test_that('blockedCV completes spatial block cross-validation.', { skip_on_cran() ##Set up a model ##Set up arbitrary data projection <- '+proj=tmerc' x <- c(16.48438, 17.49512, 24.74609, 22.59277, 16.48438) y <- c(59.736328125, 55.1220703125, 55.0341796875, 61.142578125, 59.736328125) xy <- cbind(x, y) xy <- cbind(x, y) SpatialPoly <- st_sfc(st_polygon(list(xy)), crs = projection) ##Old coordinate names #Make random points #Random presence only dataset PO <- st_as_sf(st_sample(SpatialPoly, 100, crs = projection)) st_geometry(PO) <- 'geometry' ##Add random variable PO$numvar <- runif(n = nrow(PO)) PO$factvar <- sample(x = c('a','b'), size = nrow(PO), replace = TRUE) PO$species <- sample(x = c('fish'), size = nrow(PO), replace = TRUE) #Random presence absence dataset PA <- st_as_sf(st_sample(SpatialPoly, 100, crs = projection)) PA$PAresp <- sample(x = c(0,1), size = nrow(PA), replace = TRUE) #Add trial name PA$trial <- sample(x = c(1,2,3), size = nrow(PA), replace = TRUE) PA$pointcov <- runif(n = nrow(PA)) PA$binommark <- sample(x = 2:3, size = nrow(PA), replace = TRUE) PA$marktrial <- sample(x = 3:5, size = nrow(PA), replace = TRUE) PA$species <- sample(x = c('bird'), nrow(PA), replace = TRUE) mesh <- INLA::inla.mesh.2d(boundary = INLA::inla.sp2segment(SpatialPoly), max.edge = 2, crs = inlabru::fm_crs(projection)) #iPoints <- inlabru::ipoints(samplers = SpatialPoly, domain = mesh) iPoints <- inlabru::fm_int(samplers = SpatialPoly, domain = mesh) ##Make PA a data.frame object coordnames <- c('long', 'lat') responseCounts <- 'count' responsePA <- 'PAresp' trialName <- 'trial' markNames <- c('numvar', 'factvar', 'binommark') marksFamily <- c('gaussian', 'multinomial', 'binomial') markTrial = 'marktrial' pointCovs <- 'pointcov' speciesName <- 'species' obj <- startISDM(PA, Projection = projection, Mesh = mesh, IPS = iPoints, trialsPA = trialName, responseCounts = responseCounts, responsePA = responsePA,pointsSpatial = NULL) obj$spatialBlock(k = 2, rows_cols = c(2,1)) #expect_true('.__block_index__' %in% names(obj$.__enclos_env__$private$modelData$PO$PO)) expect_true('.__block_index__' %in% names(obj$.__enclos_env__$private$modelData$PA$PA)) ##run model blocked <- blockedCV(data = obj, options = list(control.inla=list(int.strategy='eb'))) expect_setequal(class(blocked), c("blockedCV", "list")) expect_setequal(names(blocked), c( "DIC_fold_1", "DIC_fold_2",'Formula')) expect_equal(class(blocked$Formula), 'formula') expect_output(print(blocked), 'Spatial block cross-validation score:') expect_output(print(blocked), 'mean DIC score:') obj2 <- startSpecies(PA, Projection = projection, Mesh = mesh, IPS = iPoints, trialsPA = trialName, responseCounts = responseCounts, responsePA = responsePA,pointsSpatial = NULL, speciesName = speciesName) obj2$spatialBlock(k = 2, rows_cols = c(2,1)) expect_true('.__block_index__' %in% names(obj2$.__enclos_env__$private$modelData$PA$PA_bird)) blocked2 <- blockedCV(data = obj2, options = list(control.inla=list(int.strategy='eb'))) expect_setequal(class(blocked2), c("blockedCV", "list")) expect_setequal(names(blocked2), c( "DIC_fold_1", "DIC_fold_2",'Formula')) expect_equal(class(blocked2$Formula), 'formula') expect_output(print(blocked2), 'Spatial block cross-validation score:') expect_output(print(blocked2), 'mean DIC score:') })