check_prior: Check if Prior is Informative

Description Usage Arguments Value References Examples

View source: R/check_prior.R

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

1
check_prior(model, method = "gelman", simulate_priors = TRUE, ...)

Arguments

model

A stanreg, stanfit, or brmsfit 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

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
## Not run: 
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")
  plot(si(model)) # can provide visual confirmation to the Lakeland method
}

## End(Not run)

DominiqueMakowski/bayestestR documentation built on July 27, 2021, 4:12 p.m.