new methods and cleaned up docs

[mattansb]

• New methods docs now in ?bayesfactor_methods
• Better function docs / sections
• Update BF vignette
  • Cleanup the vignette to focus on the ideas.
  • Include order restrictions vs null
• Add support for stanfit (rstan) and CmdStanMCMC (cmdstanr)
  • model via bridgesampling (for cmdstan needs Add support for bayesfactor_models(<cmdstan>) #739)
  • parameters / restrictions / si (should be easy since we have .draws methods in place)
  • diagnostic_draws
  • describe_posterior
  • equivalence_test
  • p_direction
  • p_map
  • p_rope
  • rope
  • p_significance
  • weighted_posteriors (for cmdstan needs Add support for bayesfactor_models(<cmdstan>) #739)

[gemini-code-assist]

Summary of Changes

Hello @mattansb, I'm Gemini Code Assist¹! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed!

This pull request focuses on enhancing the usability and clarity of the Bayes factor functionalities within the bayestestR package. It introduces a centralized documentation hub for Bayes factor methods and refactors the underlying S3 method dispatch to improve code organization and maintainability. The changes aim to provide a more consistent and informative experience for users working with Bayes factor objects.

Highlights

• New Unified Bayes Factor Methods Documentation: A new dedicated documentation page, ?bayesfactor_methods, has been added to centralize information regarding various methods for Bayes factor objects, including interpretation, transitivity, and prior/posterior considerations.
• Consolidation of S3 Methods: S3 methods for Bayes factor objects (e.g., as.numeric, as.matrix, as.logical, as.vector) have been consolidated under a new internal bayestestRBF class, streamlining method dispatch and reducing redundancy across individual Bayes factor functions.
• Improved Function Documentation: Existing Bayes factor functions (bayesfactor_inclusion, bayesfactor_models, bayesfactor_parameters, bayesfactor_restricted, si) have received updated and cleaned-up documentation, with references to the new unified methods page and clearer explanations.

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[gemini-code-assist]

Code Review

This pull request introduces a significant and beneficial refactoring by centralizing Bayes factor methods and their documentation into a new R/bayesfactor-methods.R file. This greatly improves code maintainability and consistency across the package by using a new bayestestRBF parent class. The documentation has also been cleaned up nicely. I've found a couple of minor issues to address: a small regression in functionality in the new print method and a typo in a warning message.

[codecov]

Codecov Report

❌ Patch coverage is 61.41732% with 49 lines in your changes missing coverage. Please review.
✅ Project coverage is 55.58%. Comparing base (6a8cb98) to head (585bff3).
⚠️ Report is 59 commits behind head on main.

Files with missing lines	Patch %	Lines
R/diagnostic_posterior.R	0.00%	16 Missing ⚠️
R/bayesfactor-methods.R	82.19%	13 Missing ⚠️
R/utils_bayesfactor.R	0.00%	11 Missing ⚠️
R/bayesfactor_models.R	75.00%	3 Missing ⚠️
R/print.equivalence_test.R	0.00%	2 Missing ⚠️
R/effective_sample.R	0.00%	1 Missing ⚠️
R/mcse.R	0.00%	1 Missing ⚠️
R/utils_check_collinearity.R	50.00%	1 Missing ⚠️
R/utils_clean_stan_parameters.R	50.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #738      +/-   ##
==========================================
+ Coverage   54.33%   55.58%   +1.25%     
==========================================
  Files          64       67       +3     
  Lines        6000     6196     +196     
==========================================
+ Hits         3260     3444     +184     
- Misses       2740     2752      +12     

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