#   )})
# BF2 <- BF(cor2,hypothesis="am_with_vs= .1")
# PHPexplo <- matrix(
#   c(.49,  .09,  .42),nrow=1,byrow=T)
# # exploratory hypothesis test on the correlation
# test_that("BF.cor_test exploratory hypotheses on correlations correctly evaluated", {
#   expect_equivalent(
#     BF2$PHP_exploratory,PHPexplo, tolerance = .1
#   )})
# # confirmatory hypothesis test on the correlation
# test_that("BF.cor_test confirmatory hypotheses on correlations correctly evaluated", {
#   expect_equivalent(
#     log(BF2$BFmatrix_confirmatory[1,2]),.93, tolerance = .1
#   )})

# # test with combinations between continuous and ordinal (categorical) outcome variables
# set.seed(187)
# mtcars_test <- mtcars[,c(1,2,9,10)]
# mtcars_test[,2] <- as.ordered(mtcars_test[,2])
# mtcars_test[,3] <- as.factor(mtcars_test[,3])
# mtcars_test[,4] <- as.integer(mtcars_test[,4])
# cor4 <- cor_test(mtcars_test)
# BF4 <- BF(cor4)
# test_that("BF.cor_test exploratory hypotheses on correlations mixed measurement levels", {
#   expect_equivalent(
#     BF4$PHP_exploratory[,1],c(0,.074,.06,.075,.061,.00), tolerance = .1
#   )})