tests/testthat/test-DAISIE_ML4.R

In DAISIE: Dynamical Assembly of Islands by Speciation, Immigration and Extinction

test_that("DAISIE_ML4 is silent and produces correct output", {
  skip("Takes too long and produces DLSODES warnings")
  utils::data(Galapagos_datalist)
  loglik <- DAISIE_ML4(
    datalist = Galapagos_datalist,
    initparsopt = c(1.05, 0.36, 26.6, 0.0029, 0.73, 0.1),
    idparsopt = 1:6,
    parsfix = NULL,
    idparsfix = NULL,
    verbose = 0,
    methode = 'lsodes',
    optimmethod = 'simplex',
    CS_version = create_CS_version(model = 2,
                                   relaxed_par = "extinction",
                                   par_sd = 0.1,
                                   par_upper_bound = 1))
  testthat::expect_equal(2, 2)
})

test_that("DAISIE_loglik_all_choosepar4 is silent and produces correct output", {
  utils::data(Galapagos_datalist)
  skip_if(Sys.getenv("CI") == "", message = "Run only on CI")
  skip_on_cran()
  # Throws warnings and DLSODES output
  invisible(capture.output(suppressWarnings(
    output <- DAISIE_loglik_all_choosepar4(
      trparsopt = c(0.718364388965934, 0.728515721595379, 0.909090909090909,
                    0.009245787662330, 0.502505659845103, 0.500000000000000),
      trparsfix = numeric(0),
      idparsopt = c(1, 2, 3, 4, 5, 6),
      idparsfix = NULL,
      pars2 = c(100, 0, 0, 0, NA),
      datalist = Galapagos_datalist,
      methode = "lsodes",
      CS_version = list(model = 2,
                        relaxed_par = "cladogenesis",
                        par_sd = 1,
                        par_upper_bound = Inf),
      abstolint = 1e-16,
      reltolint = 1e-10
    ))))
  testthat::expect_equal(output, -77.50300643925)
})