Changelog
Source:NEWS.md
bayestestR 0.13.1
CRAN release: 20230407
Changes
Improved speed performance when functions are called using
do.call()
.Improved speed performance to
bayesfactor_models()
forbrmsfit
objects that already included amarglik
element in the model object.
New functionality

as.logical()
forbayesfactor_restricted()
results, extracts the boolean vector(s) the mark which draws are part of the order restriction.
Bug fixes
p_map()
gains a newnull
argument to specify any non0 nulls.Fixed nonworking examples for
ci(method = "SI")
.Fixed wrong calculation of rope range for model objects in
describe_posterior()
.Some smaller bug fixes.
bayestestR 0.13.0
CRAN release: 20220918
Breaking
The minimum needed R version has been bumped to
3.6
.contr.equalprior(contrasts = FALSE)
(previouslycontr.orthonorm
) no longer returns an identity matrix, but a shifteddiag(n)  1/n
, for consistency.
New functionality

p_to_bf()
, to convert pvalues into Bayes factors. For more accurate approximate Bayes factors, usebic_to_bf()
. 
bayestestR now supports objects of class
rvar
from package posterior. 
contr.equalprior
(previouslycontr.orthonorm
) gains two new functions:contr.equalprior_pairs
andcontr.equalprior_deviations
to aide in setting more intuitive priors.
Changes
 has been renamed
contr.equalprior
to be more explicit about its function. 
p_direction()
now accepts objects of classparameters_model()
(fromparameters::model_parameters()
), to compute probability of direction for parameters of frequentist models.
bayestestR 0.12.1
CRAN release: 20220502
Breaking
Bayesfactor_models()
for frequentist models now relies on the updatedinsight::get_loglikelihood()
. This might change some results for REML based models. See documentation.estimate_density()
argumentgroup_by
is renamedat
.All
distribution_*(random = FALSE)
functions now rely onppoints()
, which will result in slightly different results, especially with smalln
s.Uncertainty estimation now defaults to
"eti"
(formerly was"hdi"
).
Changes
bayestestR functions now support
draws
objects from package posterior.rope_range()
now handles log(normal)families and models with logtransformed outcomes.New function
spi()
, to compute shortest probability intervals. Furthermore, the"spi"
option was added as new method to compute uncertainty intervals.
Bug fixes

bci()
for some objects incorrectly returned the equaltailed intervals.
bayestestR 0.11.1
New functions

describe_posterior()
gains aplot()
method, which is a short cut forplot(estimate_density(describe_posterior()))
.
bayestestR 0.11
Bug fixes
Fixed issues related to last brms update.
Fixed bug in
describe_posterior.BFBayesFactor()
where Bayes factors were missing from out put ( #442 ).
bayestestR 0.10.0
CRAN release: 20210531
Breaking
 All Bayes factors are now returned as
log(BF)
(column namelog_BF
). Printing is unaffected. To retrieve the raw BFs, you can runexp(result$log_BF)
.
New functions

bci()
(and its aliasbcai()
) to compute biascorrected and accelerated bootstrap intervals. Along with this new function,ci()
anddescribe_posterior()
gain a newci_method
type,"bci"
.
bayestestR 0.9.0
CRAN release: 20210408
Breaking
The default
ci
width has been changed to 0.95 instead of 0.89 (see here). This should not come as a surprise to the longtime users ofbayestestR
as we have been warning about this impending change for a while now :)Column names for
bayesfactor_restricted()
are nowp_prior
andp_posterior
(wasPrior_prob
andPosterior_prob
), to be consistent withbayesfactor_inclusion()
output.Removed the experimental function
mhdior
.
General
Support for
blavaan
models.Support for
blrm
models (rmsb).Support for
BGGM
models (BGGM).check_prior()
anddescribe_prior()
should now also work for more ways of prior definition in models from rstanarm or brms.
Bug fixes
Fixed bug in
print()
method for themediation()
function.Fixed remaining inconsistencies with CI values, which were not reported as fraction for
rope()
.Fixed issues with special prior definitions in
check_prior()
,describe_prior()
andsimulate_prior()
.
bayestestR 0.8.2
CRAN release: 20210126
Changes to functions
 All
.stanreg
methods gain acomponent
argument, to also include auxiliary parameters.
Bug fixes
bayesfactor_parameters()
no longer errors for no reason when computing extremely un/likely direction hypotheses.bayesfactor_pointull()
/bf_pointull()
are nowbayesfactor_pointnull()
/bf_pointnull()
(can you spot the difference? #363 ).
bayestestR 0.8.0
CRAN release: 20201205
New functions

