https://github.com/cran/bayestestR
Tip revision: 79b3ea026adbb877bc1921a9cf1ea0eae067cb63 authored by Dominique Makowski on 12 February 2024, 11:40:02 UTC
version 0.13.2
version 0.13.2
Tip revision: 79b3ea0
test-bayesfactor_parameters.R
test_that("bayesfactor_parameters data frame", {
skip_if_not_or_load_if_installed("logspline", "2.1.21")
Xprior <- data.frame(
x = distribution_normal(1e4),
y = distribution_normal(1e4)
)
Xposterior <- data.frame(
x = distribution_normal(1e4, mean = 0.5),
y = distribution_normal(1e4, mean = -0.5)
)
# point
bfsd <- bayesfactor_parameters(Xposterior, prior = Xprior, null = 0, direction = 0, verbose = FALSE)
expect_equal(bfsd$log_BF, c(0.12, 0.12), tolerance = 0.1)
bfsd <- bayesfactor_parameters(Xposterior, prior = Xprior, null = 0, direction = 1, verbose = FALSE)
expect_equal(bfsd$log_BF, c(0.44, -0.35), tolerance = 0.1)
bfsd <- bayesfactor_parameters(Xposterior, prior = Xprior, null = 0, direction = -1, verbose = FALSE)
expect_equal(bfsd$log_BF, c(-0.35, 0.44), tolerance = 0.1)
bfsd <- bayesfactor_parameters(Xposterior, prior = Xprior, null = 0.5, direction = 0, verbose = FALSE)
expect_equal(bfsd$log_BF, c(-0.12, 0.37), tolerance = 0.1)
expect_warning(bayesfactor_parameters(Xposterior, Xprior))
w <- capture_warnings(bfsd <- bayesfactor_parameters(Xposterior))
expect_match(w, "Prior", all = FALSE)
expect_match(w, "40", all = FALSE)
expect_equal(bfsd$log_BF, c(0, 0), tolerance = 0.1)
# interval
expect_warning(
bfsd <- bayesfactor_parameters(Xposterior, prior = Xprior, null = c(-.1, .1), direction = 0),
regexp = NA
)
expect_equal(bfsd$log_BF, c(0.13, 0.13), tolerance = 0.1)
bfsd <- bayesfactor_parameters(Xposterior, prior = Xprior, null = c(-.1, .1), direction = 1)
expect_equal(bfsd$log_BF, c(0.47, -0.39), tolerance = 0.1)
bfsd <- bayesfactor_parameters(Xposterior, prior = Xprior, null = c(-.1, .1), direction = -1)
expect_equal(bfsd$log_BF, c(-0.39, 0.47), tolerance = 0.1)
# interval with inf
bfsd <- bayesfactor_parameters(Xposterior, prior = Xprior, null = c(-.1, Inf))
expect_equal(bfsd$log_BF, c(-0.81, 0.80), tolerance = 0.1)
bfsd <- bayesfactor_parameters(Xposterior, prior = Xprior, null = c(-Inf, .1))
expect_equal(bfsd$log_BF, c(0.80, -0.81), tolerance = 0.1)
})
test_that("bayesfactor_parameters RSTANARM", {
skip_on_cran()
skip_if_offline()
skip_if_not_or_load_if_installed("logspline", "2.1.21")
skip_if_not_or_load_if_installed("rstanarm")
skip_if_not_or_load_if_installed("httr")
fit <- suppressMessages(stan_glm(mpg ~ ., data = mtcars, refresh = 0))
set.seed(333)
fit_p <- unupdate(fit, verbose = FALSE)
expect_warning(BF2 <- bayesfactor_parameters(fit, fit_p))
set.seed(333)
BF1 <- bayesfactor_parameters(fit, verbose = FALSE)
BF3 <- bayesfactor_parameters(insight::get_parameters(fit), insight::get_parameters(fit_p), verbose = FALSE)
expect_equal(BF1, BF2)
expect_equal(BF1[["Parameter"]], BF3[["Parameter"]])
expect_equal(BF1[["log_BF"]], BF3[["log_BF"]])
model_flat <- suppressMessages(
stan_glm(extra ~ group, data = sleep, prior = NULL, refresh = 0)
)
suppressMessages(
expect_error(bayesfactor_parameters(model_flat))
)
skip_on_ci()
fit10 <- update(fit, chains = 10, iter = 5100, warmup = 100)
suppressMessages(
expect_warning(bayesfactor_parameters(fit10), regexp = NA)
)
})
# bayesfactor_parameters BRMS ---------------------------------------------
test_that("bayesfactor_parameters BRMS", {
skip_if_offline()
skip_if_not_or_load_if_installed("logspline", "2.1.21")
skip_if_not_or_load_if_installed("httr")
skip_if_not_or_load_if_installed("brms")
skip_if_not_or_load_if_installed("cmdstanr")
brms_mixed_6 <- insight::download_model("brms_mixed_6")
set.seed(222)
brms_mixed_6_p <- unupdate(brms_mixed_6)
bfsd1 <- suppressWarnings(bayesfactor_parameters(brms_mixed_6, brms_mixed_6_p, effects = "fixed"))
set.seed(222)
bfsd2 <- suppressWarnings(bayesfactor_parameters(brms_mixed_6, effects = "fixed"))
expect_equal(bfsd1$log_BF, bfsd2$log_BF, tolerance = 0.11)
brms_mixed_1 <- insight::download_model("brms_mixed_1")
expect_error(bayesfactor_parameters(brms_mixed_1))
})