Nothing
## Test confint() methods
var_nms <- c(".estimate", ".se", ".crit", ".lower_ci", ".upper_ci")
## first derivatives of all smooths...
test_that("Point-wise confidence interval for a first derivatives of a GAM works", {
skip_if_not_installed("withr")
withr::local_options(lifecycle_verbosity = "quiet")
fd <- fderiv(m_gam)
ci <- confint(fd, type = "confidence")
expect_s3_class(ci, "confint.fderiv")
expect_s3_class(ci, "data.frame")
expect_named(ci, expected = c("term", "lower", "est", "upper"))
expect_warning(confint(fd, level = c(0.95, 0.8), type = "confidence"))
expect_error(confint(fd, parm = "s(x4)", type = "confidence"))
})
test_that("Simultaneous interval for a first derivatives of a GAM works", {
skip_if_not_installed("withr")
withr::local_options(lifecycle_verbosity = "quiet")
fd <- fderiv(m_gam)
ci <- withr::with_seed(
42,
confint(fd, parm = "x1", type = "simultaneous", nsim = 1000)
)
expect_s3_class(ci, "confint.fderiv")
expect_s3_class(ci, "data.frame")
expect_named(ci, expected = c("term", "lower", "est", "upper"))
})
test_that("Point-wise confidence interval for a GAM works", {
skip_if_not_installed("withr")
withr::local_options(lifecycle_verbosity = "quiet")
ci <- confint(m_gam, parm = "s(x1)", type = "confidence")
expect_s3_class(ci, "confint.gam")
expect_s3_class(ci, "tbl_df")
expect_named(ci, expected = c(".smooth", ".type", ".by", "x1", var_nms))
})
test_that("Simultaneous interval for a GAM works", {
skip_if_not_installed("withr")
withr::local_options(lifecycle_verbosity = "quiet")
ci <- withr::with_seed(
42,
confint(m_gam, parm = "s(x1)", type = "simultaneous", nsim = 100)
)
expect_s3_class(ci, "confint.gam")
expect_s3_class(ci, "tbl_df")
expect_named(ci, expected = c(".smooth", ".type", ".by", "x1", var_nms))
})
## 2d smooth
test_that("Point-wise confidence interval for a 2d smooth works", {
skip_if_not_installed("withr")
withr::local_options(lifecycle_verbosity = "quiet")
ci <- confint(su_m_bivar_te, parm = "te(x,z)", type = "confidence")
expect_s3_class(ci, "confint.gam")
expect_s3_class(ci, "tbl_df")
expect_named(ci, expected = c(".smooth", ".type", ".by", "x", "z", var_nms))
})
test_that("Simultaneous interval for a 2d smooth works", {
skip_if_not_installed("withr")
withr::local_options(lifecycle_verbosity = "quiet")
ci <- withr::with_seed(
42,
confint(su_m_bivar_te,
parm = "te(x,z)", type = "simultaneous",
nsim = 100
)
)
expect_s3_class(ci, "confint.gam")
expect_s3_class(ci, "tbl_df")
expect_named(ci, expected = c(".smooth", ".type", ".by", "x", "z", var_nms))
})
test_that("Point-wise confidence interval for a GAMM works", {
withr::local_options(lifecycle_verbosity = "quiet")
skip_if_not_installed("withr")
ci <- confint(m_gamm, parm = "s(x1)", type = "confidence")
expect_s3_class(ci, "confint.gam")
expect_s3_class(ci, "tbl_df")
expect_named(ci, expected = c(".smooth", ".type", ".by", "x1", var_nms))
})
test_that("Simultaneous interval for a GAMM works", {
skip_if_not_installed("withr")
withr::local_options(lifecycle_verbosity = "quiet")
ci <- withr::with_seed(
42,
confint(m_gamm, parm = "s(x1)", type = "simultaneous", nsim = 100)
)
expect_s3_class(ci, "confint.gam")
expect_s3_class(ci, "tbl_df")
expect_named(ci, expected = c(".smooth", ".type", ".by", "x1", var_nms))
