inst/tests/test-bym2.R

In inbo/INLA: Full Bayesian Analysis of Latent Gaussian Models using Integrated Nested Laplace Approximations

context("test 'latent bym2'")

test_that("Case 1", {
    set.seed(123)
    library(MASS)
    data(Germany)
    g = inla.read.graph(system.file("demodata/germany.graph", package="INLA"))
    Germany = cbind(Germany,region.struct=Germany$region)
    Q = -inla.graph2matrix(g)
    diag(Q) = g$nnbs
    Q = Q * exp(mean(log(diag(ginv(as.matrix(Q))))))
    tau = 1
    rho = 0.3
    n = dim(Q)[1]
    u = inla.qsample(n = 1,  Q = Q + 1e-8 * Diagonal(n),
            constr=list(A = matrix(1, 1, n), e=0), seed=1234L)
    v = rnorm(n)
    x = 1/sqrt(tau) * (sqrt(1-rho) * v + sqrt(rho) * u)
    intercept = log(Germany$E)
    y = rpois(n, lambda = exp(intercept + x))
    
    formula = y ~ 1 + f(region,
            model = "bym2", graph = g, constr=TRUE)
    r = inla(formula, family="poisson",
            data=data.frame(y, region=Germany$region))
    expect_true(abs(r$summary.hyperpar[1,"mean"] - tau) < 0.4)
    expect_true(abs(r$summary.hyperpar[2,"mean"] - rho) < 0.175)
})