INLA is not strongly dependent on random number generation (unlike MCMC!) but it does sometimes use simulation as part of the calculation. You will find that if you repeat the same command, you may get slightly different output. Hence, you may find that if you repeat the same commands as seen in the book, you might not get exactly the same answer. This is usually not a serious concern bearing in mind that the last letter of INLA stands for approximation and exact answers are not to be expected.
imod <- inla(y ~ x -1, family="gaussian", control.fixed=list(mean=uhub, prec=1/((0.05*uhub)^2)), data=hubble)
As it happens, this makes no important difference to the numerical outcome.
p104: the inla.contrib.sd function is no longer available in the INLA package. You can compute this information as bri.hyperpar.summary function as demonstrated on the following page.
p111: 3rd line of R code should now read mean(lvsamp[,'site:3'] > lvsamp[,'site:1']). At some point, the parameter labeling in INLA changed which broke the previous version of this line.
p118: Both inla() calls on this page now also require the option control.compute=list(return.marginals.predictor=TRUE) because these quantities are expensive
to compute and are not always needed.
p134: Last para. Difference between predictions and table is due to the difference between subject specific effects and population effects
p137: Third para. Difference can be explained (see errata for p134) but the analysis is still worthwhile.
p139: Section 5.7.1 should be ignored. This correction is not available in the current version of INLA because it is not regarded as sufficiently stable to be relied upon.
inla.spde2.matern has changed arguments requiringspde <- inla.spde2.matern(mesh, alpha=alpha, constr = FALSE,
prior.tau = tau0,
prior.kappa = kappa0,
theta.prior.prec = 1e5)
The value of theta.prior.prec is intentionally large to ensure prior is respected.
We must add the option control.compute=list(return.marginals.predictor=TRUE) to get
the marginal distributions needed for the subsequent calculation.