})
## confint methods for by variables
test_that("Point-wise confidence interval for a GAM with factor by variable works", {
skip_if_not_installed("withr")
withr::local_options(lifecycle_verbosity = "quiet")
ci <- confint(su_m_factor_by_x2,
parm = "s(x2)", type = "confidence",
partial_match = TRUE
)
expect_s3_class(ci, "confint.gam")
expect_s3_class(ci, "tbl_df")
expect_named(ci, expected = c(
".smooth", ".type", ".by", "x2", "fac",
var_nms
))
expect_equal(
paste0("s(x2):fac", levels(su_eg4[["fac"]])),
unique(ci[[".smooth"]])
)
})
test_that("Simultaneous confidence interval for a GAM with factor by variable works", {
skip_if_not_installed("withr")
withr::local_options(lifecycle_verbosity = "quiet")
ci <- confint(su_m_factor_by_x2,
parm = "s(x2)", type = "simultaneous",
partial_match = TRUE
)
expect_s3_class(ci, "confint.gam")
expect_s3_class(ci, "tbl_df")
expect_named(ci, expected = c(".smooth", ".type", ".by", "x2", "fac", var_nms))
expect_equal(
paste0("s(x2):fac", levels(su_eg4[["fac"]])),
unique(ci[[".smooth"]])
)
})
## Part of #80
test_that("Point-wise confidence interval for a GAM with selected factor by variable works", {
skip_if_not_installed("withr")
withr::local_options(lifecycle_verbosity = "quiet")
ci <- confint(su_m_factor_by_x2, parm = "s(x2):fac1", type = "confidence")
expect_s3_class(ci, "confint.gam")
expect_s3_class(ci, "tbl_df")
expect_named(ci, expected = c(".smooth", ".type", ".by", "x2", "fac", var_nms))
})
test_that("Point-wise confidence interval for a GAMM works", {
skip_if_not_installed("withr")
withr::local_options(lifecycle_verbosity = "quiet")
ci <- confint(m_gamm4, parm = "s(x1)", type = "confidence")
expect_s3_class(ci, "confint.gam")
expect_s3_class(ci, "tbl_df")
expect_named(ci, expected = c(".smooth", ".type", ".by", "x1", var_nms))
})
test_that("Simultaneous interval for a GAMM works", {
skip_if_not_installed("withr")
withr::local_options(lifecycle_verbosity = "quiet")
ci <- withr::with_seed(
42,
confint(m_gamm4, parm = "s(x1)", type = "simultaneous", nsim = 100)
)
expect_s3_class(ci, "confint.gam")
expect_s3_class(ci, "tbl_df")
expect_named(ci, expected = c(".smooth", ".type", ".by", "x1", var_nms))
})
## test snapshots...
test_that("confint.fderiv example output", {
skip_on_cran()
skip_on_os("win")
skip_if_not_installed("withr")
withr::local_options(lifecycle_verbosity = "quiet")
# new data to evaluate the derivatives at, say over the middle 50% of range
# of each covariate
middle <- function(x, n = 25, coverage = 0.5) {
v <- (1 - coverage) / 2
q <- quantile(x, prob = c(0 + v, 1 - v), type = 8)
seq(q[1], q[2], length = n)
}
new_data <- sapply(su_eg1[c("x0", "x1", "x2", "x3")], middle)
new_data <- data.frame(new_data)
## first derivatives of all smooths...
fd <- fderiv(m_gam, newdata = new_data)
## point-wise interval
ci <- confint(fd, type = "confidence")
expect_snapshot_output(ci)
## simultaneous interval for smooth term of x2
x2_sint <- withr::with_seed(
24,
confint(fd,
parm = "x2", type = "simultaneous", nsim = 10000,
ncores = 2
)
)
# skip_on_ci()
skip_on_covr()
skip_on_os(os = c("linux", "windows"))
expect_snapshot_output(x2_sint)
})
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