sexit()
, a function for sequential effect existence and significance testing (SEXIT).
General
Added startupmessage to warn users that default ciwidth might change in a future update.
Added support for mcmc.list objects.
Bug fixes
unupdate()
gains anewdata
argument to work withbrmsfit_multiple
models.Fixed issue in Bayes factor vignette (don’t evaluate code chunks if packages not available).
bayestestR 0.7.5
CRAN release: 20201022
New functions
Added
as.matrix()
function forbayesfactor_model
arrays.unupdate()
, a utility function to get Bayesian models unfitted from the data, representing the priors only.
Bug fixes
Fixed issue with default rope range for
BayesFactor
models.Fixed issue in collinearitycheck for
rope()
for models with less than two parameters.Fixed issue in printmethod for
mediation()
withstanmvreg
models, which displays the wrong name for the responsevalue.Fixed issue in
effective_sample()
for models with only one parameter.rope_range()
forBayesFactor
models returns nonNA
values ( #343 )
bayestestR 0.7.2
CRAN release: 20200720
New functions

mediation()
, to compute average direct and average causal mediation effects of multivariate response models (brmsfit
,stanmvreg
).
Bug fixes

bayesfactor_parameters()
works withR<3.6.0
.
bayestestR 0.7.0
CRAN release: 20200619
Changes to functions
weighted_posteriors()
can now be used with data frames.Revised
print()
fordescribe_posterior()
.Improved value formatting for Bayesfactor functions.
Bug fixes
Link transformation are now taken into account for
emmeans
objets. E.g., indescribe_posterior()
.Fix
diagnostic_posterior()
when algorithm is not “sampling”.Minor revisions to some documentations.
Fix CRAN check issues for winoldrelease.
bayestestR 0.6.0
CRAN release: 20200420
Changes to functions
describe_posterior()
now also works oneffectsize::standardize_posteriors()
.p_significance()
now also works onparameters::simulate_model()
.rope_range()
supports more (frequentis) models.
Bug fixes
Fixed issue with
plot()
data.frame
methods ofp_direction()
andequivalence_test()
.Fix check issues for forthcoming insightupdate.
bayestestR 0.5.3
CRAN release: 20200326
Changes to functions

estimate_density()
now also works on grouped data frames.
Bug fixes
Fixed bug in
weighted_posteriors()
to properly weight InterceptonlyBFBayesFactor
models.Fixed bug in
weighted_posteriors()
when models have very low posterior probability ( #286 ).Fixed bug in
describe_posterior()
,rope()
andequivalence_test()
for brmsfit models with monotonic effect.Fixed issues related to latest changes in
as.data.frame.brmsfit()
from the brms package.
bayestestR 0.5.0
CRAN release: 20200118
General
Added
p_pointnull()
as an alias top_MAP()
.Added
si()
function to compute support intervals.Added
weighted_posteriors()
for generating posterior samples averaged across models.Added
plot()
method forp_significance()
.p_significance()
now also works for brmsfitobjects.estimate_density()
now also works for MCMCglmmobjects.equivalence_test()
getseffects
andcomponent
arguments for stanreg and brmsfit models, to print specific model components.Support for mcmc objects (package coda)
Provide more distributions via
distribution()
.Added
distribution_tweedie()
.Better handling of
stanmvreg
models fordescribe_posterior()
,diagnostic_posterior()
anddescribe_prior()
.
Breaking changes
point_estimate()
: argumentcentrality
default value changed from ‘median’ to ‘all’.p_rope()
, previously as exploratory index, was renamed asmhdior()
(for Max HDI inside/outside ROPE), asp_rope()
will refer torope(..., ci = 1)
( #258 )
Bug fixes
Fixed mistake in description of
p_significance()
.Fixed error when computing BFs with
emmGrid
based on some nonlinear models ( #260 ).Fixed wrong output for percentagevalues in
print.equivalence_test()
.Fixed issue in
describe_posterior()
forBFBayesFactor
objects with more than one model.
bayestestR 0.4.0
CRAN release: 20191020
New functions / features
convert_bayesian_to_frequentist()
Convert (refit) Bayesian model as frequentistdistribution_binomial()
for perfect binomial distributionssimulate_ttest()
Simulate data with a mean differencesimulate_correlation()
Simulate correlated datasetsp_significance()
Compute the probability of Practical Significance (ps)overlap()
Compute overlap between two empirical distributionsestimate_density()
:method = "mixture"
argument added for mixture density estimation
Bug fixes
 Fixed bug in
simulate_prior()
for stanregmodels whenautoscale
was set toFALSE
bayestestR 0.3.0
CRAN release: 20190922
General
 revised
print()
methods for functions likerope()
,p_direction()
,describe_posterior()
etc., in particular for model objects with random effects and/or zeroinflation component
New functions / features
check_prior()
to check if prior is informativesimulate_prior()
to simulate model’s priors as distributionsdistribution_gamma()
to generate a (nearperfect or random) Gamma distributioncontr.bayes
function for orthogonal factor coding (implementation from Singmann & Gronau’sbfrms
, used for proper prior estimation when factor have 3 levels or more. See Bayes factor vignette ## Changes to functionsAdded support for
sim
,sim.merMod
(fromarm::sim()
) andMCMCglmm
objects to many functions (likehdi()
,ci()
,eti()
,rope()
,p_direction()
,point_estimate()
, …)describe_posterior()
gets aneffects
andcomponent
argument, to include the description of posterior samples from random effects and/or zeroinflation component.More userfriendly warning for nonsupported models in
bayesfactor()
methods
Bug fixes
Fixed bug in
bayesfactor_inclusion()
where the same interaction sometimes appeared more than once (#223)Fixed bug in
describe_posterior()
for stanreg models fitted with fullrankalgorithm
bayestestR 0.2.5
CRAN release: 20190806
Breaking changes
rope_range()
for binomial model has now a different default (.18; .18 ; instead of .055; .055)rope()
: returns a proportion (between 0 and 1) instead of a value between 0 and 100p_direction()
: returns a proportion (between 0.5 and 1) instead of a value between 50 and 100 (#168)bayesfactor_savagedickey()
:hypothesis
argument replaced bynull
as part of the newbayesfactor_parameters()
function
New functions / features
density_at()
,p_map()
andmap_estimate()
:method
argument addedrope()
:ci_method
argument addedeti()
: Computes equaltailed intervalsreshape_ci()
: Reshape CIs between wide/longbayesfactor_parameters()
: New function, replacingbayesfactor_savagedickey()
, allows for computing Bayes factors against a pointnull or an intervalnullbayesfactor_restricted()
: Function for computing Bayes factors for order restricted models
Bug fixes

