test_that("gcms_ensembles/names", { skip_on_cran() set.seed(1) sa <- sdm_area(parana, cell_size = 100000, crs = 6933) sa <- add_predictors(sa, bioc) # name changes pred_names <- c("a", "b", "c", "d", "bio1", "bio4", "bio12") sanames <- set_predictor_names(sa, pred_names) expect_true(all(pred_names == get_predictor_names(sanames))) expect_true(all(pred_names %in% colnames(sanames$grid))) expect_true(all(sanames$grid$a == sa$grid$GID0)) # expect_warning(sa <- add_scenarios(sa, scen) |> select_predictors(c("bio1", "bio12"))) # name changes pred_names <- c("a", "b") sanames <- set_predictor_names(sa, pred_names) expect_true(all(pred_names == get_predictor_names(sanames))) expect_true(all(pred_names %in% colnames(sanames$grid))) expect_true(all(pred_names %in% colnames(sanames$scenarios$grid))) expect_true(all(pred_names %in% colnames(sanames$scenarios$data$current))) expect_true(all(pred_names %in% colnames(sanames$scenarios$data$ca_ssp245_2090))) expect_true(all(sanames$grid$a == sa$grid$bio1)) expect_true(all(sanames$scenarios$grid$a == sa$scenarios$grid$bio1)) expect_true(all(sanames$scenarios$data$current$a == sa$scenarios$data$current$bio1)) expect_true(all(sanames$scenarios$data$ca_ssp245_2090$a == sa$scenarios$data$ca_ssp245_2090$bio1)) # oc <- occurrences_sdm(occ, crs = 6933) |> join_area(sa) i <- input_sdm(oc, sa) # name changes inames <- set_predictor_names(i, pred_names) expect_true(all(pred_names == get_predictor_names(inames))) expect_true(all(pred_names %in% colnames(inames$predictors$grid))) expect_true(all(pred_names %in% colnames(inames$scenarios$grid))) expect_true(all(pred_names %in% colnames(inames$scenarios$data$current))) expect_true(all(pred_names %in% colnames(inames$scenarios$data$ca_ssp245_2090))) expect_true(all(pred_names %in% colnames(inames$scenarios$data$ca_ssp245_2090))) expect_true(all(inames$predictors$grid$a == i$predictors$grid$bio1)) expect_true(all(inames$scenarios$grid$a == i$scenarios$grid$bio1)) expect_true(all(inames$scenarios$data$current$a == i$scenarios$data$current$bio1)) expect_true(all(inames$scenarios$data$ca_ssp245_2090$a == i$scenarios$data$ca_ssp245_2090$bio1)) # i <- pseudoabsences(i, method="random", n_set = 2) ctrl_sdm <- caret::trainControl(method = "boot", number = 1, classProbs = TRUE, returnResamp = "all", summaryFunction = summary_sdm, savePredictions = "all") i <- train_sdm(i, algo = c("naive_bayes"), ctrl=ctrl_sdm, variables_selected = c("bio1", "bio12")) |> suppressWarnings() i <- predict_sdm(i, th=0.8) # name changes inames <- set_scenarios_names(i, as.character(c(1:5))) expect_true(all(as.character(c(1:5)) == scenarios_names(inames))) expect_true(all(as.character(c(1:5)) == names(inames$scenarios$data))) expect_true(all(as.character(c(1:5)) == names(inames$predictions$predictions))) expect_true(all(as.character(c(1:5)) == colnames(inames$predictions$ensembles))) # # ensemble i <- gcms_ensembles(i, gcms = c("ca", "mi")) expect_true("ensembles" %in% names(i$predictions)) expect_true(all(c("matrix", "array") == class(i$predictions$ensembles))) expect_true(ncol(i$predictions$ensembles) == length(scenarios_names(i))+2) expect_true(nrow(i$predictions$ensembles) == length(species_names(i))) expect_true(all(scenarios_names(i) %in% colnames(i$predictions$ensembles))) expect_true(all(species_names(i) %in% rownames(i$predictions$ensembles))) expect_true(all(c("cell_id", "mean_occ_prob", "wmean_AUC", "committee_avg") %in% colnames(i$predictions$ensembles[,"_ssp585_2090"][[1]]))) expect_true(all(c("list") == class(i$predictions$ensembles[,"_ssp585_2090"]))) expect_true(all(c("data.frame") == class(i$predictions$ensembles[,"_ssp585_2090"][[1]]))) expect_snapshot(i) e <- i$predictions$ensembles[,"_ssp585_2090"][[1]] p1 <- i$predictions$ensembles[,"mi_ssp585_2090"][[1]] p2 <- i$predictions$ensembles[,"ca_ssp585_2090"][[1]] expect_true(all(e$cell_id == p1$cell_id)) expect_true(all(e$mean_occ_prob == (p1$mean_occ_prob + p2$mean_occ_prob) / 2)) })