tests/testthat/test_simulation_functions-sim_sad().R

In mobsim: Spatial Simulation and Scale-Dependent Analysis of Biodiversity Changes

test_that("sim_sad() - correct assertions", {
   expect_error(sim_sad(n_sim = 100L, sad_type = "lnorm"))
   expect_error(sim_sad(s_pool = NA, n_sim = 100L, sad_type = "lnorm"),
                "The argument s_pool is mandatory for the selected sad and has to be a positive integer number.")
   expect_error(sim_sad(s_pool = 3.5, n_sim = 100L, sad_type = "lnorm"),
                "s_pool has to be a positive integer number")
   expect_error(sim_sad(s_pool = 0L, n_sim = 100L, sad_type = "lnorm"),
                "s_pool has to be a positive integer number")

   expect_error(sim_sad(s_pool = 3L, sad_type = "lnorm"))
   expect_error(sim_sad(s_pool = 3L, n_sim = NA, sad_type = "lnorm"))
   expect_error(sim_sad(s_pool = 3L, n_sim = 100.5, sad_type = "lnorm"),
                "n_sim has to be a positive integer number")
   expect_error(sim_sad(s_pool = 3L, n_sim = 0L, sad_type = "lnorm"),
                "n_sim has to be a positive integer number")

   expect_error(sim_sad(s_pool = 3L, n_sim = 100L, sad_type = "lnorm",
                        sad_coef = 0.1),
                "coef must be a named list!")
   expect_error(sim_sad(s_pool = 3L, n_sim = 100L, sad_type = "wrong_sad_type"))

   expect_error(sim_sad(sad_type = "bs", sad_coef = list(S = 4L)))

   expect_warning(sim_sad(s_pool = 3L, sad_type = "bs",
                          sad_coef = list(S = 4L, N = 10L)))
   expect_warning(sim_sad(n_sim = 10L, sad_type = "bs",
                          sad_coef = list(S = 4L, N = 10L)))
})

test_that("default argument values are as expected", {
   expect_snapshot(sim_sad(s_pool = 3L, n_sim = 100L, seed = 42L))
})

test_that("sim_sad() - results are as expected", {
   expect_equal(names(sim_sad(s_pool = 3L, n_sim = 10L))[1L], "species_1")
   n_sim <- 10L
   s_pool <- 3L

   sadNorm <- sim_sad(s_pool = s_pool, n_sim = n_sim, sad_type = "lnorm",
                      fix_s_sim = TRUE)
   expect_equal(sum(sadNorm), n_sim)
   expect_equal(length(sadNorm), s_pool)

   sadBs <- sim_sad(sad_type = "bs", sad_coef = list(S = s_pool, N = n_sim),
                    fix_s_sim = TRUE)
   expect_equal(sum(sadBs), n_sim)
   expect_equal(length(sadBs), s_pool)

   sadGamma <- sim_sad(s_pool = s_pool, n_sim = n_sim, sad_type = "gamma",
                       sad_coef = list(shape = 1, scale = 1), fix_s_sim = TRUE)
   expect_equal(sum(sadGamma), n_sim)
   expect_equal(length(sadGamma), s_pool)

   sadGeom <- sim_sad(s_pool = s_pool, n_sim = n_sim, sad_type = "geom",
                      sad_coef = list(prob = 0.5), fix_s_sim = TRUE)
   expect_equal(sum(sadGeom), n_sim)
   expect_equal(length(sadGeom), s_pool)

   sadLs <- sim_sad(sad_type = "ls", sad_coef = list(N = n_sim, alpha = 3),
                    fix_s_sim = TRUE)
   expect_equal(sum(sadLs), n_sim)

   # expect_equal(sum(sim_sad(sad_type = "mzsm", sad_coef = list(n = 3L, J = n_sim, theta = 4))), n_sim)

   sadNbinom <- sim_sad(s_pool = s_pool, n_sim = n_sim, sad_type = "nbinom",
                        sad_coef = list(size = 100L, prob = 0.5),
                        fix_s_sim = TRUE)
   expect_equal(sum(sadNbinom), n_sim)
   expect_equal(length(sadNbinom), s_pool)

   sadPareto <- sim_sad(s_pool = s_pool, n_sim = n_sim, sad_type = "pareto",
                        sad_coef = list(shape = 2), fix_s_sim = TRUE)
   expect_equal(sum(sadPareto), n_sim)
   expect_equal(length(sadPareto), s_pool)

   sadPoilog <- sim_sad(s_pool = s_pool, n_sim = n_sim, sad_type = "poilog",
                        fix_s_sim = TRUE)
   expect_equal(sum(sadPoilog), n_sim)
   expect_equal(length(sadPoilog), s_pool)

   sadPower <- sim_sad(s_pool = s_pool, n_sim = n_sim, sad_type = "power",
                       sad_coef = list(s = 2), fix_s_sim = TRUE)
   expect_equal(sum(sadPower), n_sim)
   expect_equal(length(sadPower), s_pool)

