tests/testthat/test-7-plotsjSDM.R

In sjSDM: Scalable Joint Species Distribution Modeling

source("utils.R")

test_model = function(occ = NULL, env, spatial=NULL, biotic = bioticStruct(), 
                      iter = 1L, step_size = 10L, se=FALSE, family = stats::binomial(), context = "") {
  sjSDM:::check_module()
  device = is_gpu_available()
  testthat::expect_error({model = sjSDM(!!occ, env=!!env, 
                                        spatial = !!spatial, 
                                        biotic = !!biotic,
                                        iter = !!iter, 
                                        step_size = !!step_size,
                                        se = !!se,
                                        family = !!family,
                                        device=device,
                                        sampling=10L, verbose = FALSE)}, NA)
  testthat::expect_error(plot(model), NA)
}


library(sjSDM)

sim = simulate_SDM(sites = 50L, species = 12, env = 3)
X1 = sim$env_weights
Y1 = sim$response


Funcs = list(
  list(5, 2, FALSE, binomial("logit")),
  list(5, 23, FALSE, poisson()),
  list(5, 40, FALSE, gaussian()),
  list(5, 40, FALSE, "nbinom")
)
testthat::test_that("sjSDM plot-sjSDM-coef Func", {
  testthat::skip_on_cran()
  testthat::skip_on_ci()
  skip_if_no_torch()
  for(i in 1:length(Funcs)) {
    test_model(Y1, env = linear(X1), iter = Funcs[[i]][[1]], step_size =  Funcs[[i]][[2]],  se = Funcs[[i]][[3]], family =  Funcs[[i]][[4]])
  }
})


biotic = list(
  bioticStruct(4L),
  bioticStruct(4L, lambda = 0.1, alpha = 1.0)
)
testthat::test_that("sjSDM plot-sjSDM-coef Biotic", {
  testthat::skip_on_cran()
  testthat::skip_on_ci()
  skip_if_no_torch()
  for(i in 1:length(biotic)) {
    test_model(Y1, env=linear(X1), biotic = biotic[[i]])
  }
})


envs = list(
  linear(X1, ~0+X1:X2),
  linear(X1, lambda = 0.1)
)
testthat::test_that("sjSDM plot-sjSDM-coef env linear", {
  testthat::skip_on_cran()
  testthat::skip_on_ci()
  skip_if_no_torch()
  for(i in 1:length(envs)) {
    test_model(Y1, env = envs[[i]])
  }
})



SP = matrix(rnorm(100), 50, 2)
Spatial = list(
  linear(SP, ~0+X1:X2),
  linear(SP, lambda = 0.1, alpha=0.0)
)
testthat::test_that("sjSDM plot-sjSDM-coef Spatial", {
  testthat::skip_on_cran()
  testthat::skip_on_ci()
  skip_if_no_torch()
  for(i in 1:length(Spatial)) {
    test_model(Y1, env = linear(X1), spatial = Spatial[[i]])
  }
})


Spatial = list(
  linear(SP, ~0+.)
)

Env = list(
  linear(X1, lambda = 0.1, alpha=0.5)
)
testthat::test_that("sjSDM plot-sjSDM-coef Mix", {
  testthat::skip_on_cran()
  testthat::skip_on_ci()
  skip_if_no_torch()
  for(i in 1:length(Spatial)) {
    test_model(Y1, env = Env[[i]], spatial = Spatial[[i]])
    test_model(Y1, env = Env[[i]], spatial = Spatial[[i]],se=TRUE)
  }
})