skip_if_not_installed("survival")
m1 <- survival::survfit(survival::Surv(time, status) ~ sex + age + ph.ecog, data = survival::lung)
test_that("model_info", {
expect_true(model_info(m1)$is_logit)
expect_false(model_info(m1)$is_linear)
})
test_that("find_predictors", {
expect_identical(find_predictors(m1), list(conditional = c("sex", "age", "ph.ecog")))
expect_null(find_predictors(m1, effects = "random"))
})
test_that("find_response", {
expect_identical(find_response(m1), "survival::Surv(time, status)")
expect_identical(find_response(m1, combine = FALSE), c("time", "status"))
})
test_that("link_inverse", {
expect_equal(link_inverse(m1)(0.2), plogis(0.2), tolerance = 1e-5)
})
test_that("get_data", {
expect_identical(nrow(get_data(m1)), 227L)
expect_named(get_data(m1), c("time", "status", "sex", "age", "ph.ecog"))
})
test_that("find_formula", {
expect_length(find_formula(m1), 1)
expect_equal(
find_formula(m1),
list(conditional = as.formula(
"survival::Surv(time, status) ~ sex + age + ph.ecog"
)),
ignore_attr = TRUE
)
})
test_that("find_variables", {
expect_identical(find_variables(m1), list(
response = c("time", "status"),
conditional = c("sex", "age", "ph.ecog")
))
expect_identical(
find_variables(m1, flatten = TRUE),
c("time", "status", "sex", "age", "ph.ecog")
)
})
test_that("n_obs", {
expect_identical(n_obs(m1), 227L)
})
test_that("linkfun", {
expect_false(is.null(link_function(m1)))
})
test_that("is_multivariate", {
expect_false(is_multivariate(m1))
})
test_that("find_terms", {
expect_identical(
find_terms(m1),
list(
response = "Surv(time, status)",
conditional = c("sex", "age", "ph.ecog")
)
)
})
test_that("find_statistic", {
expect_null(find_statistic(m1))
})
skip_if_not_installed("withr")
withr::with_package(
"survival",
test_that("find_predictors works with strata", {
data(mtcars)
mod <- suppressWarnings(survival::clogit(
am ~ mpg + cyl + mpg:cyl + survival::strata(carb, gear),
data = mtcars
))
out <- find_predictors(mod)
expect_identical(out, list(conditional = c("mpg", "cyl"), strata = c("carb", "gear")))
# works with reserved arguments inside "strata()"
mod <- suppressWarnings(survival::clogit(
am ~ mpg + cyl + mpg:cyl + survival::strata(carb, gear, shortlabel = TRUE),
data = mtcars
))
out <- find_predictors(mod)
expect_identical(out, list(conditional = c("mpg", "cyl"), strata = c("carb", "gear")))
})
)
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