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
  • Appendix!
• 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 (Add support diagnostic_draws(<CmdStanMCMC>) #762)
  • 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 and Add insight::get_parameters(<CmdStanMCMC>) insight#1186)
• Edit NEWS.md

[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.

Using Gemini Code Assist

The full guide for Gemini Code Assist can be found on our documentation page, here are some quick tips.

Invoking Gemini

You can request assistance from Gemini at any point in your pull request via creating an issue comment (i.e. comment on the pull request page) using either /gemini <command> or @gemini-code-assist <command>. Below is a summary of the supported commands.

Feature	Command	Description
Code Review	/gemini review	Performs a code review for the current pull request in its current state.
Pull Request Summary	/gemini summary	Provides a summary of the current pull request in its current state.
Comment	@gemini-code-assist	Responds in comments when explicitly tagged, both in issue comments and review comments.
Help	/gemini help	Displays a list of available commands.

Customization

To customize Gemini Code Assist for GitHub experience, repository maintainers can create a configuration file and/or provide a custom code review style guide (such as PEP-8 for Python) by creating and adding files to a .gemini/ folder in the base of the repository. Detailed instructions can be found here.

Limitations & Feedback

Gemini Code Assist may make mistakes. Please leave feedback on any instances where its feedback is incorrect or counter productive. You can react with 👍 and 👎 on @gemini-code-assist comments. If you're interested in giving your feedback about your experience with Gemini Code Assist for Github and other Google products, sign up here.

You can also get AI-powered code generation, chat, as well as code reviews directly in the IDE at no cost with the Gemini Code Assist IDE Extension.

Footnotes

1. Review the Privacy Notices, Generative AI Prohibited Use Policy, Terms of Service, and learn how to configure Gemini Code Assist in GitHub here. Gemini can make mistakes, so double check it and use code with caution. ↩

[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     

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

[strengejacke]

gogogo!

[mattansb]

I think it'll be better to run AIR after merging this with main to avoid any issues.

[strengejacke]

Yes, I think you can ignore the formatting warnings for now.

[strengejacke]

There was a conflict, please check whether the correct commit was chosen to resolve the conflict.

[mattansb]

I suspect not. Perhaps it is better to keep this out-of-sync until this PR matures out of its "draft" status.

Thanks!

[strengejacke]

Nice work! Once this PR is merged, we can have a new release! (so, hurry up! 😬 )

[mattansb]

Is there a deadline for the release?

[strengejacke]

No