tests/testthat/test_simulation_functions-thomas_process.r

In MoBiodiv/MoBspatial: Spatial Simulation and Scale-Dependent Analysis of Biodiversity Changes

# sim_thomas_coords, sim_thomas_community, rThomas_rcpp, 
test_that("sim_thomas_community() - default argument values are as expected", {
  expect_snapshot(sim_thomas_community(s_pool = 3L, n_sim = 100L, seed = 42L))
})

test_that("sim_thomas_coords() - default argument values are as expected", {
  expect_snapshot(sim_thomas_coords(abund_vec = 1:4, seed = 42L))
})

test_that("rThomas_rcpp() - default argument values are as expected", {
  set.seed(42L)
  expect_snapshot(rThomas_rcpp(n_points = 100L, n_mother_points = 2L,
                               xmother = NA, ymother = NA, sigma = 0.2))
  expect_snapshot(rThomas_rcpp(n_points = 100L, n_mother_points = 2L,
                               xmother = 0.5, ymother = 0.5, sigma = 0.2))
  expect_snapshot({rThomas_rcpp(n_points = 100L, n_mother_points = 2L,
                               xmother = c(0.2, 0.8), ymother = c(0.2, 0.8),
                               sigma = 0.2)})
})

test_that("sim_thomas_community() calls sim_sad() correctly", {
  s_pool <- 10L
  n_sim <- 100L
  
  sad1 <- sim_sad(s_pool = s_pool, n_sim = n_sim, fix_s_sim = TRUE, seed = 42L)
  sim1 <- sim_thomas_community(s_pool = s_pool, n_sim = n_sim,
                               fix_s_sim = TRUE, seed = 42L)
  
  expect_equal(sum(sad1), nrow(sim1$census))
  expect_equal(length(sad1), length(table(sim1$census$species)))
})

test_that("sim_thomas_coords() - handles wrong mother_points parametres", {
  expect_error({
    # mother_points is negative
    sim_thomas_coords(abund_vec = sad1,
                      mother_points = -1)})  
  expect_error({
    # mother_points contains negative values
    sim_thomas_coords(abund_vec = sad1,
                      mother_points = sample(size = 100,
                                             x = -2:2,
                                             replace = TRUE))})  
  expect_error({
    # mother_points is too short
    sim_thomas_coords(abund_vec = sad1,
                      mother_points = rep(1, 4))})  
  expect_error({
    # mother_points is too long
    sim_thomas_coords(abund_vec = sad1,
                      mother_points = rep(1, 1000))})  
})

test_that("sim_thomas_coords() - handles wrong xmother and ymother parametres", {
  sad2 <- sim_sad(s_pool = 2, n_sim = 100)
  xmother <- lapply(1:length(sad2), function(x) runif(2, 0, 1))
  
  expect_error(sim_thomas_coords(sad2,
                                 xmother = xmother,
                                 ymother = list(c(0.2, NA), c(0.3, NA))))
  expect_error(sim_thomas_coords(sad2,
                                 xmother = xmother,
                                 ymother = list(NA, c(0.2, 0.3))))
  expect_error(sim_thomas_coords(sad2, xmother = xmother, ymother = list(2, c(0.2, 0.3))))
})

test_that("sim_thomas_coords() - handles wrong xrange and yrange parametres", {
  expect_error(sim_thomas_coords(sad2, xmother = xmother, ymother = xmother, xrange = c(0, 0.1)))   # xmother and ymother outside of range
  expect_error(sim_thomas_coords(sad2, xmother = xmother, ymother = xmother, xrange = data.frame(c(0,1), c(0,0.1))))   # xrange and y range have different class
  expect_error(sim_thomas_coords(sad2, xmother = xmother, ymother = xmother,
                                 xrange = data.frame(c(0,1,2), c(0,1,2)),
                                 yrange = data.frame(c(0,1,2), c(0,1,2))))  # xrange and yrange have too many columns
  expect_error(sim_thomas_coords(sad2, xmother = xmother, ymother = xmother,
                                 xrange = data.frame(c(0,1), c(0,1), c(0,1)),
                                 yrange = data.frame(c(0,1), c(0,1), c(0,1))))  # xrange and yrange have too many rows
})

test_that("sim_thomas_coords() - throws warnings when expected", {
  sad1 <- sim_sad(s_pool = 3L, n_sim = 10L)
  xmother <- lapply(1L:length(sad1), function(x) runif(1, 0, 1))
  ymother <- lapply(1L:length(sad1), function(x) runif(1, 0, 1))
  expect_warning(sim_thomas_coords(sad1, mother_points = 1, xmother = xmother, ymother = ymother))
  expect_warning(sim_thomas_coords(sad1, mother_points = 1, cluster_points = 2))
})

test_that("rThomas_rcpp() - behaves as expected", {
  expect_s3_class(rThomas_rcpp(20, n_mother_points = 1, xmother = .5, ymother = .5, sigma = 0.2), "data.frame")
  expect_equal(nrow(rThomas_rcpp(20, n_mother_points = 1, xmother = .5, ymother = .5, sigma = 0.2)), 20)
  expect_error(rThomas_rcpp(20, n_mother_points = 2, sigma = 0.2))
})