tests/testthat/test_stan_fit_5.R

In breathteststan: Stan-Based Fit to Gastric Emptying Curves

test_that("Non-gaussian residuals with student_t_df <10 gives result close to nlme", {
  skip_on_cran()
  skip_on_32bit()
  library(breathtestcore)
  chains = 1
  student_t_df = 5
  dose = 100
  iter = 500
  sample_minutes = 15
  data = cleanup_data(simulate_breathtest_data(n_records = 1, seed = 1000,
                                         student_t_df = student_t_df)$data)
  fit = stan_fit(data, dose = dose, student_t_df = student_t_df,
                 chains = chains, iter = iter  )
  fit_nlme = nlme_fit(data, dose = dose)
  cf = coef(fit) %>%
    left_join(coef(fit_nlme), by = c("patient_id", "parameter", "method","group")) %>%
    filter(method == "exp_beta") %>%
    mutate(rel_diff = 2*abs(value.x - value.y)/(value.x + value.y)) %>%
    select(parameter, rel_diff) %>%
    summarize(
      rel_diff = mean(rel_diff)
    )
  expect_lt(cf$rel_diff, 0.15)
})