requiet("survival")
requiet("insight")
requiet("JM")
lung <- subset(survival::lung, subset = ph.ecog %in% 0:2)
lung$sex <- factor(lung$sex, labels = c("male", "female"))
lung$ph.ecog <- factor(lung$ph.ecog, labels = c("good", "ok", "limited"))
m1 <- coxph(Surv(time, status) ~ sex + age + ph.ecog, data = 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), "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", {
## NOTE check back every now and then and see if tests still work
skip("works interactively")
expect_s3_class(get_data(m1), "data.frame")
expect_equal(dim(get_data(m1)), c(166, 10))
})
test_that("get_data: regression test for previous bug", {
## NOTE check back every now and then and see if tests still work
skip("works interactively")
dat_regression_test <- data.frame(
time = c(4, 3, 1, 1, 2, 2, 3),
status = c(1, 1, 1, 0, 1, 1, 0),
x = c(0, 2, 1, 1, 1, 0, 0),
sex = c(0, 0, 0, 0, 1, 1, 1)
)
mod <- coxph(Surv(time, status) ~ x + strata(sex),
data = dat_regression_test,
ties = "breslow"
)
expect_equal(get_data(mod), dat_regression_test, ignore_attr = TRUE)
})
test_that("get_data: regression test for data stored as list", {
## NOTE check back every now and then and see if tests still work
skip("works interactively")
dat_regression_test <- list(
time = c(4, 3, 1, 1, 2, 2, 3),
status = c(1, 1, 1, 0, 1, 1, 0),
x = c(0, 2, 1, 1, 1, 0, 0),
sex = c(0, 0, 0, 0, 1, 1, 1)
)
mod <- coxph(Surv(time, status) ~ x + strata(sex),
data = dat_regression_test,
ties = "breslow"
)
expect_equal(get_data(mod), as.data.frame(dat_regression_test), ignore_attr = TRUE)
})
test_that("find_formula", {
expect_length(find_formula(m1), 1)
expect_equal(
find_formula(m1),
list(conditional = as.formula(
"Surv(time, status) ~ sex + age + ph.ecog"
)),
ignore_attr = TRUE
)
})
test_that("find_variables", {
expect_equal(find_variables(m1), list(
response = c("time", "status"),
conditional = c("sex", "age", "ph.ecog")
))
expect_equal(
find_variables(m1, flatten = TRUE),
c("time", "status", "sex", "age", "ph.ecog")
)
})
test_that("n_obs", {
expect_equal(n_obs(m1), 226)
})
test_that("linkfun", {
expect_false(is.null(link_function(m1)))
})
test_that("is_multivariate", {
expect_false(is_multivariate(m1))
})
test_that("find_parameters", {
expect_equal(
find_parameters(m1),
list(
conditional = c("sexfemale", "age", "ph.ecogok", "ph.ecoglimited")
)
)
expect_equal(nrow(get_parameters(m1)), 4)
expect_equal(
get_parameters(m1)$Parameter,
c("sexfemale", "age", "ph.ecogok", "ph.ecoglimited")
)
})
test_that("find_terms", {
expect_equal(
find_terms(m1),
list(
response = "Surv(time, status)",
conditional = c("sex", "age", "ph.ecog")
)
)
})
test_that("find_statistic", {
expect_identical(find_statistic(m1), "z-statistic")
})
test_that("get_statistic", {
requiet("survival")
bladder1 <- bladder[bladder$enum < 5, ]
mod <- coxph(
Surv(stop, event) ~ (rx + size + number) * strata(enum),
cluster = id, bladder1, robust = TRUE
)
z1 <- get_statistic(mod)$Statistic
z2 <- coef(summary(mod))[, "z"]
expect_equal(z1, z2, ignore_attr = TRUE)
lung <- survival::lung
mod <- survival::coxph(
formula = Surv(time, status) ~ age + sex + frailty(inst),
data = lung
)
z1 <- get_statistic(mod)$Statistic
z2 <- coef(summary(mod))[, "Chisq"]
expect_equal(z1, z2, ignore_attr = TRUE)
})
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