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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: #28)
  • adding Na/NaN tests for check_ functions (fixes: #26)

Fixes

  • ability to run more than 4 chains (fixes: #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 (#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 (#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