tests/testthat/test-DAISIE_sim_trait_dep.R

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

test_that("A clean CS two trait simulation run should produce no output", {
  n_mainland_species <- 1000
  island_age <- 0.4
  clado_rate <- 0.0001 # cladogenesis rate
  ext_rate <- 2.683454548 # extinction rate (not used)
  clade_carr_cap <- 0.05  # clade-level carrying capacity
  imm_rate <- 0.001 # immigration rate
  ana_rate <- 0.1 # anagenesis rate
  trans_rate <- 0.5 # transition rate
  trait_pars <- create_trait_pars(trans_rate = trans_rate,
                                  immig_rate2 = imm_rate / 2,
                                  ext_rate2 = ext_rate * 2,
                                  ana_rate2 = ana_rate / 2,
                                  clado_rate2 = clado_rate / 2,
                                  trans_rate2 = trans_rate / 2,
                                  M2 = n_mainland_species / 2)
  island_ontogeny <- "const"
  sea_level <- "const"
  extcutoff <- 1000
  testthat::expect_silent(
    DAISIE_sim_trait_dep(
      time = island_age,
      M = n_mainland_species,
      pars = c(clado_rate, ext_rate, clade_carr_cap, imm_rate, ana_rate),
      replicates = 1,
      island_ontogeny = island_ontogeny,
      sea_level = sea_level,
      trait_pars = trait_pars,
      extcutoff = extcutoff,
      plot_sims = FALSE,
      verbose = FALSE
    )
  )
})

test_that("A divdepmodel = 'CS' two trait run with cond works as expected", {
  set.seed(Sys.time()) # Always run a different sim
  n_mainland_species <- 1000
  island_age <- 0.4
  clado_rate <- 0.0001 # cladogenesis rate
  ext_rate <- 2.683454548 # extinction rate (not used)
  clade_carr_cap <- 0.05  # clade-level carrying capacity
  imm_rate <- 0.01 # immigration rate
  ana_rate <- 0.1 # anagenesis rate
  trans_rate <- 0.5 # transition rate
  cond <- 5
  trait_pars <- create_trait_pars(trans_rate = trans_rate,
                                  immig_rate2 = imm_rate / 2,
                                  ext_rate2 = ext_rate * 2,
                                  ana_rate2 = ana_rate / 2,
                                  clado_rate2 = clado_rate / 2,
                                  trans_rate2 = trans_rate / 2,
                                  M2 = n_mainland_species / 2)
  island_ontogeny <- "const"
  sea_level <- "const"
  extcutoff <- 1000
  testthat::expect_silent(
    out <- DAISIE_sim_trait_dep(
      time = island_age,
      M = n_mainland_species,
      pars = c(clado_rate, ext_rate, clade_carr_cap, imm_rate, ana_rate),
      replicates = 1,
      island_ontogeny = island_ontogeny,
      sea_level = sea_level,
      trait_pars = trait_pars,
      extcutoff = extcutoff,
      plot_sims = FALSE,
      verbose = FALSE,
      cond = cond
    )
  )

  testthat::expect_true(out[[1]][[1]]$stt_all[nrow(out[[1]][[1]]$stt_all), 8] >= cond)
})

test_that("A divdepmodel = 'CS' two trait run cond no cond work as expected", {
  set.seed(1) # Always run the same sim
  n_mainland_species <- 1000
  island_age <- 0.4
  clado_rate <- 0.0001 # cladogenesis rate
  ext_rate <- 2.683454548 # extinction rate (not used)
  clade_carr_cap <- 0.05  # clade-level carrying capacity
  imm_rate <- 0.01 # immigration rate
  ana_rate <- 0.1 # anagenesis rate
  trans_rate <- 0.5 # transition rate
  cond <- 5
  trait_pars <- create_trait_pars(trans_rate = trans_rate,
                                  immig_rate2 = imm_rate / 2,
                                  ext_rate2 = ext_rate * 2,
                                  ana_rate2 = ana_rate / 2,
                                  clado_rate2 = clado_rate / 2,
                                  trans_rate2 = trans_rate / 2,
                                  M2 = n_mainland_species / 2)
  island_ontogeny <- "const"
  sea_level <- "const"
  extcutoff <- 1000
  testthat::expect_silent(
    out_cond <- DAISIE_sim_trait_dep(
      time = island_age,
      M = n_mainland_species,
      pars = c(clado_rate, ext_rate, clade_carr_cap, imm_rate, ana_rate),
      replicates = 1,
      island_ontogeny = island_ontogeny,
      sea_level = sea_level,
      trait_pars = trait_pars,
      extcutoff = extcutoff,
      plot_sims = FALSE,
      verbose = FALSE,
      cond = cond
    )
  )

  testthat::expect_true(
    out_cond[[1]][[1]]$stt_all[nrow(out_cond[[1]][[1]]$stt_all), 8] >= cond
  )

  set.seed(1)
  testthat::expect_silent(
    out_no_cond <- DAISIE_sim_trait_dep(
      time = island_age,
      M = n_mainland_species,
      pars = c(clado_rate, ext_rate, clade_carr_cap, imm_rate, ana_rate),
      replicates = 1,
      island_ontogeny = island_ontogeny,
      sea_level = sea_level,
      trait_pars = trait_pars,
      extcutoff = extcutoff,
      plot_sims = FALSE,
      verbose = FALSE,
      cond = 0
    )
  )

  testthat::expect_true(
    out_no_cond[[1]][[1]]$stt_all[nrow(out_no_cond[[1]][[1]]$stt_all), 8] < 5)
})

test_that("A clean IW two trait simulation run should produce no output", {
  n_mainland_species <- 1000
  island_age <- 0.4
  clado_rate <- 0.0001 # cladogenesis rate
  ext_rate <- 2.683454548 # extinction rate (not used)
  clade_carr_cap <- 0.05  # clade-level carrying capacity
  imm_rate <- 0.001 # immigration rate
  ana_rate <- 0.1 # anagenesis rate
  trans_rate <- 0.5 # transition rate
  trait_pars <- create_trait_pars(trans_rate = trans_rate,
                                  immig_rate2 = imm_rate / 2,
                                  ext_rate2 = ext_rate * 2,
                                  ana_rate2 = ana_rate / 2,
                                  clado_rate2 = clado_rate / 2,
                                  trans_rate2 = trans_rate / 2,
                                  M2 = n_mainland_species / 2)
  divdepmodel <- "IW"
  island_ontogeny <- "const"
  sea_level <- "const"
  extcutoff <- 1000
  testthat::expect_silent(
    DAISIE_sim_trait_dep(
      time = island_age,
      M = n_mainland_species,
      pars = c(clado_rate, ext_rate, clade_carr_cap, imm_rate, ana_rate),
      trait_pars = trait_pars,
      replicates = 1,
      divdepmodel = divdepmodel,
      island_ontogeny = island_ontogeny,
      sea_level = sea_level,
      extcutoff = extcutoff,
      plot_sims = FALSE,
      verbose = FALSE
    )
  )
})