bayesfactor: Bayes Factors (BF)

In bayestestR: Understand and Describe Bayesian Models and Posterior Distributions

Bayes Factors (BF)

Description

This function compte the Bayes factors (BFs) that are appropriate to the input. For vectors or single models, it will compute BFs for single parameters(), or is hypothesis is specified, BFs for restricted models(). For multiple models, it will return the BF corresponding to comparison between models() and if a model comparison is passed, it will compute the inclusion BF().

For a complete overview of these functions, read the Bayes factor vignette.

Usage

bayesfactor(
  ...,
  prior = NULL,
  direction = "two-sided",
  null = 0,
  hypothesis = NULL,
  effects = c("fixed", "random", "all"),
  verbose = TRUE,
  denominator = 1,
  match_models = FALSE,
  prior_odds = NULL
)

Arguments

...	A numeric vector, model object(s), or the output from bayesfactor_models.
prior	An object representing a prior distribution (see 'Details').
direction	Test type (see 'Details'). One of 0, "two-sided" (default, two tailed), -1, "left" (left tailed) or 1, "right" (right tailed).
null	Value of the null, either a scalar (for point-null) or a range (for a interval-null).
hypothesis	A character vector specifying the restrictions as logical conditions (see examples below).
effects	Should results for fixed effects, random effects or both be returned? Only applies to mixed models. May be abbreviated.
verbose	Toggle off warnings.
denominator	Either an integer indicating which of the models to use as the denominator, or a model to be used as a denominator. Ignored for BFBayesFactor.
match_models	See details.
prior_odds	Optional vector of prior odds for the models. See ⁠BayesFactor::priorOdds<-⁠.

Value

Some type of Bayes factor, depending on the input. See bayesfactor_parameters(), bayesfactor_models() or bayesfactor_inclusion()

Note

There is also a plot()-method implemented in the see-package.

Examples

library(bayestestR)

if (require("logspline")) {
  prior <- distribution_normal(1000, mean = 0, sd = 1)
  posterior <- distribution_normal(1000, mean = .5, sd = .3)

  bayesfactor(posterior, prior = prior, verbose = FALSE)
}
## Not run: 
# rstanarm models
# ---------------
if (require("rstanarm")) {
  model <- stan_lmer(extra ~ group + (1 | ID), data = sleep)
  bayesfactor(model, verbose = FALSE)
}

## End(Not run)

if (require("logspline")) {
  # Frequentist models
  # ---------------
  m0 <- lm(extra ~ 1, data = sleep)
  m1 <- lm(extra ~ group, data = sleep)
  m2 <- lm(extra ~ group + ID, data = sleep)

  comparison <- bayesfactor(m0, m1, m2)
  comparison

  bayesfactor(comparison)
}

bayestestR documentation built on April 7, 2023, 5:09 p.m.