tests/testthat/test-cumulative-coefficients.R

In adibender/pammtools: Piece-Wise Exponential Additive Mixed Modeling Tools for Survival Analysis

context("Test cumulative coefficients functionality")

test_that("Cumulative coefficients work", {

  df <- tumor[1:30, c("days", "status", "age")]
  df$x1 <- as.factor(rep(letters[1:3], each = nrow(df) / 3L))

  ## pam
  ped <- as_ped(df, formula = Surv(days, status)~ x1 + age)
  pam <- mgcv::gam(ped_status ~ s(tend) + x1 + age, data = ped,
    family = poisson(), offset = offset)
  cumu_coef_pam <- get_cumu_coef(pam, ped, terms = c("age", "x1"), nsim = 20L)
  expect_data_frame(cumu_coef_pam, nrows = 36L, ncols = 6L)
  expect_equal(unique(cumu_coef_pam$variable), c("age", "x1 (b)", "x1 (c)"))
  cumu_coef_pam <- get_cumu_coef(pam, ped, terms = c("(Intercept)", "age"))
  expect_data_frame(cumu_coef_pam, nrows = 24L, ncols = 6L)

})