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bayestestR 0.12.1

CRAN release: 2022-05-02

Breaking

  • Bayesfactor_models() for frequentist models now relies on the updated insight::get_loglikelihood(). This might change some results for REML based models. See documentation.

  • estimate_density() argument group_by is renamed at.

  • All distribution_*(random = FALSE) functions now rely on ppoints(), which will result in slightly different results, especially with small ns.

  • 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 log-transformed 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 equal-tailed intervals.

bayestestR 0.11.5

CRAN release: 2021-10-30

  • Fixes failing tests in CRAN checks.

bayestestR 0.11.1

New functions

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: 2021-05-31

Breaking

  • All Bayes factors are now returned as log(BF) (column name log_BF). Printing is unaffected. To retrieve the raw BFs, you can run exp(result$log_BF).

New functions

  • bci() (and its alias bcai()) to compute bias-corrected and accelerated bootstrap intervals. Along with this new function, ci() and describe_posterior() gain a new ci_method type, "bci".

Changes

  • contr.bayes has been renamed contr.orthonorm to be more explicit about its function.

bayestestR 0.9.0

CRAN release: 2021-04-08

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 long-time users of bayestestR as we have been warning about this impending change for a while now :)

  • Column names for bayesfactor_restricted() are now p_prior and p_posterior (was Prior_prob and Posterior_prob), to be consistent with bayesfactor_inclusion() output.

  • Removed the experimental function mhdior.

General

  • Support for blavaan models.

  • Support for blrm models (rmsb).

  • Support for BGGM models (BGGM).

  • check_prior() and describe_prior() should now also work for more ways of prior definition in models from rstanarm or brms.

Bug fixes

bayestestR 0.8.2

CRAN release: 2021-01-26

General

  • Support for bamlss models.

  • Roll-back R dependency to R >= 3.4.

Changes to functions

  • All .stanreg methods gain a component argument, to also include auxiliary parameters.

Bug fixes

bayestestR 0.8.0

CRAN release: 2020-12-05

New functions

  • sexit(), a function for sequential effect existence and significance testing (SEXIT).

General

  • Added startup-message to warn users that default ci-width might change in a future update.

  • Added support for mcmc.list objects.

Bug fixes

  • unupdate() gains a newdata argument to work with brmsfit_multiple models.

  • Fixed issue in Bayes factor vignette (don’t evaluate code chunks if packages not available).

bayestestR 0.7.5

CRAN release: 2020-10-22

New functions

  • Added as.matrix() function for bayesfactor_model arrays.

  • unupdate(), a utility function to get Bayesian models un-fitted from the data, representing the priors only.

Changes to functions

  • ci() supports emmeans - both Bayesian and frequentist ( #312 - cross fix with parameters)

Bug fixes

  • Fixed issue with default rope range for BayesFactor models.

  • Fixed issue in collinearity-check for rope() for models with less than two parameters.

  • Fixed issue in print-method for mediation() with stanmvreg-models, which displays the wrong name for the response-value.

  • Fixed issue in effective_sample() for models with only one parameter.

  • rope_range() for BayesFactor models returns non-NA values ( #343 )

bayestestR 0.7.2

CRAN release: 2020-07-20

New functions

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

Bug fixes

bayestestR 0.7.0

CRAN release: 2020-06-19

General

  • Preliminary support for stanfit objects.

  • Added support for bayesQR objects.

Changes to functions

Bug fixes

  • Link transformation are now taken into account for emmeans objets. E.g., in describe_posterior().

  • Fix diagnostic_posterior() when algorithm is not “sampling”.

  • Minor revisions to some documentations.

  • Fix CRAN check issues for win-old-release.

bayestestR 0.6.0

CRAN release: 2020-04-20

Changes to functions

Bug fixes

bayestestR 0.5.3

CRAN release: 2020-03-26

General

  • Support for bcplm objects (package cplm)

Changes to functions

Bug fixes

bayestestR 0.5.0

CRAN release: 2020-01-18

General

Breaking changes

  • point_estimate(): argument centrality default value changed from ‘median’ to ‘all’.

  • p_rope(), previously as exploratory index, was renamed as mhdior() (for Max HDI inside/outside ROPE), as p_rope() will refer to rope(..., ci = 1) ( #258 )

Bug fixes

  • Fixed mistake in description of p_significance().

  • Fixed error when computing BFs with emmGrid based on some non-linear models ( #260 ).

  • Fixed wrong output for percentage-values in print.equivalence_test().

  • Fixed issue in describe_posterior() for BFBayesFactor-objects with more than one model.

bayestestR 0.4.0

CRAN release: 2019-10-20

New functions / features

Bug fixes

  • Fixed bug in simulate_prior() for stanreg-models when autoscale was set to FALSE

bayestestR 0.3.0

CRAN release: 2019-09-22

General

New functions / features

  • check_prior() to check if prior is informative

  • simulate_prior() to simulate model’s priors as distributions

  • distribution_gamma() to generate a (near-perfect or random) Gamma distribution

  • contr.bayes function for orthogonal factor coding (implementation from Singmann & Gronau’s bfrms, used for proper prior estimation when factor have 3 levels or more. See Bayes factor vignette ## Changes to functions

  • Added support for sim, sim.merMod (from arm::sim()) and MCMCglmm-objects to many functions (like hdi(), ci(), eti(), rope(), p_direction(), point_estimate(), …)

  • describe_posterior() gets an effects and component argument, to include the description of posterior samples from random effects and/or zero-inflation component.

  • More user-friendly warning for non-supported models in bayesfactor()-methods

Bug fixes

bayestestR 0.2.5

CRAN release: 2019-08-06

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 100

  • p_direction(): returns a proportion (between 0.5 and 1) instead of a value between 50 and 100 (#168)

  • bayesfactor_savagedickey(): hypothesis argument replaced by null as part of the new bayesfactor_parameters() function

New functions / features

Minor changes

Bug fixes

bayestestR 0.2.2

CRAN release: 2019-06-20

Breaking changes

New functions / features

Minor changes

  • Improved tutorial 2

Bug fixes

bayestestR 0.2.0

CRAN release: 2019-05-29

Breaking changes

New functions / features

Minor changes

  • Improved documentation

  • Improved testing

  • p_direction(): improved printing

  • rope() for model-objects now returns the HDI values for all parameters as attribute in a consistent way

  • Changes legend-labels in plot.equivalence_test() to align plots with the output of the print()-method (#78)

Bug fixes

  • hdi() returned multiple class attributes (#72)

  • Printing results from hdi() failed when ci-argument had fractional parts for percentage values (e.g. ci = .995).

  • plot.equivalence_test() did not work properly for brms-models (#76).

bayestestR 0.1.0

CRAN release: 2019-04-08

  • CRAN initial publication and 0.1.0 release

  • Added a NEWS.md file to track changes to the package