test_that('intModel is able to initialize a dataSDM object as well as correctly add the data to the integrated model', { skip_on_cran() ##Set up arbitrary data 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$binommark <- sample(x = 2:5, size = nrow(PA), replace = TRUE) PA$marktrial <- sample(x = 0:1, size = nrow(PA), replace = TRUE) PA$species <- sample(x = c('bird'), nrow(PA), replace = TRUE) mesh <- INLA::inla.mesh.2d(boundary = INLA::inla.sp2segment(SpatialPoly), max.edge = 2, crs = inlabru::fm_crs(projection)) #iPoints <- inlabru::ipoints(samplers = SpatialPoly, domain = mesh) iPoints <- inlabru::fm_int(samplers = SpatialPoly, domain = mesh) ##Make PA a data.frame object PA$long <- st_coordinates(PA)[,1] PA$lat <- st_coordinates(PA)[,2] st_geometry(PA) <- NULL PA <- data.frame(PA) coordnames <- c('long', 'lat') responseCounts <- 'count' responsePA <- 'PAresp' trialName <- 'trial' markNames <- c('numvar', 'factvar', 'binommark') marksFamily <- c('gaussian', 'multinomial', 'binomial') markTrial = 'marktrial' pointCovs <- 'pointcov' speciesName <- 'species' obj <- intModel(PO, PA, Coordinates = coordnames, Projection = projection, Mesh = mesh, IPS = iPoints, trialsPA = trialName, responseCounts = responseCounts, responsePA = responsePA, markNames = markNames, markFamily = marksFamily, speciesName = speciesName) expect_true(all(class(obj) == c('dataSDM', 'R6'))) expect_setequal(names(obj$.__enclos_env__$private$modelData), c("PO", "PA")) ##Test warnings: No data added expect_warning(intModel(Coordinates = coordnames, Projection = projection, Mesh = mesh, IPS = iPoints, trialsPA = trialName, responseCounts = responseCounts, responsePA = responsePA, markNames = markNames, markFamily = marksFamily, speciesName = speciesName)) ##Test error: Coordinates length > 2 expect_error(intModel(PO, PA, Coordinates = c('x','y','z'), Projection = projection, Mesh = mesh, IPS = iPoints, trialsPA = trialName, responseCounts = responseCounts, responsePA = responsePA, markNames = markNames, markFamily = marksFamily, speciesName = speciesName)) ##Test error: Coordinates[1] == Coordinates[2] expect_error(intModel(PO, PA, Coordinates = c('x','x'), Projection = projection, Mesh = mesh, IPS = iPoints, trialsPA = trialName, responseCounts = responseCounts, responsePA = responsePA, markNames = markNames, markFamily = marksFamily, speciesName = speciesName)) ##Test error: proj not CRS expect_error(intModel(PO, PA, Coordinates = coordnames, Projection = list(), Mesh = mesh, IPS = iPoints, trialsPA = trialName, responseCounts = responseCounts, responsePA = responsePA, markNames = markNames, markFamily = marksFamily, speciesName = speciesName)) ##Test error: INLAmesh not an inla.mesh object expect_error(intModel(PO, PA, Coordinates = coordnames, Projection = Projection, Mesh = list(), IPS = iPoints, trialsPA = trialName, responseCounts = responseCounts, responsePA = responsePA, markNames = markNames, markFamily = marksFamily, speciesName = speciesName)) })