demo/prior.R

In INLAtools: Functionalities for the 'INLA' Package

library(INLAtools)
old.par <- par(no.readonly = TRUE)

## Setting the prior parameters
prior.par <- c(1, 0.5) # P(sigma > 1) = 0.5
cmodel <- cgeneric(
  model = "iid", n = 10,
  param = prior.par)

## prior summaries: sigma and log-precision
(lamb <- -log(prior.par[2])/prior.par[1])
(smedian <- qexp(0.5, lamb))
(smean <- 1/lamb)

## mode: at the minimum of - log-prior
(lpmode <- optimize(function(x)
  -prior(cmodel, theta = x),
  c(-10, 30))$minimum)
## mean: integral of x*f(x)dx
(lpmean <- integrate(function(x)
  exp(prior(cmodel, theta = matrix(x, 1)))*x,
  -10, 30)$value)

## prior visualization: log(precision) and sigma
par(mfrow = c(1, 2))
plot(function(x)
 exp(prior(cmodel, theta = matrix(x, nrow=1))),
  -3, 3, n = 601, xlab = "log-precision",
  ylab = "density")
abline(v = lpmode, lwd = 3, col = 2)
rug(-2*log(smedian), lwd = 3, col = 3)
rug(lpmean, lwd = 3, col = 4)
plot(function(x)
 exp(prior(cmodel,
  theta = matrix(
    -2*log(x),
    nrow = 1))+log(2)-log(x)),
  1/100, 10, n = 1000,
  xlab = expression(sigma),
  ylab = "density")
plot(function(x) dexp(x, lamb),
   1/100, 10, n = 1000,
   add = TRUE, lty = 2, col = 2)
rug(smedian, lwd = 3, col = 3)
rug(smean, lwd = 3, col = 4)

par(old.par)