test_that('datasetOut is able to correctly remove the correct datasets and metadata from the integrated model.', { ##First generate a model: ##Just import a model?? projection <- '+proj=tmerc' #Make random shape to generate points on 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) 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$species <- sample(x = c('fish'), size = nrow(PO), replace = TRUE) #Random presence absence dataset PA <- st_as_sf(st_sample(SpatialPoly, 100, crs = projection)) st_geometry(PA) <- 'geometry' PA$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$binommark <- sample(x = 0:1, size = nrow(PA), replace = TRUE) PA$marktrial <- sample(x = 2:5, size = nrow(PA), replace = TRUE) PA$species <- sample(x = c('bird'), nrow(PA), replace = TRUE) mesh <- INLA::inla.mesh.2d(boundary = INLA::inla.sp2segment(SpatialPoly), max.edge = 2, crs = inlabru::fm_crs(projection)) #iPoints <- inlabru::ipoints(samplers = SpatialPoly, domain = mesh) iPoints <- inlabru::fm_int(samplers = SpatialPoly, domain = mesh) coordnames <- c('long', 'lat') responseCounts <- 'count' responsePA <- 'PAresp' trialName <- 'trial' markNames <- c('numvar', 'factvar', 'binommark') marksFamily <- c('gaussian', 'multinomial', 'binomial') markTrial = 'marktrial' pointCovs <- 'pointcov' speciesName <- 'species' cov <- terra::rast(st_as_sf(SpatialPoly), crs = projection) terra::values(cov) <- rgamma(n = terra::ncell(cov), shape = 2) names(cov) <- 'covariate' obj <- startISDM(PO, PA, Projection = projection, Mesh = mesh, spatialCovariates = cov, IPS = iPoints, trialsPA = trialName, responseCounts = responseCounts, responsePA = responsePA, pointsIntercept = TRUE,pointsSpatial = NULL) spatMod <- fitISDM(data = obj, options = list(control.inla=list(int.strategy='eb'))) ##Remove PO from the model outPO <- datasetOut(model = spatMod, dataset = 'PO', predictions = T) expect_setequal(class(outPO), c("datasetOut", "list")) expect_true(names(outPO) == 'Leaving_out_PO') expect_output(print(outPO),'Changes in fixed values by leaving out PO:') expect_output(print(outPO), 'Leave-one-out cross-validation score:') #ie no fish from dataset PO expect_setequal(outPO$Leaving_out_PO$names.fixed, c("covariate", "PA_intercept")) expect_setequal(names(outPO$Leaving_out_PO$bru_info$lhoods), 'PA_PAresp') expect_setequal(outPO$Leaving_out_PO$source, 'PA') expect_false('PO' %in% names(outPO$Leaving_out_PO$species$speciesIn)) expect_false('PO' %in% names(outPO$Leaving_out_PO$marks$marksIn)) expect_length(outPO$Leaving_out_PO$optionsJoint$control.family, 1) #Try copy spatial obj2 <- startISDM(PO, PA, Projection = projection, Mesh = mesh, IPS = iPoints, trialsPA = trialName, responseCounts = responseCounts, responsePA = responsePA, pointsIntercept = TRUE) spatMod2 <- fitISDM(data = obj2, options = list(control.inla=list(int.strategy='eb'))) outPO2 <- datasetOut(model = spatMod2, dataset = 'PO', predictions = T) expect_true('PA_spatial' %in% names(outPO2$Leaving_out_PO$summary.random)) expect_identical(deparse1(outPO2$Leaving_out_PO$componentsJoint), '~PA_intercept(1) + PA_spatial(main = geometry, model = PO_field) - 1') })