tests/testthat/test-survival_ln_mixture-fit.R

In lnmixsurv: Bayesian Mixture Log-Normal Survival Model

test_that("outcome must be Surv object", {
  expect_error(
    survival_ln_mixture(y ~ x, sim_data$data)
  )
})

test_that("only right censored data supported", {
  expect_error(
    survival_ln_mixture(survival::Surv(y, delta, type = "left") ~ x, sim_data$data)
  )
})

test_that("events at time zero are not supported", {
  data_new <- sim_data$data
  data_new$y[1] <- 0
  expect_error(
    survival_ln_mixture(survival::Surv(y, delta, type = "left") ~ x, sim_data$data)
  )
})

test_that("when using ~NULL, intercept must be TRUE", {
  expect_error(
    survival_ln_mixture(survival::Surv(y, delta) ~ NULL, sim_data$data, intercept = FALSE)
  )
})

test_that("survival_ln_mixture doesnt work with xy specification", {
  expect_error(
    survival_ln_mixture(sim_data$data$y, sim_data$data$x)
  )
})

test_that("survival_ln_mixture works with intercept only fit", {
  mod <- readRDS(test_path("fixtures", "ln_fit_with_intercept_only.rds"))
  expect_equal(tidy(mod)$estimate, c(3.44, 4.02, 4.83), tolerance = 1)
})

test_that("fit works as expected with simulated data", {
  mod <- readRDS(test_path("fixtures", "ln_fit_with_covariates.rds"))
  post_summary <- posterior::summarise_draws(mod$posterior, estimate = stats::median, std.error = stats::mad)
  colnames(post_summary)[1] <- "term"
  post_tidy <- tidy(mod, effects = c("fixed", "auxiliary"))
  
  expected_result <- structure(
    list(term = c(
      "(Intercept)_1", "x1_1", "(Intercept)_2",
      "x1_2", "phi_1", "phi_2", "eta_1"
    ), estimate = c(
      4.05, 0.81, 3.43, 0.487, 26.7, 3.18, 0.505
    ), std.error = c(
      0.00668, 0.00942, 0.0172, 0.0203, 1.34, 0.114, 0.0109
    )),
    row.names = c(NA, -7L), 
    class = c("draws_summary", "tbl_df", "tbl", "data.frame"), 
    num_args = list())

  expect_equal(mod$nobs, 10000)
  expect_equal(post_summary, post_tidy, tolerance = 1)
  expect_equal(post_summary, expected_result, tolerance = 1)
})