https://github.com/cran/bayestestR
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Tip revision: 68a979e69aa2a1e57017730e1397470d5614d216 authored by Dominique Makowski on 02 September 2021, 23:10 UTC
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NEWS.md
# 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

## 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

## Breaking

* The default `ci` width has been changed to 0.95 instead of 0.89 (see
  [here](https://github.com/easystats/bayestestR/discussions/250)). 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

* Fixed bug in `print()` method for the `mediation()` 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()` and `simulate_prior()`.

# bayestestR 0.8.2

## 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

* `bayesfactor_parameters()` no longer errors for no reason when computing
  extremely un/likely direction hypotheses.

* `bayesfactor_pointull()` / `bf_pointull()` are now `bayesfactor_pointnull()` /
  `bf_pointnull()` (can *you* spot the difference? #363 ).

# bayestestR 0.8.0

## 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

## 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

## New functions

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

## Bug fixes

- `bayesfactor_parameters()` works with `R<3.6.0`.

# bayestestR 0.7.0

## General

- Preliminary support for *stanfit* objects.

- Added support for *bayesQR* objects.

## Changes to functions

- `weighted_posteriors()` can now be used with data frames.

- Revised `print()` for `describe_posterior()`.

- Improved value formatting for Bayesfactor 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

## Changes to functions

- `describe_posterior()` now also works on
  `effectsize::standardize_posteriors()`.

- `p_significance()` now also works on `parameters::simulate_model()`.

- `rope_range()` supports more (frequentis) models.

## Bug fixes

- Fixed issue with `plot()` `data.frame`-methods of `p_direction()` and
  `equivalence_test()`.

- Fix check issues for forthcoming insight-update.

# bayestestR 0.5.3

## General

- Support for *bcplm* objects (package **cplm**)

## Changes to functions

- `estimate_density()` now also works on grouped data frames.

## Bug fixes

- Fixed bug in `weighted_posteriors()` to properly weight Intercept-only
  `BFBayesFactor` models.

- Fixed bug in `weighted_posteriors()` when models have very low posterior
  probability ( #286 ).

- Fixed bug in `describe_posterior()`, `rope()` and `equivalence_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

## General

- Added `p_pointnull()` as an alias to `p_MAP()`.

- Added `si()` function to compute support intervals.

- Added `weighted_posteriors()` for generating posterior samples averaged across
  models.

- Added `plot()`-method for `p_significance()`.

- `p_significance()` now also works for *brmsfit*-objects.

- `estimate_density()` now also works for *MCMCglmm*-objects.

- `equivalence_test()` gets `effects` and `component` 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 for `describe_posterior()`,
  `diagnostic_posterior()` and `describe_prior()`.

## 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

## New functions / features

- `convert_bayesian_to_frequentist()` Convert (refit) Bayesian model as
  frequentist

- `distribution_binomial()` for perfect binomial distributions

- `simulate_ttest()` Simulate data with a mean difference

- `simulate_correlation()` Simulate correlated datasets

- `p_significance()` Compute the probability of Practical Significance (ps)

- `overlap()` Compute overlap between two empirical distributions

- `estimate_density()`: `method = "mixture"` argument added for mixture density
  estimation

## Bug fixes

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

# bayestestR 0.3.0

## General

- revised `print()`-methods for functions like `rope()`, `p_direction()`,
  `describe_posterior()` etc., in particular for model objects with random
  effects and/or zero-inflation component

## 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`](https://github.com/bayesstuff/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

- 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
  fullrank-algorithm

# bayestestR 0.2.5

## 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](https://github.com/easystats/bayestestR/issues/168))

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

## New functions / features

- `density_at()`, `p_map()` and `map_estimate()`: `method` argument added

- `rope()`: `ci_method` argument added

- `eti()`: Computes equal-tailed intervals

- `reshape_ci()`: Reshape CIs between wide/long

- `bayesfactor_parameters()`: New function, replacing
  `bayesfactor_savagedickey()`, allows for computing Bayes factors against a
  *point-null* or an *interval-null*

- `bayesfactor_restricted()`: Function for computing Bayes factors for order
  restricted models

## Minor changes

## Bug fixes

- `bayesfactor_inclusion()` now works with `R < 3.6`.

# bayestestR 0.2.2

## Breaking changes

- `equivalence_test()`: returns capitalized output (e.g., `Rejected` instead of
  `rejected`)

- `describe_posterior.numeric()`: `dispersion` defaults to `FALSE` for
  consistency with the other methods

## New functions / features

- `pd_to_p()` and `p_to_pd()`: Functions to convert between probability of
  direction (pd) and p-value

- Support of `emmGrid` objects: `ci()`, `rope()`, `bayesfactor_savagedickey()`,
  `describe_posterior()`, ...

## Minor changes

- Improved tutorial 2

## Bug fixes

- `describe_posterior()`: Fixed column order restoration

- `bayesfactor_inclusion()`: Inclusion BFs for matched models are more inline
  with JASP results.

# bayestestR 0.2.0

## Breaking changes

- plotting functions now require the installation of the `see` package

- `estimate` argument name in `describe_posterior()` and `point_estimate()`
  changed to `centrality`

- `hdi()`, `ci()`, `rope()` and `equivalence_test()` default `ci` to `0.89`

- `rnorm_perfect()` deprecated in favour of `distribution_normal()`

- `map_estimate()` now returns a single value instead of a dataframe and the
  `density` parameter has been removed. The MAP density value is now accessible
  via `attributes(map_output)$MAP_density`

## New functions / features

- `describe_posterior()`, `describe_prior()`, `diagnostic_posterior()`: added
  wrapper function

- `point_estimate()` added function to compute point estimates

- `p_direction()`: new argument `method` to compute pd based on AUC

- `area_under_curve()`: compute AUC

- `distribution()` functions have been added

- `bayesfactor_savagedickey()`, `bayesfactor_models()` and
  `bayesfactor_inclusion()` functions has been added

- Started adding plotting methods (currently in the
  [`see`](https://github.com/easystats/see) package) for `p_direction()` and
  `hdi()`

- `probability_at()` as alias for `density_at()`

- `effective_sample()` to return the effective sample size of Stan-models

- `mcse()` to return the Monte Carlo standard error of Stan-models

## 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 initial publication and [0.1.0
  release](https://github.com/easystats/bayestestR/releases/tag/v0.1.0)

- Added a `NEWS.md` file to track changes to the package
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