tests/testthat/test-coxph.R

In performance: Assessment of Regression Models Performance

skip_if_not_installed("survival")
lung <- survival::lung

lung <- subset(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 <- survival::coxph(survival::Surv(time, status) ~ sex + age + ph.ecog, data = lung)

test_that("r2", {
  expect_equal(r2_nagelkerke(m1), c(`Nagelkerke's R2` = 0.1203544), tolerance = 1e-3)
  expect_equal(r2(m1), list(R2 = c(`Nagelkerke's R2` = 0.1203544)), tolerance = 1e-3, ignore_attr = TRUE)
})

test_that("model_performance", {
  perf <- suppressWarnings(model_performance(m1, verbose = FALSE))

  expect_equal(perf$AIC, 1457.19458886438, tolerance = 1e-3)
  expect_equal(perf$BIC, 1469.5695896676, tolerance = 1e-3)
  expect_equal(perf$R2_Nagelkerke, 0.1203544, tolerance = 1e-3)
  expect_equal(perf$RMSE, 0.882014942836432, tolerance = 1e-3)
})

test_that("r2", {
  expect_error(r2_xu(m1))
})