   # expect_equal(sum(sim_sad(s_pool = 3L, n_sim = n_sim, sad_type = "powbend", sad_coef = list(s = 2, omega = 3))), n_sim)

   sadWeibull <- sim_sad(s_pool = s_pool, n_sim = n_sim, sad_type = "weibull",
                         sad_coef = list(shape = 2), fix_s_sim = TRUE)
   expect_equal(sum(sadWeibull), n_sim)
   expect_equal(length(sadWeibull), s_pool)
})

test_that("sim_sad() - edge case s_pool = 1", {
   n_sim <- 100L
   s_pool <- 1L
   sad1lnorm <- sim_sad(s_pool = s_pool, n_sim = n_sim, sad_type = "lnorm", sad_coef = list(cv_abund = 1))

   expect_equal(sum(sad1lnorm), n_sim)
   expect_equal(length(sad1lnorm), s_pool)

   sad1bs <- sim_sad(sad_type = "bs", sad_coef = list(S = s_pool, N = n_sim))

   expect_equal(sum(sad1bs), n_sim)
   expect_equal(length(sad1bs), s_pool)

   expect_error(sim_sad(s_pool = 1, n_sim = 0))
})


test_that("sim_sad() - respects seed argument", {
   expect_equal(
      sim_sad(sad_type = "lnorm", s_pool = 10L, n_sim = 500L, seed = 42L),
      sim_sad(sad_type = "lnorm", s_pool = 10L, n_sim = 500L, seed = 42L)
   )
   expect_equal(
      sim_sad(sad_type = "bs", sad_coef = list(S = 4L, N = 10L), seed = 42L),
      sim_sad(sad_type = "bs", sad_coef = list(S = 4L, N = 10L), seed = 42L)
   )
   expect_equal(
      sim_sad(sad_type = "gamma", s_pool = 10L, n_sim = 500L, sad_coef = list(shape = 1, scale = 1), seed = 42L),
      sim_sad(sad_type = "gamma", s_pool = 10L, n_sim = 500L, sad_coef = list(shape = 1, scale = 1), seed = 42L)
   )
   expect_equal(
      sim_sad(sad_type = "geom",  s_pool = 10L, n_sim = 500L, sad_coef = list(prob = 0.5), seed = 42L),
      sim_sad(sad_type = "geom",  s_pool = 10L, n_sim = 500L, sad_coef = list(prob = 0.5), seed = 42L)
   )
   expect_equal(
      sim_sad(sad_type = "ls", sad_coef = list(N = 500L, alpha = 3), seed = 42L),
      sim_sad(sad_type = "ls", sad_coef = list(N = 500L, alpha = 3), seed = 42L)
   )
   expect_equal(
      sim_sad(sad_type = "nbinom", s_pool = 10L, n_sim = 500L, sad_coef = list(size = 100L, prob = 0.5), seed = 42L),
      sim_sad(sad_type = "nbinom", s_pool = 10L, n_sim = 500L, sad_coef = list(size = 100L, prob = 0.5), seed = 42L)
   )
   expect_equal(
      sim_sad(sad_type = "pareto", s_pool = 10L, n_sim = 500L, sad_coef = list(shape = 2), seed = 42L),
      sim_sad(sad_type = "pareto", s_pool = 10L, n_sim = 500L, sad_coef = list(shape = 2), seed = 42L)
   )
   expect_equal(
      sim_sad(sad_type = "poilog", s_pool = 10L, n_sim = 500L, seed = 42L),
      sim_sad(sad_type = "poilog", s_pool = 10L, n_sim = 500L, seed = 42L)
   )
   expect_equal(
      sim_sad(sad_type = "power", s_pool = 10L, n_sim = 500L, sad_coef = list(s = 2), seed = 42L),
      sim_sad(sad_type = "power", s_pool = 10L, n_sim = 500L, sad_coef = list(s = 2), seed = 42L)
   )
   expect_equal(
      sim_sad(sad_type = "weibull", s_pool = 10L, n_sim = 500L, sad_coef = list(shape = 2), seed = 42L),
      sim_sad(sad_type = "weibull", s_pool = 10L, n_sim = 500L, sad_coef = list(shape = 2), seed = 42L)
   )
})