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version 0.2.17

Features

• adding informed prior distributions for dichotomous and time to event outcomes based on Cochrane Database of Systematic Reviews to prior_informed() function
• adding bridge object convenience function bridge_object() (fixes: https://github.com/FBartos/BayesTools/issues/28)
• adding Na/NaN tests for check_ functions (fixes: https://github.com/FBartos/BayesTools/issues/26)

Fixes

• ability to run more than 4 chains (fixes: https://github.com/FBartos/BayesTools/issues/20)

version 0.2.16

Features

• update an existing JAGS fit with JAGS_extend() function
• new element of the autofit_control argument in JAGS_fit(): "restarts" allows to restart model initialization up to restarts times in case of failure

version 0.2.15

Fixes

• fixing repeated print of previous prior distribution in model_summary_table() in case of prior_none()

version 0.2.14

Features

• adding contrast = "meandif" to the prior_factor function which generates identical prior distributions for difference between the grand mean and each factor level
• adding contrast = "independent" to the prior_factor function which generates independent identical prior distributions for each factor level
• remove_column function for removing columns from BayesTools_table objects without breaking the attributes etc…
• adding empty table functions (https://github.com/FBartos/BayesTools/issues/10)
• adding remove_parameters argument to model_summary_table()
• adding multivariate point distribution functions
• adding point prior distribution as option to prior_factor with "meandif" and "orthonormal" contrasts
• adding marginal_posterior() function which creates marginal prior and posterior distributions (according to a model formula specification)
• adding Savage_Dickey_BF() function to compute density ratio Bayes factors based on marginal_posterior objects
• adding marginal_inference() function to combine information from marginal_posterior() and Savage_Dickey_BF()
• adding marginal_estimates_table() function to summarize marginal_inference() objects
• adding plot_marginal() function to visualize marginal_inference() objects

Changes

• contrast = "meandif" is now the default setting for prior_factor function
• depreciating transform_orthonormal argument in favor of more general transform_factors argument
• switching dummy contrast/factor attributes to treatment for consistency (https://github.com/FBartos/BayesTools/issues/23)

Fixes

• zero length inputs to check_bool(), check_char(), check_real(), check_int(), and check_list() do not throw error if allow_NULL = TRUE
• properly aggregating identical priors in the plotting function (previously overlying multiple spikes on top of each other when attributes did not match)
• student-t allowed as a prior distribution name
• fixing factor contrast settings in JAGS_evaluate_formula
• fixing spike prior transformations

version 0.2.13

Features

• runjags_estimates_table() function can now handle factor transformations
• plot_posterior function can now handle factor transformations
• ability to remove parameters from the runjags_estimates_table() function via the remove_parameters argument

Fixes

• inability to deal with constant intercept in marglik formula calculation
• runjags_estimates_table() function can now remove factor spike prior distributions
• marginal likelihood calculation for factor prior distributions with spike
• mixing samples from vector priors of length 1
• same prior distributions not always combined together properly when part of them was generated via the formula interface

version 0.2.12

Features

• stan_estimates_summary() function
• reducing dependency on runjags/rjags

Fixes

• dealing with posterior samples from rstan
• dealing with vector posterior samples
• fixing MCMC error of SD calculation for transformed samples (previously reported 100 times lower)

version 0.2.11

Features

• adding Bernoulli prior distribution
• adding spike and slab type of prior distributions (without marginal likelihood computations/model-averaging capabilities)
• new vignette comparing Bayes factor computation via marginal likelihood and spike and slab priors

Fixes

• when a transformation is applied, JAGS summary tables now produce the mean of the transformed variable (previous versions incorrectly returned transformation of the mean)

