Description Usage Arguments Details Value Setting the correct prior Interpreting Bayes Factors References Examples
View source: R/bayesfactor_restricted.R
This method computes Bayes factors for comparing a model with an order restrictions on its parameters
with the fully unrestricted model. Note that this method should only be used for confirmatory analyses.
The bf_*
function is an alias of the main function.
For more info, in particular on specifying correct priors for factors with more than 2 levels, see the Bayes factors vignette.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49  bayesfactor_restricted(
posterior,
hypothesis,
prior = NULL,
verbose = TRUE,
...
)
bf_restricted(posterior, hypothesis, prior = NULL, verbose = TRUE, ...)
## S3 method for class 'stanreg'
bayesfactor_restricted(
posterior,
hypothesis,
prior = NULL,
verbose = TRUE,
effects = c("fixed", "random", "all"),
component = c("conditional", "zi", "zero_inflated", "all"),
...
)
## S3 method for class 'brmsfit'
bayesfactor_restricted(
posterior,
hypothesis,
prior = NULL,
verbose = TRUE,
effects = c("fixed", "random", "all"),
component = c("conditional", "zi", "zero_inflated", "all"),
...
)
## S3 method for class 'blavaan'
bayesfactor_restricted(
posterior,
hypothesis,
prior = NULL,
verbose = TRUE,
...
)
## S3 method for class 'emmGrid'
bayesfactor_restricted(
posterior,
hypothesis,
prior = NULL,
verbose = TRUE,
...
)

posterior 
A 
hypothesis 
A character vector specifying the restrictions as logical conditions (see examples below). 
prior 
An object representing a prior distribution (see Details). 
verbose 
Toggle off warnings. 
... 
Currently not used. 
effects 
Should results for fixed effects, random effects or both be returned? Only applies to mixed models. May be abbreviated. 
component 
Should results for all parameters, parameters for the conditional model or the zeroinflated part of the model be returned? May be abbreviated. Only applies to brmsmodels. 
This method is used to compute Bayes factors for orderrestricted models vs unrestricted
models by setting an order restriction on the prior and posterior distributions
(Morey & Wagenmakers, 2013).
(Though it is possible to use bayesfactor_restricted()
to test interval restrictions,
it is more suitable for testing order restrictions; see examples).
A data frame containing the (log) Bayes factor representing evidence against the unrestricted model.
prior
For the computation of Bayes factors, the model priors must be proper priors
(at the very least they should be not flat, and it is preferable that
they be informative); As the priors for the alternative get wider, the
likelihood of the null value(s) increases, to the extreme that for completely
flat priors the null is infinitely more favorable than the alternative (this
is called the JeffreysLindleyBartlett paradox). Thus, you should
only ever try (or want) to compute a Bayes factor when you have an informed
prior.
(Note that by default, brms::brm()
uses flat priors for fixedeffects;
See example below.)
It is important to provide the correct prior
for meaningful results.
When posterior
is a numerical vector, prior
should also be a numerical vector.
When posterior
is a data.frame
, prior
should also be a data.frame
, with matching column order.
When posterior
is a stanreg
or brmsfit
model:
prior
can be set to NULL
, in which case prior samples are drawn internally.
prior
can also be a model equivalent to posterior
but with samples from the priors only. See unupdate()
.
Note: When posterior
is a brmsfit_multiple
model, prior
must be provided.
When posterior
is an emmGrid
object:
prior
should be the stanreg
or brmsfit
model used to create the emmGrid
objects.
prior
can also be an emmGrid
object equivalent to posterior
but created with a model of priors samples only.
Note: When the emmGrid
has undergone any transformations ("log"
, "response"
, etc.), or regrid
ing, then prior
must be an emmGrid
object, as stated above.
A Bayes factor greater than 1 can be interpreted as evidence against the null, at which one convention is that a Bayes factor greater than 3 can be considered as "substantial" evidence against the null (and vice versa, a Bayes factor smaller than 1/3 indicates substantial evidence in favor of the nullmodel) (Wetzels et al. 2011).
Morey, R. D., & Wagenmakers, E. J. (2014). Simple relation between Bayesian orderrestricted and pointnull hypothesis tests. Statistics & Probability Letters, 92, 121124.
Morey, R. D., & Rouder, J. N. (2011). Bayes factor approaches for testing interval null hypotheses. Psychological methods, 16(4), 406.
Morey, R. D. (Jan, 2015). Multiple Comparisons with BayesFactor, Part 2 – order restrictions. Retrived from https://richarddmorey.org/category/orderrestrictions/.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54  library(bayestestR)
prior < data.frame(
X = rnorm(100),
X1 = rnorm(100),
X3 = rnorm(100)
)
posterior < data.frame(
X = rnorm(100, .4),
X1 = rnorm(100, .2),
X3 = rnorm(100)
)
hyps < c(
"X > X1 & X1 > X3",
"X > X1"
)
bayesfactor_restricted(posterior, hypothesis = hyps, prior = prior)
## Not run:
# rstanarm models
# 
if (require("rstanarm") && require("emmeans")) {
fit_stan < stan_glm(mpg ~ wt + cyl + am,
data = mtcars, refresh = 0
)
hyps < c(
"am > 0 & cyl < 0",
"cyl < 0",
"wt  cyl > 0"
)
bayesfactor_restricted(fit_stan, hypothesis = hyps)
# emmGrid objects
# 
# replicating http://bayesfactor.blogspot.com/2015/01/multiplecomparisonswithbayesfactor2.html
disgust_data < read.table(url("http://www.learnbayes.org/disgust_example.txt"), header = TRUE)
contrasts(disgust_data$condition) < contr.orthonorm # see vignette
fit_model < stan_glm(score ~ condition, data = disgust_data, family = gaussian())
em_condition < emmeans(fit_model, ~condition)
hyps < c("lemon < control & control < sulfur")
bayesfactor_restricted(em_condition, prior = fit_model, hypothesis = hyps)
# > # Bayes Factor (OrderRestriction)
# >
# > Hypothesis P(Prior) P(Posterior) BF
# > lemon < control & control < sulfur 0.17 0.75 4.49
# > 
# > Bayes factors for the restricted model vs. the unrestricted model.
}
## End(Not run)

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