Variance and correlations measures for prediction components
Calculates local and integrated variance and correlation measures as introduced by Yuan et al. (2017).
devel.cvmeasure(joint, prediction1, prediction2, samplers = NULL, mesh = NULL)
joint |
A joint |
prediction1 |
A |
prediction2 |
A |
samplers |
A SpatialPolygon object describing the area for which to compute the cummulative variance measure. |
mesh |
The |
Variance and correlations measures.
Y. Yuan, F. E. Bachl, F. Lindgren, D. L. Brochers, J. B. Illian, S. T. Buckland, H. Rue, T. Gerrodette. 2017. Point process models for spatio-temporal distance sampling data from a large-scale survey of blue whales. https://arxiv.org/abs/1604.06013
if (bru_safe_inla()) { # Load Gorilla data data("gorillas", package = "inlabru") # Use RColorBrewer library(RColorBrewer) # Fit a model with two components: # 1) A spatial smooth SPDE # 2) A spatial covariate effect (vegetation) pcmatern <- INLA::inla.spde2.pcmatern(gorillas$mesh, prior.sigma = c(0.1, 0.01), prior.range = c(0.01, 0.01) ) cmp <- coordinates ~ vegetation(gorillas$gcov$vegetation, model = "factor_contrast") + spde(coordinates, model = pcmatern) - Intercept(1) fit <- lgcp(cmp, gorillas$nests, samplers = gorillas$boundary, domain = list(coordinates = gorillas$mesh), options = list(control.inla = list(int.strategy = "eb")) ) # Predict SPDE and vegetation at the mesh vertex locations vrt <- vertices(gorillas$mesh) pred <- predict( fit, vrt, ~ list( joint = spde + vegetation, field = spde, veg = vegetation ) ) # Plot component mean multiplot(ggplot() + gg(gorillas$mesh, color = pred$joint$mean) + coord_equal() + theme(legend.position = "bottom"), ggplot() + gg(gorillas$mesh, color = pred$field$mean) + coord_equal() + theme(legend.position = "bottom"), ggplot() + gg(gorillas$mesh, color = pred$veg$mean) + coord_equal() + theme(legend.position = "bottom"), cols = 3 ) # Plot component variance multiplot(ggplot() + gg(gorillas$mesh, color = pred$joint$var) + coord_equal() + theme(legend.position = "bottom"), ggplot() + gg(gorillas$mesh, color = pred$field$var) + coord_equal() + theme(legend.position = "bottom"), ggplot() + gg(gorillas$mesh, color = pred$veg$var) + coord_equal() + theme(legend.position = "bottom"), cols = 3 ) # Calculate variance and correlation measure vm <- devel.cvmeasure(pred$joint, pred$field, pred$veg) lprange <- range(vm$var.joint, vm$var1, vm$var2) # Variance contribution of the components csc <- scale_fill_gradientn(colours = brewer.pal(9, "YlOrRd"), limits = lprange) boundary <- gorillas$boundary plot.1 <- ggplot() + gg(gorillas$mesh, color = vm$var.joint, mask = boundary) + csc + coord_equal() + ggtitle("joint") + theme(legend.position = "bottom") plot.2 <- ggplot() + gg(gorillas$mesh, color = vm$var1, mask = boundary) + csc + coord_equal() + ggtitle("SPDE") + theme(legend.position = "bottom") plot.3 <- ggplot() + gg(gorillas$mesh, color = vm$var2, mask = boundary) + csc + coord_equal() + ggtitle("vegetation") + theme(legend.position = "bottom") multiplot(plot.1, plot.2, plot.3, cols = 3) # Covariance of SPDE field and vegetation ggplot() + gg(gorillas$mesh, color = vm$cov) # Correlation between field and vegetation ggplot() + gg(gorillas$mesh, color = vm$cor) # Variance and correlation integrated over space vm.int <- devel.cvmeasure(pred$joint, pred$field, pred$veg, samplers = ipoints(gorillas$boundary, gorillas$mesh), mesh = gorillas$mesh ) vm.int }
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