check_prior: Check if Prior is Informative

In DominiqueMakowski/bayestestR: Understand and Describe Bayesian Models and Posterior Distributions

Check if Prior is Informative

Description

Performs a simple test to check whether the prior is informative to the posterior. This idea, and the accompanying heuristics, were discussed in this blogpost.

Usage

check_prior(model, method = "gelman", simulate_priors = TRUE, ...)

Arguments

model	A stanreg, stanfit, brmsfit, blavaan, or MCMCglmm object.
method	Can be "gelman" or "lakeland". For the "gelman" method, if the SD of the posterior is more than 0.1 times the SD of the prior, then the prior is considered as informative. For the "lakeland" method, the prior is considered as informative if the posterior falls within the ⁠95%⁠ HDI of the prior.
simulate_priors	Should prior distributions be simulated using simulate_prior() (default; faster) or sampled via unupdate() (slower, more accurate).
...	Currently not used.

Value

A data frame with two columns: The parameter names and the quality of the prior (which might be "informative", "uninformative") or "not determinable" if the prior distribution could not be determined).

References

https://statmodeling.stat.columbia.edu/2019/08/10/

Examples

library(bayestestR)
if (require("rstanarm")) {
  model <- stan_glm(mpg ~ wt + am, data = mtcars, chains = 1, refresh = 0)
  check_prior(model, method = "gelman")
  check_prior(model, method = "lakeland")

  # An extreme example where both methods diverge:
  model <- stan_glm(mpg ~ wt,
    data = mtcars[1:3, ],
    prior = normal(-3.3, 1, FALSE),
    prior_intercept = normal(0, 1000, FALSE),
    refresh = 0
  )
  check_prior(model, method = "gelman")
  check_prior(model, method = "lakeland")
  # can provide visual confirmation to the Lakeland method
  plot(si(model, verbose = FALSE))
}

DominiqueMakowski/bayestestR documentation built on April 3, 2024, 7:02 p.m.