bayesfactor_inclusion()
now works withR < 3.6
.
bayestestR 0.2.2
CRAN release: 20190620
Breaking changes
equivalence_test()
: returns capitalized output (e.g.,Rejected
instead ofrejected
)describe_posterior.numeric()
:dispersion
defaults toFALSE
for consistency with the other methods
New functions / features
pd_to_p()
andp_to_pd()
: Functions to convert between probability of direction (pd) and pvalueSupport of
emmGrid
objects:ci()
,rope()
,bayesfactor_savagedickey()
,describe_posterior()
, …
Bug fixes
describe_posterior()
: Fixed column order restorationbayesfactor_inclusion()
: Inclusion BFs for matched models are more inline with JASP results.
bayestestR 0.2.0
CRAN release: 20190529
Breaking changes
plotting functions now require the installation of the
see
packageestimate
argument name indescribe_posterior()
andpoint_estimate()
changed tocentrality
hdi()
,ci()
,rope()
andequivalence_test()
defaultci
to0.89
rnorm_perfect()
deprecated in favour ofdistribution_normal()
map_estimate()
now returns a single value instead of a dataframe and thedensity
parameter has been removed. The MAP density value is now accessible viaattributes(map_output)$MAP_density
New functions / features
describe_posterior()
,describe_prior()
,diagnostic_posterior()
: added wrapper functionpoint_estimate()
added function to compute point estimatesp_direction()
: new argumentmethod
to compute pd based on AUCarea_under_curve()
: compute AUCdistribution()
functions have been addedbayesfactor_savagedickey()
,bayesfactor_models()
andbayesfactor_inclusion()
functions has been addedStarted adding plotting methods (currently in the
see
package) forp_direction()
andhdi()
probability_at()
as alias fordensity_at()
effective_sample()
to return the effective sample size of Stanmodelsmcse()
to return the Monte Carlo standard error of Stanmodels
Minor changes
Improved documentation
Improved testing
p_direction()
: improved printingrope()
for modelobjects now returns the HDI values for all parameters as attribute in a consistent wayChanges legendlabels in
plot.equivalence_test()
to align plots with the output of theprint()
method (#78)
bayestestR 0.1.0
CRAN release: 20190408
CRAN initial publication and 0.1.0 release
Added a
NEWS.md
file to track changes to the package