test_that("min_ressources works", { # Load input array data(fish_PCR_rep_seq_read) # Load covariate data (Distance to sea) data(distance_cov) # Build the covariate array applied to sites on the psi level covariates <- covarray(protocol = 'PCR_rep_seq_read', array = fish_PCR_rep_seq_read, cov_list = list(Distance = list(cov_data = distance_cov$Distance, level = 'psi', dimension = 'site'))) # Run the 'PCR_rep_seq_read' model on the input array with the distance covariate model <- Nemodel(protocol = 'PCR_rep_seq_read', array = fish_PCR_rep_seq_read, covariates = covariates) unlink('model.txt') # Calculate the minimum number of samples, PCR replicates, and sequencing depth # required to ascertain species absence with 95% confidence result <- min_resources(model = model, resources = c('J', 'K', 'M')) # Test expect_equal(all(result@J_min$median == floor(result@J_min$median)), TRUE) expect_equal(all(result@J_min$hdi1 == floor(result@J_min$hdi1)), TRUE) expect_equal(all(result@J_min$hdi2 == floor(result@J_min$hdi2)), TRUE) expect_equal(all(result@K_min$median == floor(result@K_min$median)), TRUE) expect_equal(all(result@K_min$hdi1 == floor(result@K_min$hdi1)), TRUE) expect_equal(all(result@K_min$hdi2 == floor(result@K_min$hdi2)), TRUE) expect_equal(all(result@M_min$median == floor(result@M_min$median)), TRUE) expect_equal(all(result@M_min$hdi1 == floor(result@M_min$hdi1)), TRUE) expect_equal(all(result@M_min$hdi2 == floor(result@M_min$hdi2)), TRUE) })