tests/testthat/test-check_multi_daisie_data.R

In joshwlambert/DAISIEmainland: Simulates Data for Phylogenetic Data on Islands for DAISIE with the Addition of Mainland Dynamics

test_that("use", {
  daisie_mainland_data <- DAISIEmainland::sim_island_with_mainland(
    total_time = 1,
    m = 100,
    island_pars = c(1, 1, 50, 0.1, 1),
    mainland_ex = 0.5,
    mainland_sample_prob = 1,
    mainland_sample_type = "complete",
    replicates = 1,
    verbose = FALSE
  )
  ideal_multi_daisie_data <- daisie_mainland_data$ideal_multi_daisie_data
  empirical_multi_daisie_data <-
    daisie_mainland_data$empirical_multi_daisie_data
  expect_silent(check_multi_daisie_data(ideal_multi_daisie_data))
  expect_silent(check_multi_daisie_data(empirical_multi_daisie_data))
  expect_error(
    check_multi_daisie_data(ideal_multi_daisie_data[[1]]),
    "'multi_daisie_data' must be a list of 'daisie_data'"
  )
  expect_error(
    check_multi_daisie_data(empirical_multi_daisie_data[[1]]),
    "'multi_daisie_data' must be a list of 'daisie_data'"
  )

  # Only run locally, as DAISIE's output cannot be suppressed
  if (1 == 2) {
    # This is where daisie_data is used
    loglik <- DAISIE::DAISIE_ML_CS(
      datalist = empirical_daisie_data[[1]],
      initparsopt = c(1, 1, 50, 0.1, 1),
      idparsopt = 1:5,
      parsfix = NULL,
      idparsfix = NULL,
      ddmodel = 11,
      methode = "odeint::runge_kutta_fehlberg78",
      optimmethod = "simplex",
      jitter = 1e-5
    )
  }
})