inference_inla {makemyprior}

Run inference

Description

This function helps you run inference with INLA using a prior object from make_prior. You must have INLA installed to run this. INLA can be installed with: install.packages("INLA", repos = c(getOption("repos"), INLA = "https://inla.r-inla-download.org/R/stable"), dep = TRUE). Also see r-inla.org.

Usage

inference_inla(prior_obj, use_likelihood = TRUE, print_prior = TRUE, ...)

Arguments

prior_obj

An object from make_prior, from makemyprior_gui, from inference_stan, or from inference_inla (for refitting model)

use_likelihood

Whether to sample from the prior only (FALSE, can be used for e.g. debugging or to look at the priors on variance parameters when using an HD prior, see also Details), or to use the likelihood and data to get the posterior (TRUE, default).

print_prior

Whether to print a text with the chosen prior or not (default TRUE)

...

Other values to be sent to INLA. Useful arguments include Ntrials for the binomial likelihood and E (mean E_i in E_i*exp(eta_i)) for the Poisson likelihood. We set the default value of num.threads to 1 (this can however be changed). See inla for details. Can be anything sent to inla except for control.expert and arguments that specify priors.

Details

Jeffreys' prior is improper. If use_likelihood = FALSE and Jeffreys' prior is used for the total variance, the prior will be changed to a Gaussian(0,1) prior on the log total variance. This means that it does not make sense to look at the variances/standard deviations/precisions, but the variance proportions will be correct. Note that this is only an issue when sampling from the prior (i.e., not using the likelihood).

Value

A named list with a prior object (prior), an inla-object (inla) and some data inla requires (inla_data).

Examples

## Not run: 

vignette("make_prior", package = "makemyprior")

## End(Not run)

ex_prior <- makemyprior_example_model()
if (interactive() && requireNamespace("INLA")){
  posterior <- inference_inla(ex_prior)
  plot(posterior)
}