tests/testthat/test_dnnsurv.R

In survivalmodels: Models for Survival Analysis

skip_on_os("windows")
skip_if_not_installed("keras")

test_that("silent", {
  expect_silent({fit <- dnnsurv(Surv(time, status) ~ ., data = rats[1:50, ], verbose = FALSE,
                                validation_split = 0.3)})
  expect_silent({predict(fit, newdata = rats[51:100, ])})
})

test_that("errors", {
  expect_error(dnnsurv(Surv(time, status) ~ ., data = rats[1:50, ], cuts = NULL, cutpoints = NULL),
               "One of")
})

test_that("custom", {
  expect_silent(dnnsurv(Surv(time, status) ~ ., data = rats[1:10, 1:4], verbose = FALSE,
                        cuts = 3,
                        custom_model = build_keras_net(5L, 1L)))
})

test_that("early stopping", {
  expect_silent(dnnsurv(Surv(time, status) ~ ., data = rats[1:10, 1:4], verbose = FALSE,
                        early_stopping = TRUE, validation_split = 0.3))
})

fit <- dnnsurv(Surv(time, status) ~ ., data = rats[1:50, ], verbose = FALSE,
               cuts = 5)

test_that("predict", {
  p <- predict(fit, type = "all", distr6 = FALSE)
  expect_is(p, "list")
  expect_is(p$surv, "matrix")
  expect_is(p$risk, "numeric")
  expect_equal(length(p$risk), 50)
  expect_equal(dim(p$surv), c(50, 5))
})

test_that("predict distr6", {
  if (!requireNamespace("distr6", quietly = TRUE)) {
    skip("distr6 not installed.")
  }
  p <- predict(fit, type = "all", distr6 = TRUE)
  expect_is(p, "list")
  expect_is(p$surv, "Matdist")
  expect_equal(nrow(distr6::gprm(p$surv, "cdf")), 50)
  p <- predict(fit, type = "survival")
  expect_is(p, "matrix")
})

test_that("auto sanity", {
  sanity_check(
    model = "dnnsurv",
    pars = list(epochs = 100L, validation_split = 0.3)
  )
})