Changes

• runjags_XXX_table functions are now also exported as JAGS_XXX_functions for consistency with the rest of the code

version 0.2.10

Features

• trace, density, and autocorrelation diagnostic plots for JAGS models

version 0.2.9

Fixes

• dealing with NaNs in inclusion Bayes factors due to overflow with very large marginal likelihoods

version 0.2.8

Fixes

• dealing with point prior distributions in JAGS_marglik_parameters_formula function
• posterior samples dropping name in runjags_estimates_table function
• ensemble_summary_table and ensemble_diagnostics_table function can create table without model components

version 0.2.7

Features

• JAGS_evaluate_formula for evaluating formulas based on data and posterior samples (for creating predictions etc)
  
• JAGS_parameter_names for transforming formula names into the JAGS syntax

version 0.2.6

Features

• plot_models implementation for factor predictors
• format_parameter_names for cleaning parameter names from JAGS
• mean, sd, and var functions now return the corresponding values for differences from the mean for the orthonormal prior distributions

Fixes

• proper splitting of transformed posterior samples based on orthonormal contrasts in runjags_summary_table function (previous version crashed under other than default fit_JAGS settings)
• always showing name of the comparison group for treatment contrasts in runjags_summary_table function
• better handling of transformed parameter names in plot_models function

version 0.2.5

Features

• add_column function for extending BayesTools_table objects without breaking the attributes etc…
• ability to suppress the formula parameter prefix in BayesTools_table functions with with formula_prefix argument

Fixes

• allowing to pass point prior distributions for factor type predictors

version 0.2.4

Features

• adding possibility to multiply a (formula) prior parameter by another term (via multiply_by attribute passed with the prior)
• t-test example vignette

version 0.2.3

Fixes

• fixing error from trying to rename formula parameters in BayesTools tables when multiple parameters were nested within a component

version 0.2.2

Fixes

• fixing layering of prior and posterior plots in plot_posterior (posterior is now plotted over the prior)

version 0.2.1

Fixes

• fixing JAGS code for multivariate-t prior distribution

version 0.2.0

Changes

• ensemble inference, summary, and plot functions now extract the prior list from attribute of the fit objects (previously, the prior_list needed to be passed for each model within the model_list as the priors argument

Features

• adding formula interface for fitting and computing marginal likelihood of JAGS models
• adding factor prior distributions (with treatment and orthonormal contrasts)

version 0.1.4

Fixes

• fixing DOIs in the references file
• adds marglik argument inclusion_BF to deal with over/underflow (Issue #9)
• better passing of BF names through the ensemble_inference_table() (Issue #11)

Features

• adding logBF and BF01 options to ensemble_summary_table (Issue #7)

version 0.1.3

Features

• prior_informed function for creating informed prior distributions based on the past psychological and medical research

version 0.1.2

Fixes

• prior.plot can’t plot “spike” with plot_type == "ggplot" (Issue #6)
• MCMC error/SD print names in BayesTools tables (Issue #8)
• JAGS_bridgesampling_posterior unable to add a parameter via add_parameters

Features

• interpret function for creating textual summaries based on inference and samples objects

version 0.1.1

Fixes

• plot_posterior fails with only mu & PET samples (Issue #5)
• ordering by “probabilities” does not work in ‘plot_models’ (Issue #3)
• BF goes to NaN when only a single model is present in ‘models_inference’ (Issue #2)
• summary tables unit tests unable to deal with numerical precision
• problems with aggregating samples across multiple spikes in `plot_posterior’

Features

• allow density.prior with range lower == upper (Issue #4)
• moving rstan towards suggested packages

version 0.1.0

• published on CRAN

version 0.0.0.9010

• plotting functions for models

version 0.0.0.9009

• plotting functions for posterior samples

version 0.0.0.9008

• plotting functions for mixture of priors

version 0.0.0.9007

• improvements to prior plotting functions

version 0.0.0.9006

• ensemble and model summary tables functions

version 0.0.0.9005

• posterior mixing functions

version 0.0.0.9004

• model-averaging functions

version 0.0.0.9003

• JAGS fitting related functions

version 0.0.0.9002

• JAGS bridgesampling related functions

version 0.0.0.9001

• JAGS model building related functions

version 0.0.0.9000

• priors and related methods

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.