tests/testthat/test_BC_model.R

In agarciaEE/NINA: Niche Interaction Network Analyses

context("Testing")

test_that("Succes", {

  library(NINA)

  g1_EN = EN_model(env_data, occ_data1,  cluster = "env", n.clus = 5)
  g2_EN = EN_model(env_data, occ_data2,  cluster = g1_EN$clus)

  g2_BCcomp <- BC_model(g2_EN, g1_EN, A.matrix = int_matrix, C.matrix = NULL, method = "composition", cor  = F, type = "region")
  g2_BCdens <- BC_model(g2_EN, g1_EN, A.matrix = int_matrix, C.matrix = NULL, method = "denstities", cor  = T, type = "region")

  expect_equal(class(g2_BCcomp), c("NINA", "BCmodel"))

  expect_equal(raster::nlayers(g2_BCdens$maps), length(levels(occ_data2$species)))

  expect_equal(class(g2_BCdens$pca), c("pca", "dudi"))

  pred = g2_BCdens$pred.dis
  expect_equal(nrow(pred), nrow(na.exclude(raster::getValues(env_data))))

  expect_equal(length(g2_BCdens$z.mod), 5)

  expect_equal(length(g2_BCdens$w), 5)

  g1_EN = EN_model(env_data, occ_data1)
  g2_EN = EN_model(env_data, occ_data2)
  g2_BC <- BC_model(g2_EN, g1_EN, A.matrix = int_matrix, C.matrix = NULL, method = "composition", type = "global")

  expect_equal(length(g2_BC$z.mod), 5)

  expect_equal(length(g2_BC$w), 5)

  EN_sp1 = EN_model(raster::as.data.frame(env_data, xy = T), occ_data1, bootstraps = 5, save.bootstraps = F, save.model = F, assemble.models = T, split.data = T)
  EN_sp2 = EN_model(raster::as.data.frame(env_data, xy = T), occ_data2, bootstraps = 5, save.bootstraps = F, save.model = F, assemble.models = F, split.data = T)

  expect_equal(class(EN_sp2), c("NINA", "modelsList"))

  BC_sp2 <- lapply(1:length(EN_sp2), function(i) BC_model(EN_sp2[[i]], EN_sp1[[i]], D = 0, A.matrix = int_matrix, C.matrix = NULL, type = "global"))

  expect_equal(class(BC_sp2), c("list"))

  BC_sp2_ensemble = assemble_models(BC_sp2, method = "AUC")

  expect_equal(all(names(BC_sp2[[1]]$maps) %in% unique(occ_data2$species)), TRUE)

  expect_equal(length(BC_sp2), 5)

  expect_equal(class(BC_sp2_ensemble), c("NINA", "BCmodel"))

})