test_that("blank test", { expect_null(NULL) }) test_local <- FALSE # FALSE for CRAN #### local check if (test_local) { load(file = system.file("extdata", "exdata.rda", package = "spmodel")) load(file = system.file("extdata", "exdata_poly.rda", package = "spmodel")) load(file = system.file("extdata", "exdata_Mpoly.rda", package = "spmodel")) load(file = system.file("extdata", "exdata_Upoly.rda", package = "spmodel")) ################################ ########### row standardized ################################ test_that("the model runs for connected sites", { spcov_type <- "car" expect_error(spautor(y ~ x, exdata_poly, spcov_type), NA) expect_error(spautor(y ~ x, exdata_poly, spcov_type, estmethod = "ml"), NA) spcov_initial_val <- spcov_initial(spcov_type, de = 1, ie = 1, range = 0.5, known = "de") expect_error(spautor(y ~ x, exdata_poly, spcov_initial = spcov_initial_val), NA) expect_error(spautor(y ~ x, exdata_poly, spcov_initial = spcov_initial_val, estmethod = "ml"), NA) spcov_type <- "sar" expect_error(spautor(y ~ x, exdata_poly, spcov_type), NA) expect_error(spautor(y ~ x, exdata_poly, spcov_type, estmethod = "ml"), NA) spcov_initial_val <- spcov_initial(spcov_type, de = 1, ie = 1, range = 0.5, known = "de") expect_error(spautor(y ~ x, exdata_poly, spcov_initial = spcov_initial_val), NA) expect_error(spautor(y ~ x, exdata_poly, spcov_initial = spcov_initial_val, estmethod = "ml"), NA) }) test_that("the model runs for connected sites given W", { spcov_type <- "car" W <- 1 * Matrix::Matrix(sf::st_intersects(exdata_poly, sparse = FALSE), sparse = TRUE) expect_error(spautor(y ~ x, exdata_poly, spcov_type, W = W), NA) if (test_local) { expect_error(spautor(y ~ x, exdata_poly, spcov_type, W = W, estmethod = "ml"), NA) spcov_initial_val <- spcov_initial(spcov_type, de = 1, ie = 1, range = 0.5, known = "de") expect_error(spautor(y ~ x, exdata_poly, spcov_initial = spcov_initial_val, W = W), NA) expect_error(spautor(y ~ x, exdata_poly, spcov_initial = spcov_initial_val, W = W, estmethod = "ml"), NA) } spcov_type <- "sar" expect_error(spautor(y ~ x, exdata_poly, spcov_type, W = W), NA) if (test_local) { expect_error(spautor(y ~ x, exdata_poly, spcov_type, W = W, estmethod = "ml"), NA) spcov_initial_val <- spcov_initial(spcov_type, de = 1, ie = 1, range = 0.5, known = "de") expect_error(spautor(y ~ x, exdata_poly, spcov_initial = spcov_initial_val, W = W), NA) expect_error(spautor(y ~ x, exdata_poly, spcov_initial = spcov_initial_val, W = W, estmethod = "ml"), NA) } }) test_that("the model runs for connected sites (partition group)", { spcov_type <- "car" expect_error(spautor(y ~ x, exdata_poly, spcov_type, partition_factor = ~group), NA) if (test_local) { expect_error(spautor(y ~ x, exdata_poly, spcov_type, partition_factor = ~group, estmethod = "ml"), NA) spcov_initial_val <- spcov_initial(spcov_type, de = 1, ie = 1, range = 0.5, known = "de") expect_error(spautor(y ~ x, exdata_poly, spcov_initial = spcov_initial_val, partition_factor = ~group), NA) expect_error(spautor(y ~ x, exdata_poly, spcov_initial = spcov_initial_val, partition_factor = ~group, estmethod = "ml"), NA) } spcov_type <- "sar" expect_error(spautor(y ~ x, exdata_poly, spcov_type, partition_factor = ~group), NA) if (test_local) { expect_error(spautor(y ~ x, exdata_poly, spcov_type, partition_factor = ~group, estmethod = "ml"), NA) spcov_initial_val <- spcov_initial(spcov_type, de = 1, ie = 1, range = 0.5, known = "de") expect_error(spautor(y ~ x, exdata_poly, spcov_initial = spcov_initial_val, partition_factor = ~group), NA) expect_error(spautor(y ~ x, exdata_poly, spcov_initial = spcov_initial_val, partition_factor = ~group, estmethod = "ml"), NA) } }) test_that("the model runs for connected sites (random group)", { spcov_type <- "car" expect_error(spautor(y ~ x, exdata_poly, spcov_type, random = ~group), NA) if (test_local) { expect_error(spautor(y ~ x, exdata_poly, spcov_type, random = ~group, estmethod = "ml"), NA) spcov_initial_val <- spcov_initial(spcov_type, de = 1, ie = 1, range = 0.5, known = "de") expect_error(spautor(y ~ x, exdata_poly, spcov_initial = spcov_initial_val, random = ~group), NA) expect_error(spautor(y ~ x, exdata_poly, spcov_initial = spcov_initial_val, random = ~group, estmethod = "ml"), NA) } spcov_initial_val <- spcov_initial(spcov_type, de = 1, ie = 1, range = 0.5, known = "de") randcov_initial_val <- randcov_initial(group = 1, known = "group") expect_error(spautor(y ~ x, exdata_poly, spcov_initial = spcov_initial_val, random = ~group, randcov_initial = randcov_initial_val), NA) if (test_local) { expect_error(spautor(y ~ x, exdata_poly, spcov_initial = spcov_initial_val, random = ~group, randcov_initial = randcov_initial_val, estmethod = "ml"), NA) } spcov_type <- "sar" expect_error(spautor(y ~ x, exdata_poly, spcov_type, random = ~group), NA) if (test_local) { expect_error(spautor(y ~ x, exdata_poly, spcov_type, random = ~group, estmethod = "ml"), NA) spcov_initial_val <- spcov_initial(spcov_type, de = 1, ie = 1, range = 0.5, known = "de") expect_error(spautor(y ~ x, exdata_poly, spcov_initial = spcov_initial_val, random = ~group), NA) expect_error(spautor(y ~ x, exdata_poly, spcov_initial = spcov_initial_val, random = ~group, estmethod = "ml"), NA) } randcov_initial_val <- randcov_initial(group = 1, known = "group") expect_error(spautor(y ~ x, exdata_poly, spcov_initial = spcov_initial_val, random = ~group, randcov_initial = randcov_initial_val), NA) if (test_local) { expect_error(spautor(y ~ x, exdata_poly, spcov_initial = spcov_initial_val, random = ~group, randcov_initial = randcov_initial_val, estmethod = "ml"), NA) } }) test_that("the model runs for connected sites (partition and random group)", { spcov_type <- "car" expect_error(spautor(y ~ x, exdata_poly, spcov_type, random = ~group, partition_factor = ~group), NA) if (test_local) { expect_error(spautor(y ~ x, exdata_poly, spcov_type, random = ~group, partition_factor = ~group, estmethod = "ml"), NA) spcov_initial_val <- spcov_initial(spcov_type, de = 1, ie = 1, range = 0.5, known = "de") expect_error(spautor(y ~ x, exdata_poly, spcov_initial = spcov_initial_val, random = ~group, partition_factor = ~group), NA) expect_error(spautor(y ~ x, exdata_poly, spcov_initial = spcov_initial_val, random = ~group, partition_factor = ~group, estmethod = "ml"), NA) } spcov_type <- "sar" expect_error(spautor(y ~ x, exdata_poly, spcov_type, random = ~group, partition_factor = ~group), NA) if (test_local) { expect_error(spautor(y ~ x, exdata_poly, spcov_type, random = ~group, partition_factor = ~group, estmethod = "ml"), NA) spcov_initial_val <- spcov_initial(spcov_type, de = 1, ie = 1, range = 0.5, known = "de") expect_error(spautor(y ~ x, exdata_poly, spcov_initial = spcov_initial_val, random = ~group, partition_factor = ~group), NA) expect_error(spautor(y ~ x, exdata_poly, spcov_initial = spcov_initial_val, random = ~group, partition_factor = ~group, estmethod = "ml"), NA) } }) test_that("the model runs for unconnected sites", { spcov_type <- "car" expect_error(spautor(y ~ x, exdata_Upoly, spcov_type), NA) if (test_local) { expect_error(spautor(y ~ x, exdata_Upoly, spcov_type, estmethod = "ml"), NA) spcov_initial_val <- spcov_initial(spcov_type, de = 1, ie = 1, range = 0.5, known = "de") expect_error(spautor(y ~ x, exdata_Upoly, spcov_initial = spcov_initial_val), NA) expect_error(spautor(y ~ x, exdata_Upoly, spcov_initial = spcov_initial_val, estmethod = "ml"), NA) } spcov_type <- "sar" expect_error(spautor(y ~ x, exdata_Upoly, spcov_type), NA) if (test_local) { expect_error(spautor(y ~ x, exdata_Upoly, spcov_type, estmethod = "ml"), NA) spcov_initial_val <- spcov_initial(spcov_type, de = 1, ie = 1, range = 0.5, known = "de") expect_error(spautor(y ~ x, exdata_Upoly, spcov_initial = spcov_initial_val), NA) expect_error(spautor(y ~ x, exdata_Upoly, spcov_initial = spcov_initial_val, estmethod = "ml"), NA) } }) test_that("the model runs for unconnected sites (partition group)", { spcov_type <- "car" expect_error(spautor(y ~ x, exdata_Upoly, spcov_type, partition_factor = ~group), NA) if (test_local) { expect_error(spautor(y ~ x, exdata_Upoly, spcov_type, partition_factor = ~group, estmethod = "ml"), NA) spcov_initial_val <- spcov_initial(spcov_type, de = 1, ie = 1, range = 0.5, known = "de") expect_error(spautor(y ~ x, exdata_Upoly, spcov_initial = spcov_initial_val, partition_factor = ~group), NA) expect_error(spautor(y ~ x, exdata_Upoly, spcov_initial = spcov_initial_val, partition_factor = ~group, estmethod = "ml"), NA) } spcov_type <- "sar" expect_error(spautor(y ~ x, exdata_Upoly, spcov_type, partition_factor = ~group), NA) if (test_local) { expect_error(spautor(y ~ x, exdata_Upoly, spcov_type, partition_factor = ~group, estmethod = "ml"), NA) spcov_initial_val <- spcov_initial(spcov_type, de = 1, ie = 1, range = 0.5, known = "de") expect_error(spautor(y ~ x, exdata_Upoly, spcov_initial = spcov_initial_val, partition_factor = ~group), NA) expect_error(spautor(y ~ x, exdata_Upoly, spcov_initial = spcov_initial_val, partition_factor = ~group, estmethod = "ml"), NA) } }) test_that("the model runs for unconnected sites (random group)", { spcov_type <- "car" expect_error(spautor(y ~ x, exdata_Upoly, spcov_type, random = ~group), NA) if (test_local) { expect_error(spautor(y ~ x, exdata_Upoly, spcov_type, random = ~group, estmethod = "ml"), NA) spcov_initial_val <- spcov_initial(spcov_type, de = 1, ie = 1, range = 0.5, known = "de") expect_error(spautor(y ~ x, exdata_Upoly, spcov_initial = spcov_initial_val, random = ~group, estmethod = "ml"), NA) } spcov_type <- "sar" expect_error(spautor(y ~ x, exdata_Upoly, spcov_type, random = ~group), NA) if (test_local) { expect_error(spautor(y ~ x, exdata_Upoly, spcov_type, random = ~group, estmethod = "ml"), NA) spcov_initial_val <- spcov_initial(spcov_type, de = 1, ie = 1, range = 0.5, known = "de") expect_error(spautor(y ~ x, exdata_Upoly, spcov_initial = spcov_initial_val, random = ~group, estmethod = "ml"), NA) } }) test_that("the model runs for unconnected sites (partition and random group)", { spcov_type <- "car" expect_error(spautor(y ~ x, exdata_Upoly, spcov_type, random = ~group, partition_factor = ~group), NA) if (test_local) { expect_error(spautor(y ~ x, exdata_Upoly, spcov_type, random = ~group, partition_factor = ~group, estmethod = "ml"), NA) spcov_initial_val <- spcov_initial(spcov_type, de = 1, ie = 1, range = 0.5, known = "de") expect_error(spautor(y ~ x, exdata_Upoly, spcov_initial = spcov_initial_val, random = ~group, partition_factor = ~group, estmethod = "ml"), NA) } spcov_type <- "sar" expect_error(spautor(y ~ x, exdata_Upoly, spcov_type, random = ~group, partition_factor = ~group), NA) if (test_local) { expect_error(spautor(y ~ x, exdata_Upoly, spcov_type, random = ~group, partition_factor = ~group, estmethod = "ml"), NA) spcov_initial_val <- spcov_initial(spcov_type, de = 1, ie = 1, range = 0.5, known = "de") expect_error(spautor(y ~ x, exdata_Upoly, spcov_initial = spcov_initial_val, random = ~group, partition_factor = ~group, estmethod = "ml"), NA) } }) test_that("the model runs for missing sites", { spcov_type <- "car" expect_error(spautor(y ~ x, exdata_Mpoly, spcov_type), NA) if (test_local) { expect_error(spautor(y ~ x, exdata_Mpoly, spcov_type, estmethod = "ml"), NA) spcov_initial_val <- spcov_initial(spcov_type, de = 1, ie = 1, range = 0.5, known = "de") expect_error(spautor(y ~ x, exdata_Mpoly, spcov_initial = spcov_initial_val, estmethod = "ml"), NA) } spcov_type <- "sar" expect_error(spautor(y ~ x, exdata_Mpoly, spcov_type), NA) if (test_local) { expect_error(spautor(y ~ x, exdata_Mpoly, spcov_type, estmethod = "ml"), NA) spcov_initial_val <- spcov_initial(spcov_type, de = 1, ie = 1, range = 0.5, known = "de") expect_error(spautor(y ~ x, exdata_Mpoly, spcov_initial = spcov_initial_val, estmethod = "ml"), NA) } }) test_that("the model runs for missing sites (partition group)", { spcov_type <- "car" expect_error(spautor(y ~ x, exdata_Mpoly, spcov_type, partition_factor = ~group), NA) if (test_local) { expect_error(spautor(y ~ x, exdata_Mpoly, spcov_type, partition_factor = ~group, estmethod = "ml"), NA) spcov_initial_val <- spcov_initial(spcov_type, de = 1, ie = 1, range = 0.5, known = "de") expect_error(spautor(y ~ x, exdata_Mpoly, spcov_initial = spcov_initial_val, partition_factor = ~group, estmethod = "ml"), NA) } spcov_type <- "sar" expect_error(spautor(y ~ x, exdata_Mpoly, spcov_type, partition_factor = ~group), NA) if (test_local) { expect_error(spautor(y ~ x, exdata_Mpoly, spcov_type, partition_factor = ~group, estmethod = "ml"), NA) spcov_initial_val <- spcov_initial(spcov_type, de = 1, ie = 1, range = 0.5, known = "de") expect_error(spautor(y ~ x, exdata_Mpoly, spcov_initial = spcov_initial_val, partition_factor = ~group, estmethod = "ml"), NA) } }) test_that("the model runs for missing sites (random group)", { spcov_type <- "car" expect_error(spautor(y ~ x, exdata_Mpoly, spcov_type, random = ~group), NA) if (test_local) { expect_error(spautor(y ~ x, exdata_Mpoly, spcov_type, random = ~group, estmethod = "ml"), NA) spcov_initial_val <- spcov_initial(spcov_type, de = 1, ie = 1, range = 0.5, known = "de") expect_error(spautor(y ~ x, exdata_Mpoly, spcov_initial = spcov_initial_val, random = ~group, estmethod = "ml"), NA) } spcov_type <- "sar" expect_error(spautor(y ~ x, exdata_Mpoly, spcov_type, random = ~group), NA) if (test_local) { expect_error(spautor(y ~ x, exdata_Mpoly, spcov_type, random = ~group, estmethod = "ml"), NA) spcov_initial_val <- spcov_initial(spcov_type, de = 1, ie = 1, range = 0.5, known = "de") expect_error(spautor(y ~ x, exdata_Mpoly, spcov_initial = spcov_initial_val, random = ~group, estmethod = "ml"), NA) } }) test_that("the model runs for connected sites (partition and random group)", { spcov_type <- "car" expect_error(spautor(y ~ x, exdata_Mpoly, spcov_type, random = ~group, partition_factor = ~group), NA) if (test_local) { expect_error(spautor(y ~ x, exdata_Mpoly, spcov_type, random = ~group, partition_factor = ~group, estmethod = "ml"), NA) spcov_initial_val <- spcov_initial(spcov_type, de = 1, ie = 1, range = 0.5, known = "de") expect_error(spautor(y ~ x, exdata_poly, spcov_initial = spcov_initial_val, random = ~group, partition_factor = ~group, estmethod = "ml"), NA) } spcov_type <- "sar" expect_error(spautor(y ~ x, exdata_Mpoly, spcov_type, random = ~group, partition_factor = ~group), NA) if (test_local) { expect_error(spautor(y ~ x, exdata_Mpoly, spcov_type, random = ~group, partition_factor = ~group, estmethod = "ml"), NA) spcov_initial_val <- spcov_initial(spcov_type, de = 1, ie = 1, range = 0.5, known = "de") expect_error(spautor(y ~ x, exdata_poly, spcov_initial = spcov_initial_val, random = ~group, partition_factor = ~group, estmethod = "ml"), NA) } }) ################################ ########### row unstandardized ################################ test_that("the model runs for connected sites", { spcov_type <- "car" expect_error(spautor(y ~ x, exdata_poly, spcov_type, row_st = FALSE), NA) if (test_local) { expect_error(spautor(y ~ x, exdata_poly, spcov_type, row_st = FALSE, estmethod = "ml"), NA) spcov_initial_val <- spcov_initial(spcov_type, de = 1, ie = 1, range = 0.1, known = "de") expect_error(spautor(y ~ x, exdata_poly, spcov_initial = spcov_initial_val, row_st = FALSE, estmethod = "ml"), NA) } spcov_type <- "sar" expect_error(spautor(y ~ x, exdata_poly, spcov_type, row_st = FALSE), NA) if (test_local) { expect_error(spautor(y ~ x, exdata_poly, spcov_type, row_st = FALSE, estmethod = "ml"), NA) spcov_initial_val <- spcov_initial(spcov_type, de = 1, ie = 1, range = 0.1, known = "de") expect_error(spautor(y ~ x, exdata_poly, spcov_initial = spcov_initial_val, row_st = FALSE, estmethod = "ml"), NA) } }) test_that("the model runs for connected sites given W", { spcov_type <- "car" W <- 1 * Matrix::Matrix(sf::st_intersects(exdata_poly, sparse = FALSE), sparse = TRUE) Wp <- W / rowSums(W) M <- 1 / rowSums(W) expect_error(spautor(y ~ x, exdata_poly, spcov_type, W = W, row_st = FALSE), NA) expect_error(spautor(y ~ x, exdata_poly, spcov_type, W = Wp, row_st = FALSE, M = M), NA) if (test_local) { expect_error(spautor(y ~ x, exdata_poly, spcov_type, W = W, row_st = FALSE, estmethod = "ml"), NA) expect_error(spautor(y ~ x, exdata_poly, spcov_type, W = Wp, row_st = FALSE, M = M, estmethod = "ml"), NA) spcov_initial_val <- spcov_initial(spcov_type, de = 1, ie = 1, range = 0.1, known = "de") expect_error(spautor(y ~ x, exdata_poly, spcov_initial = spcov_initial_val, W = W, row_st = FALSE), NA) expect_error(spautor(y ~ x, exdata_poly, spcov_initial = spcov_initial_val, W = Wp, row_st = FALSE, M = M), NA) expect_error(spautor(y ~ x, exdata_poly, spcov_initial = spcov_initial_val, W = W, row_st = FALSE, estmethod = "ml"), NA) expect_error(spautor(y ~ x, exdata_poly, spcov_initial = spcov_initial_val, W = Wp, row_st = FALSE, M = M, estmethod = "ml"), NA) } spcov_type <- "sar" expect_error(spautor(y ~ x, exdata_poly, spcov_type, W = W, row_st = FALSE), NA) expect_error(spautor(y ~ x, exdata_poly, spcov_type, W = Wp, row_st = FALSE), NA) if (test_local) { expect_error(spautor(y ~ x, exdata_poly, spcov_type, W = W, row_st = FALSE, estmethod = "ml"), NA) expect_error(spautor(y ~ x, exdata_poly, spcov_type, W = Wp, row_st = FALSE, estmethod = "ml"), NA) spcov_initial_val <- spcov_initial(spcov_type, de = 1, ie = 1, range = 0.1, known = "de") expect_error(spautor(y ~ x, exdata_poly, spcov_initial = spcov_initial_val, W = W, row_st = FALSE), NA) expect_error(spautor(y ~ x, exdata_poly, spcov_initial = spcov_initial_val, W = Wp, row_st = FALSE), NA) expect_error(spautor(y ~ x, exdata_poly, spcov_initial = spcov_initial_val, W = W, row_st = FALSE, estmethod = "ml"), NA) expect_error(spautor(y ~ x, exdata_poly, spcov_initial = spcov_initial_val, W = Wp, row_st = FALSE, estmethod = "ml"), NA) } }) test_that("the model runs for connected sites (partition group)", { spcov_type <- "car" expect_error(spautor(y ~ x, exdata_poly, spcov_type, partition_factor = ~group, row_st = FALSE), NA) if (test_local) { expect_error(spautor(y ~ x, exdata_poly, spcov_type, partition_factor = ~group, row_st = FALSE, estmethod = "ml"), NA) spcov_initial_val <- spcov_initial(spcov_type, de = 1, ie = 1, range = 0.1, known = "de") expect_error(spautor(y ~ x, exdata_poly, spcov_initial = spcov_initial_val, partition_factor = ~group, row_st = FALSE), NA) expect_error(spautor(y ~ x, exdata_poly, spcov_initial = spcov_initial_val, partition_factor = ~group, row_st = FALSE, estmethod = "ml"), NA) } spcov_type <- "sar" expect_error(spautor(y ~ x, exdata_poly, spcov_type, partition_factor = ~group, row_st = FALSE), NA) if (test_local) { expect_error(spautor(y ~ x, exdata_poly, spcov_type, partition_factor = ~group, row_st = FALSE, estmethod = "ml"), NA) spcov_initial_val <- spcov_initial(spcov_type, de = 1, ie = 1, range = 0.1, known = "de") expect_error(spautor(y ~ x, exdata_poly, spcov_initial = spcov_initial_val, partition_factor = ~group, row_st = FALSE), NA) expect_error(spautor(y ~ x, exdata_poly, spcov_initial = spcov_initial_val, partition_factor = ~group, row_st = FALSE, estmethod = "ml"), NA) } }) test_that("the model runs for connected sites (random group)", { spcov_type <- "car" expect_error(spautor(y ~ x, exdata_poly, spcov_type, random = ~group, row_st = FALSE), NA) if (test_local) { expect_error(spautor(y ~ x, exdata_poly, spcov_type, random = ~group, row_st = FALSE, estmethod = "ml"), NA) spcov_initial_val <- spcov_initial(spcov_type, de = 1, ie = 1, range = 0.1, known = "de") expect_error(spautor(y ~ x, exdata_poly, spcov_initial = spcov_initial_val, random = ~group, row_st = FALSE), NA) expect_error(spautor(y ~ x, exdata_poly, spcov_initial = spcov_initial_val, random = ~group, row_st = FALSE, estmethod = "ml"), NA) } spcov_initial_val <- spcov_initial(spcov_type, de = 1, ie = 1, range = 0.1, known = "de") randcov_initial_val <- randcov_initial(group = 1, known = "group") expect_error(spautor(y ~ x, exdata_poly, spcov_initial = spcov_initial_val, random = ~group, randcov_initial = randcov_initial_val, row_st = FALSE), NA) spcov_type <- "sar" expect_error(spautor(y ~ x, exdata_poly, spcov_type, random = ~group, row_st = FALSE), NA) if (test_local) { expect_error(spautor(y ~ x, exdata_poly, spcov_type, random = ~group, row_st = FALSE, estmethod = "ml"), NA) spcov_initial_val <- spcov_initial(spcov_type, de = 1, ie = 1, range = 0.1, known = "de") expect_error(spautor(y ~ x, exdata_poly, spcov_initial = spcov_initial_val, random = ~group, row_st = FALSE), NA) expect_error(spautor(y ~ x, exdata_poly, spcov_initial = spcov_initial_val, random = ~group, row_st = FALSE, estmethod = "ml"), NA) } spcov_initial_val <- spcov_initial(spcov_type, de = 1, ie = 1, range = 0.1, known = "de") randcov_initial_val <- randcov_initial(group = 1, known = "group") expect_error(spautor(y ~ x, exdata_poly, spcov_initial = spcov_initial_val, random = ~group, randcov_initial = randcov_initial_val, row_st = FALSE), NA) }) test_that("the model runs for connected sites (partition and random group)", { spcov_type <- "car" expect_error(spautor(y ~ x, exdata_poly, spcov_type, random = ~group, partition_factor = ~group, row_st = FALSE), NA) if (test_local) { expect_error(spautor(y ~ x, exdata_poly, spcov_type, random = ~group, partition_factor = ~group, row_st = FALSE, estmethod = "ml"), NA) spcov_initial_val <- spcov_initial(spcov_type, de = 1, ie = 1, range = 0.1, known = "de") expect_error(spautor(y ~ x, exdata_poly, spcov_initial = spcov_initial_val, random = ~group, partition_factor = ~group, row_st = FALSE), NA) expect_error(spautor(y ~ x, exdata_poly, spcov_initial = spcov_initial_val, random = ~group, partition_factor = ~group, row_st = FALSE, estmethod = "ml"), NA) } spcov_type <- "sar" expect_error(spautor(y ~ x, exdata_poly, spcov_type, random = ~group, partition_factor = ~group, row_st = FALSE), NA) if (test_local) { expect_error(spautor(y ~ x, exdata_poly, spcov_type, random = ~group, partition_factor = ~group, row_st = FALSE, estmethod = "ml"), NA) spcov_initial_val <- spcov_initial(spcov_type, de = 1, ie = 1, range = 0.1, known = "de") expect_error(spautor(y ~ x, exdata_poly, spcov_initial = spcov_initial_val, random = ~group, partition_factor = ~group, row_st = FALSE), NA) expect_error(spautor(y ~ x, exdata_poly, spcov_initial = spcov_initial_val, random = ~group, partition_factor = ~group, row_st = FALSE, estmethod = "ml"), NA) } }) test_that("the model runs for unconnected sites", { spcov_type <- "car" expect_error(spautor(y ~ x, exdata_Upoly, spcov_type, row_st = FALSE), NA) if (test_local) { expect_error(spautor(y ~ x, exdata_Upoly, spcov_type, row_st = FALSE, estmethod = "ml"), NA) spcov_initial_val <- spcov_initial(spcov_type, de = 1, ie = 1, range = 0.1, known = "de") expect_error(spautor(y ~ x, exdata_Upoly, spcov_initial = spcov_initial_val, row_st = FALSE, estmethod = "reml"), NA) expect_error(spautor(y ~ x, exdata_Upoly, spcov_initial = spcov_initial_val, row_st = FALSE, estmethod = "ml"), NA) } spcov_type <- "sar" expect_error(spautor(y ~ x, exdata_Upoly, spcov_type, row_st = FALSE), NA) if (test_local) { expect_error(spautor(y ~ x, exdata_Upoly, spcov_type, row_st = FALSE, estmethod = "ml"), NA) spcov_initial_val <- spcov_initial(spcov_type, de = 1, ie = 1, range = 0.1, known = "de") expect_error(spautor(y ~ x, exdata_Upoly, spcov_initial = spcov_initial_val, row_st = FALSE, estmethod = "reml"), NA) expect_error(spautor(y ~ x, exdata_Upoly, spcov_initial = spcov_initial_val, row_st = FALSE, estmethod = "ml"), NA) } }) test_that("the model runs for unconnected sites (partition group)", { spcov_type <- "car" expect_error(spautor(y ~ x, exdata_Upoly, spcov_type, partition_factor = ~group, row_st = FALSE), NA) if (test_local) { expect_error(spautor(y ~ x, exdata_Upoly, spcov_type, partition_factor = ~group, row_st = FALSE, estmethod = "ml"), NA) spcov_initial_val <- spcov_initial(spcov_type, de = 1, ie = 1, range = 0.1, known = "de") expect_error(spautor(y ~ x, exdata_Upoly, spcov_initial = spcov_initial_val, partition_factor = ~group, row_st = FALSE, estmethod = "reml"), NA) expect_error(spautor(y ~ x, exdata_Upoly, spcov_initial = spcov_initial_val, partition_factor = ~group, row_st = FALSE, estmethod = "ml"), NA) } spcov_type <- "sar" expect_error(spautor(y ~ x, exdata_Upoly, spcov_type, partition_factor = ~group, row_st = FALSE), NA) if (test_local) { expect_error(spautor(y ~ x, exdata_Upoly, spcov_type, partition_factor = ~group, row_st = FALSE, estmethod = "ml"), NA) spcov_initial_val <- spcov_initial(spcov_type, de = 1, ie = 1, range = 0.1, known = "de") expect_error(spautor(y ~ x, exdata_Upoly, spcov_initial = spcov_initial_val, partition_factor = ~group, row_st = FALSE, estmethod = "reml"), NA) expect_error(spautor(y ~ x, exdata_Upoly, spcov_initial = spcov_initial_val, partition_factor = ~group, row_st = FALSE, estmethod = "ml"), NA) } }) test_that("the model runs for unconnected sites (random group)", { spcov_type <- "car" expect_error(spautor(y ~ x, exdata_Upoly, spcov_type, random = ~group, row_st = FALSE), NA) if (test_local) { expect_error(spautor(y ~ x, exdata_Upoly, spcov_type, random = ~group, row_st = FALSE, estmethod = "ml"), NA) spcov_initial_val <- spcov_initial(spcov_type, de = 1, ie = 1, range = 0.1, known = "de") expect_error(spautor(y ~ x, exdata_Upoly, spcov_initial = spcov_initial_val, random = ~group, row_st = FALSE, estmethod = "reml"), NA) expect_error(spautor(y ~ x, exdata_Upoly, spcov_initial = spcov_initial_val, random = ~group, row_st = FALSE, estmethod = "ml"), NA) } spcov_type <- "sar" expect_error(spautor(y ~ x, exdata_Upoly, spcov_type, random = ~group, row_st = FALSE), NA) if (test_local) { expect_error(spautor(y ~ x, exdata_Upoly, spcov_type, random = ~group, row_st = FALSE, estmethod = "ml"), NA) spcov_initial_val <- spcov_initial(spcov_type, de = 1, ie = 1, range = 0.1, known = "de") expect_error(spautor(y ~ x, exdata_Upoly, spcov_initial = spcov_initial_val, random = ~group, row_st = FALSE, estmethod = "reml"), NA) expect_error(spautor(y ~ x, exdata_Upoly, spcov_initial = spcov_initial_val, random = ~group, row_st = FALSE, estmethod = "ml"), NA) } }) test_that("the model runs for unconnected sites (partition and random group)", { spcov_type <- "car" expect_error(spautor(y ~ x, exdata_Upoly, spcov_type, random = ~group, partition_factor = ~group, row_st = FALSE), NA) if (test_local) { expect_error(spautor(y ~ x, exdata_Upoly, spcov_type, random = ~group, partition_factor = ~group, row_st = FALSE, estmethod = "ml"), NA) spcov_initial_val <- spcov_initial(spcov_type, de = 1, ie = 1, range = 0.1, known = "de") expect_error(spautor(y ~ x, exdata_Upoly, spcov_initial = spcov_initial_val, random = ~group, partition_factor = ~group, row_st = FALSE), NA) expect_error(spautor(y ~ x, exdata_Upoly, spcov_initial = spcov_initial_val, random = ~group, partition_factor = ~group, row_st = FALSE, estmethod = "ml"), NA) } spcov_type <- "sar" expect_error(spautor(y ~ x, exdata_Upoly, spcov_type, random = ~group, partition_factor = ~group, row_st = FALSE), NA) if (test_local) { expect_error(spautor(y ~ x, exdata_Upoly, spcov_type, random = ~group, partition_factor = ~group, row_st = FALSE, estmethod = "ml"), NA) spcov_initial_val <- spcov_initial(spcov_type, de = 1, ie = 1, range = 0.1, known = "de") expect_error(spautor(y ~ x, exdata_Upoly, spcov_initial = spcov_initial_val, random = ~group, partition_factor = ~group, row_st = FALSE), NA) expect_error(spautor(y ~ x, exdata_Upoly, spcov_initial = spcov_initial_val, random = ~group, partition_factor = ~group, row_st = FALSE, estmethod = "ml"), NA) } }) test_that("the model runs for missing sites", { spcov_type <- "car" expect_error(spautor(y ~ x, exdata_Mpoly, spcov_type, row_st = FALSE), NA) if (test_local) { expect_error(spautor(y ~ x, exdata_Mpoly, spcov_type, row_st = FALSE, estmethod = "ml"), NA) spcov_initial_val <- spcov_initial(spcov_type, de = 1, ie = 1, range = 0.1, known = "de") expect_error(spautor(y ~ x, exdata_Mpoly, spcov_initial = spcov_initial_val, row_st = FALSE), NA) expect_error(spautor(y ~ x, exdata_Mpoly, spcov_initial = spcov_initial_val, row_st = FALSE, estmethod = "ml"), NA) } spcov_type <- "sar" expect_error(spautor(y ~ x, exdata_Mpoly, spcov_type, row_st = FALSE), NA) if (test_local) { expect_error(spautor(y ~ x, exdata_Mpoly, spcov_type, row_st = FALSE, estmethod = "ml"), NA) spcov_initial_val <- spcov_initial(spcov_type, de = 1, ie = 1, range = 0.1, known = "de") expect_error(spautor(y ~ x, exdata_Mpoly, spcov_initial = spcov_initial_val, row_st = FALSE), NA) expect_error(spautor(y ~ x, exdata_Mpoly, spcov_initial = spcov_initial_val, row_st = FALSE, estmethod = "ml"), NA) } }) test_that("the model runs for missing sites (partition group)", { spcov_type <- "car" expect_error(spautor(y ~ x, exdata_Mpoly, spcov_type, partition_factor = ~group, row_st = FALSE), NA) if (test_local) { expect_error(spautor(y ~ x, exdata_Mpoly, spcov_type, partition_factor = ~group, row_st = FALSE, estmethod = "ml"), NA) spcov_initial_val <- spcov_initial(spcov_type, de = 1, ie = 1, range = 0.1, known = "de") expect_error(spautor(y ~ x, exdata_Mpoly, spcov_initial = spcov_initial_val, partition_factor = ~group, row_st = FALSE, estmethod = "ml"), NA) } spcov_type <- "sar" expect_error(spautor(y ~ x, exdata_Mpoly, spcov_type, partition_factor = ~group, row_st = FALSE), NA) if (test_local) { expect_error(spautor(y ~ x, exdata_Mpoly, spcov_type, partition_factor = ~group, row_st = FALSE, estmethod = "ml"), NA) spcov_initial_val <- spcov_initial(spcov_type, de = 1, ie = 1, range = 0.1, known = "de") expect_error(spautor(y ~ x, exdata_Mpoly, spcov_initial = spcov_initial_val, partition_factor = ~group, row_st = FALSE, estmethod = "ml"), NA) } }) test_that("the model runs for missing sites (random group)", { spcov_type <- "car" expect_error(spautor(y ~ x, exdata_Mpoly, spcov_type, random = ~group, row_st = FALSE), NA) if (test_local) { expect_error(spautor(y ~ x, exdata_Mpoly, spcov_type, random = ~group, row_st = FALSE, estmethod = "ml"), NA) spcov_initial_val <- spcov_initial(spcov_type, de = 1, ie = 1, range = 0.1, known = "de") expect_error(spautor(y ~ x, exdata_Mpoly, spcov_initial = spcov_initial_val, random = ~group, row_st = FALSE), NA) expect_error(spautor(y ~ x, exdata_Mpoly, spcov_initial = spcov_initial_val, random = ~group, row_st = FALSE, estmethod = "ml"), NA) } spcov_type <- "sar" expect_error(spautor(y ~ x, exdata_Mpoly, spcov_type, random = ~group, row_st = FALSE), NA) if (test_local) { expect_error(spautor(y ~ x, exdata_Mpoly, spcov_type, random = ~group, row_st = FALSE, estmethod = "ml"), NA) spcov_initial_val <- spcov_initial(spcov_type, de = 1, ie = 1, range = 0.1, known = "de") expect_error(spautor(y ~ x, exdata_Mpoly, spcov_initial = spcov_initial_val, random = ~group, row_st = FALSE), NA) expect_error(spautor(y ~ x, exdata_Mpoly, spcov_initial = spcov_initial_val, random = ~group, row_st = FALSE, estmethod = "ml"), NA) } }) test_that("examples run", { spmod <- spautor(y ~ x, exdata_poly, "car") expect_output(print(spmod)) expect_error(summary(spmod), NA) expect_error(tidy(spmod), NA) # random effects spmod <- expect_error(spautor(y ~ x, exdata_poly, "car", random = ~group), NA) spmod <- expect_error(spautor(y ~ x, exdata_poly, "car", random = ~ (x | group) + (x | subgroup)), NA) # partition factor spmod <- expect_error(spautor(y ~ x, exdata_poly, "car", partition_factor = ~group), NA) # combining spmod <- expect_error(spautor(y ~ x, exdata_poly, "car", random = ~group, partition_factor = ~group), NA) # spcov_initial spcov_initial_val <- spcov_initial("car", range = 0.5, known = "range") spmod <- expect_error(spautor(y ~ x, exdata_poly, spcov_initial = spcov_initial_val), NA) # randcov_initial ("group" is shorthand for "1 | group") randcov_initial_val <- randcov_initial(1, nm = "group", known = "group") spmod <- expect_error(spautor(y ~ x, exdata_poly, "car", randcov_initial = randcov_initial_val), NA) }) test_that("errors occur", { W <- 1 * sf::st_intersects(exdata_poly, sparse = FALSE) diag(W) <- 0 M <- seq_len(NROW(exdata_poly)) expect_error(spautor(y ~ x, exdata_poly, "car", W = W, row_st = FALSE, M = M)) expect_error(spautor(y ~ x, exdata_poly, "car", partition_factor = ~ group + subgroup)) expect_error(suppressWarnings(spautor(y ~ as.factor(x) + group, exdata_poly, "car"))) exdata_poly3 <- exdata_poly exdata_poly3$y <- as.character(exdata_poly3$y) expect_error(spautor(y ~ x, exdata_poly3, "car")) expect_error(spautor(as.character(y) ~ x, exdata_poly, "car")) exdata_poly3$y <- as.factor(exdata_poly3$y) expect_error(spautor(y ~ x, exdata_poly3, "car")) expect_error(spautor(as.factor(y) ~ x, exdata_poly, "car")) expect_error(spautor(y ~ x, exdata_poly, "xyz")) expect_error(spautor(y ~ x, exdata_poly, "exponential")) expect_error(spautor(y ~ x, exdata, "car")) expect_error(spautor(y ~ x, exdata_poly, "car", estmethod = "xyz")) exdata_poly4 <- exdata_poly exdata_poly4$x2 <- exdata_poly4$x expect_error(suppressWarnings(spautor(y ~ x + x2, exdata_poly4, "car"))) exdata_poly4$x[1] <- NA expect_error(spautor(y ~ x, exdata_poly4, "car")) }) test_that("additional covr", { # spatial profiling spcov_initial_val <- spcov_initial("car", ie = 0.5) # just can't be zero and known expect_error(spautor(formula = y ~ x, data = exdata_poly, spcov_initial = spcov_initial_val), NA) # partition factor with one level and random effects exdata_poly$part <- as.factor(1) expect_error(spautor(formula = y ~ x, data = exdata_poly, "car", random = ~group, partition_factor = ~part), NA) exdata_Upoly$part <- as.factor(1) expect_error(spautor(formula = y ~ x, data = exdata_Upoly, "car", random = ~group, partition_factor = ~part), NA) exdata_Mpoly$part <- as.factor(1) expect_error(spautor(formula = y ~ x, data = exdata_Mpoly, "car", random = ~group, partition_factor = ~part), NA) }) test_that("messages occur", { expect_message(spautor(y ~ x, exdata_poly)) spcov_initial_val <- spcov_initial("car") expect_message(spautor(y ~ x, exdata_poly, "car", spcov_initial = spcov_initial_val)) }) test_that("no variance error works", { exdata_poly$novar <- 1 expect_error(spautor(novar ~ x, exdata_poly, "car")) }) test_that("range negative works", { spcov_type <- "car" expect_error(spautor(y ~ x, exdata_poly, spcov_type, range_positive = FALSE), NA) spcov_type <- "sar" expect_error(spautor(y ~ x, exdata_poly, spcov_type, range_positive = FALSE), NA) }) }