if (
requiet("survival") &&
requiet("lme4") &&
requiet("nlme") &&
requiet("bdsmatrix") &&
requiet("coxme")) {
set.seed(1234)
lung$inst2 <- sample(1:10, size = nrow(lung), replace = TRUE)
lung <- subset(lung, subset = ph.ecog %in% 0:2)
lung$ph.ecog <- factor(lung$ph.ecog, labels = c("good", "ok", "limited"))
d <<- lung
m1 <- coxme(Surv(time, status) ~ ph.ecog + age + (1 | inst), d)
m2 <- coxme(Surv(time, status) ~ ph.ecog + age + (1 | inst) + (1 | inst2), d)
test_that("model_info", {
expect_true(model_info(m1)$is_logit)
expect_false(model_info(m1)$is_linear)
})
test_that("find_predictors", {
expect_identical(find_predictors(m1), list(conditional = c("ph.ecog", "age")))
expect_identical(
find_predictors(m1, effects = "random"),
list(random = "inst")
)
expect_identical(find_predictors(m2), list(conditional = c("ph.ecog", "age")))
expect_identical(find_predictors(m2, effects = "random"), list(random = c("inst", "inst2")))
})
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)
expect_equal(link_inverse(m2)(0.2), plogis(0.2), tolerance = 1e-5)
})
test_that("get_data", {
expect_equal(nrow(get_data(m1)), 225)
expect_equal(
colnames(get_data(m1)),
c(
"time",
"status",
"ph.ecog",
"age",
"inst"
)
)
expect_equal(
colnames(get_data(m2)),
c(
"time",
"status",
"ph.ecog",
"age",
"inst",
"inst2"
)
)
})
test_that("find_formula", {
expect_length(find_formula(m1), 2)
expect_equal(
find_formula(m1),
list(
conditional = as.formula("Surv(time, status) ~ ph.ecog + age"),
random = as.formula("~1 | inst")
),
ignore_attr = TRUE
)
expect_length(find_formula(m2), 2)
expect_equal(
find_formula(m2),
list(
conditional = as.formula("Surv(time, status) ~ ph.ecog + age"),
random = list(as.formula("~1 | inst"), as.formula("~1 | inst2"))
),
ignore_attr = TRUE
)
})
test_that("find_terms", {
expect_equal(
find_terms(m1),
list(
response = "Surv(time, status)",
conditional = c("ph.ecog", "age"),
random = "inst"
)
)
expect_equal(
find_terms(m1, flatten = TRUE),
c("Surv(time, status)", "ph.ecog", "age", "inst")
)
expect_equal(
find_terms(m2),
list(
response = "Surv(time, status)",
conditional = c("ph.ecog", "age"),
random = c("inst", "inst2")
)
)
expect_equal(
find_terms(m2, flatten = TRUE),
c("Surv(time, status)", "ph.ecog", "age", "inst", "inst2")
)
})
test_that("find_variables", {
expect_equal(
find_variables(m1),
list(
response = c("time", "status"),
conditional = c("ph.ecog", "age"),
random = "inst"
)
)
expect_equal(
find_variables(m1, flatten = TRUE),
c("time", "status", "ph.ecog", "age", "inst")
)
expect_equal(
find_variables(m2),
list(
response = c("time", "status"),
conditional = c("ph.ecog", "age"),
random = c("inst", "inst2")
)
)
expect_equal(
find_variables(m2, flatten = TRUE),
c("time", "status", "ph.ecog", "age", "inst", "inst2")
)
})
test_that("n_obs", {
expect_equal(n_obs(m1), 225)
expect_equal(n_obs(m2), 225)
})
test_that("get_response", {
expect_equal(colnames(get_response(m1)), c("time", "status"))
expect_equal(nrow(get_response(m1)), 225)
expect_equal(colnames(get_response(m1)), c("time", "status"))
expect_equal(nrow(get_response(m2)), 225)
})
test_that("linkfun", {
expect_false(is.null(link_function(m1)))
expect_false(is.null(link_function(m2)))
})
test_that("is_multivariate", {
expect_false(is_multivariate(m1))
})
test_that("find_parameters", {
expect_equal(
find_parameters(m1),
list(
conditional = c("ph.ecogok", "ph.ecoglimited", "age"),
random = "inst"
)
)
expect_equal(
find_parameters(m2),
list(
conditional = c("ph.ecogok", "ph.ecoglimited", "age"),
random = c("inst", "inst2")
)
)
expect_equal(nrow(get_parameters(m1)), 3)
expect_equal(
get_parameters(m1)$Parameter,
c("ph.ecogok", "ph.ecoglimited", "age")
)
expect_equal(nrow(get_parameters(m2)), 3)
expect_equal(
get_parameters(m2)$Parameter,
c("ph.ecogok", "ph.ecoglimited", "age")
)
expect_length(get_parameters(m2, effects = "random"), 2)
})
test_that("find_statistic", {
expect_identical(find_statistic(m1), "z-statistic")
expect_identical(find_statistic(m2), "z-statistic")
})
}
Generated by dwww version 1.15 on Sat May 18 08:42:55 CEST 2024.