Double Bayesian Predictive Stacking for Spatial Analysis - Tutotial

We provide a brief tutorial of the spBPS package. Here we shows the implementation of the Double Bayesian Predictive Stacking on synthetically univariate generated data. In particular, we focus on parallel computing using the packages parallel, doParallel; but it is not mandatory: it suffices to make it sequential. For any further details please refer to (Presicce and Banerjee 2024). More examples, for multivariate data, are available in documentation, and functions help.

library(spBPS)

Working packages

library(foreach)
library(parallel)
library(doParallel)
library(tictoc)
library(MBA)
library(classInt)
library(RColorBrewer)
library(sp)
library(fields)
library(mvnfast)
library(abind)

Data generation

We generate data from the model detailed in Equation (2.4) (Presicce and Banerjee 2024), over a unit square.

# dimensions
n <- 1000
u <- 250
p <- 2
q <- 1

# parameters
B <- c(-0.75, 1.85)
tau2 <- 0.25
sigma2 <- 1
delta <- tau2/sigma2
phi <- 4

set.seed(4-8-15-16-23-42)
# generate sintethic data
crd <- matrix(runif((n+u) * 2), ncol = 2)
X_or <- cbind(rep(1, n+u), matrix(runif((p-1)*(n+u)), ncol = (p-1)))
D <- spBPS:::arma_dist(crd)
Rphi <- exp(-phi * D)
W_or <- matrix(0, n+u) + mniw::rmNorm(1, rep(0, n+u), sigma2*Rphi)
Y_or <- X_or %*% B + W_or + mniw::rmNorm(1, rep(0, n+u), diag(delta*sigma2, n+u))

# train data
crd_s <- crd[1:n, ]
X <- X_or[1:n, ]
W <- W_or[1:n, ]
Y <- Y_or[1:n, ]

# prediction data
crd_u <- crd[-(1:n), ]
X_u <- X_or[-(1:n), ]
W_u <- W_or[-(1:n), ]
Y_u <- Y_or[-(1:n), ]

Setting priors and hyperparameters

# priors 
priors <- list(mu_B = matrix(0, nrow = p, ncol = q),
               V_r = diag(10, p),
               Psi = diag(1, q),
               nu = 3)

# hyperparameters values
alfa_seq <- c(0.7, 0.8, 0.9)
phi_seq <- c(3, 4, 5)
hyperpar <- list(alpha = alfa_seq, phi = phi_seq)

Setting dimensions

# subset dimension
subset_size <- 100

# number of posterior draws
R <- 200

# number of computational cores
n_core <- 1

Double BPS parallel fit

Parallel implementation, exploiting 1 computing core.

out <- spBPS(data = list(Y = Y, X = X),
      priors = priors,
      coords = crd_s,
      hyperpar = hyperpar,
      subset_size = subset_size,
      combine_method = "bps",
      draws = R,
      newdata = list(X = X_u, coords = crd_u),
      n_cores = n_core)

Results collection

# statistics computations W
pred_mat_W <- out$predictive$Wu
post_mean_W <- apply(pred_mat_W, c(1,2), mean)
post_qnt_W <- apply(pred_mat_W, c(1,2), quantile, c(0.025, 0.975))

# Empirical coverage for W
coverage_W <- mean(W_u >= post_qnt_W[1,,1] & W_u <= post_qnt_W[2,,1])
cat("Empirical coverage for Spatial process:", round(coverage_W, 3),"\n")
#> Empirical coverage for Spatial process: 1

# statistics computations Y
pred_mat_Y <- out$predictive$Yu
post_mean_Y <- apply(pred_mat_Y, c(1,2), mean)
post_qnt_Y <- apply(pred_mat_Y, c(1,2), quantile, c(0.025, 0.975))

# Empirical coverage for Y
coverage_Y <- mean(Y_u >= post_qnt_Y[1,,1] & Y_u <= post_qnt_Y[2,,1])
cat("Empirical coverage for Response:", round(coverage_Y, 3),"\n")
#> Empirical coverage for Response: 0.976

# Root Mean Square Prediction Error
rmspe_W <- sqrt( mean( (W_u - post_mean_W)^2 ) )
rmspe_Y <- sqrt( mean( (Y_u - post_mean_Y)^2 ) )
cat("RMSPE for Spatial process:", round(rmspe_W, 3), "\n")
#> RMSPE for Spatial process: 0.487
cat("RMSPE for Response:", round(rmspe_Y, 3), "\n")
#> RMSPE for Response: 0.624

Plot results

Presicce, Luca, and Sudipto Banerjee. 2024. “Bayesian Transfer Learning for Artificially Intelligent Geospatial Systems: A Predictive Stacking Approach.” arXiv Preprint, preprint, arXiv:2410.09504. https://doi.org/10.48550/arXiv.2410.09504.