Remove all remnants of default 89% CI

[mattansb]

Closes #753

[gemini-code-assist]

Summary of Changes

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This pull request standardizes the default credible interval to 95% across the bayestestR package. The changes ensure that all relevant functions, documentation, and examples consistently use 95% as the primary credible interval, thereby enhancing the package's usability and adherence to widely accepted statistical conventions. This update simplifies user experience by removing the previous 89% default and providing clearer guidance on CI interpretation.

Highlights

• Default Credible Interval Update: The default credible interval (CI) used throughout the package has been updated from 89% to 95% to align with common statistical practices and improve consistency.
• Documentation and Examples Alignment: Extensive updates were made across R files, man pages, and vignettes to reflect the new 95% default CI in function descriptions, examples, and detailed explanations of Bayesian concepts like HDI and ROPE.
• Code Readability Improvements: Many function signatures were reformatted to enhance code readability and maintainability, particularly in ci, equivalence_test, hdi, mediation, and rope functions.
• Clarification of CI Properties: Detailed explanations regarding the stability and advantages of 89% vs. 95% CIs were updated, emphasizing the importance of checking Effective Sample Size (ESS) and Monte Carlo Standard Error (MCSE) for interval precision.

Changelog

• R/ci.R
  • Updated example usage of ci() to include 0.95 CI.
  • Reformatted function arguments for better readability.
• R/equivalence_test.R
  • Updated documentation to refer to 95% HDI instead of 89% HDI.
  • Reformatted function arguments for better readability.
• R/hdi.R
  • Updated documentation to refer to 95% CI as default.
  • Revised detailed explanation of 89% vs 95% intervals to emphasize checking ESS/MCSE.
  • Reformatted function arguments for better readability.
• R/mediation.R
  • Updated documentation to specify 95% credible intervals as default.
  • Reformatted function arguments and alert messages for clarity.
• R/rope.R
  • Updated function title and documentation to refer to 95% HDI as default.
  • Reformatted function arguments and alert messages for clarity.
• README.Rmd
  • Updated examples for hdi() and eti() to remove explicit ci = 0.89.
  • Updated ROPE description to mention 95% HDI as default.
• man/bci.Rd
  • Updated documentation to reflect 95% CI as default.
  • Revised details on 89% vs 95% intervals.
• man/ci.Rd
  • Updated example usage of ci() to include 0.95 CI.
• man/distribution.Rd
  • Updated parameter descriptions for n and mu.
• man/equivalence_test.Rd
  • Updated documentation to refer to 95% HDI instead of 89% HDI.
• man/eti.Rd
  • Updated documentation to reflect 95% CI as default.
  • Revised details on 89% vs 95% intervals.
• man/hdi.Rd
  • Updated documentation to reflect 95% CI as default.
  • Revised details on 89% vs 95% intervals.
• man/mediation.Rd
  • Updated documentation to specify 95% credible intervals as default.
• man/rope.Rd
  • Updated function title and documentation to refer to 95% HDI as default.
• man/sexit.Rd
  • Updated documentation to reflect 95% CI as default.
• man/spi.Rd
  • Updated documentation to reflect 95% CI as default.
• vignettes/bayestestR.Rmd
  • Updated vignette metadata and text to refer to 95% Credible Interval.
• vignettes/credible_interval.Rmd
  • Updated vignette metadata, R code formatting, and text to reflect the new default CI and clarify details on 89% vs 95% intervals.
• vignettes/example2.Rmd
  • Updated vignette metadata, R code formatting, and text to reflect 95% CI in examples and descriptions.
• vignettes/mediation.Rmd
  • Updated vignette text to specify 95% credible intervals as default.
• vignettes/region_of_practical_equivalence.Rmd
  • Updated vignette metadata and removed text discussing 89% HDI as a better choice.

Activity

• The pull request addresses and closes issue Default CI for ROPE in vignette #753, indicating resolution of a specific task or bug.
• The author, mattansb, implemented comprehensive changes across multiple R source files and documentation, suggesting a thorough review and update process.
• Numerous function signatures were reformatted for improved code consistency and readability, making future maintenance easier.
• Alert messages within the code were also adjusted for better user communication.

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[Copilot]

Pull request overview

This PR updates the package documentation (vignettes, README, and Rd/roxygen docs) to remove outdated references to a default 89% interval—especially around ROPE—and align narrative examples with the current 95% default.

Changes:

• Updated vignettes/README/Rd docs to remove “default 89% CI/HDI” language and reference 95% where appropriate.
• Refined explanatory text around CI stability/ESS/MCSE in CI/HDI/ETI documentation.
• Reformatted several R functions (rope/ci/equivalence_test/mediation/hdi) for readability without intended behavioral changes.

Reviewed changes

Copilot reviewed 21 out of 21 changed files in this pull request and generated 8 comments.

Show a summary per file

File	Description
vignettes/region_of_practical_equivalence.Rmd	Removes vignette text claiming default 89% HDI for ROPE.
vignettes/mediation.Rmd	Updates vignette text to 95% default credible intervals for mediation.
vignettes/example2.Rmd	Updates CI text to 95% and reformats chunks/markdown (currently has broken fences).
vignettes/credible_interval.Rmd	Expands discussion of 89% vs 95% and adds MCSE/ESS guidance (currently has duplication).
vignettes/bayestestR.Rmd	Updates getting-started vignette to reference 95% credible intervals.
man/spi.Rd	Minor Rd wording/formatting updates for CI default text.
man/sexit.Rd	Minor Rd wording/formatting updates for CI default text.
man/rope.Rd	Updates ROPE title/description and default interval wording (needs alignment with implementation).
man/mediation.Rd	Updates mediation docs to state 95% default credible intervals.
man/hdi.Rd	Updates HDI details text (MCSE/ESS guidance and formatting).
man/eti.Rd	Updates ETI details text (MCSE/ESS guidance and formatting).
man/equivalence_test.Rd	Updates equivalence test docs to reference 95% interval wording and formatting.
man/distribution.Rd	Improves argument descriptions for distribution helpers.
man/ci.Rd	Updates examples to include 0.95 in CI vectors.
man/bci.Rd	Updates BCa interval docs text (MCSE/ESS guidance and formatting).
README.Rmd	Updates README examples and ROPE default interval wording (needs alignment with implementation).
R/rope.R	Updates ROPE roxygen text/title and reformats methods (docs currently conflict with default ci_method).
R/mediation.R	Updates roxygen wording (89% -> 95%) and reformats functions for readability.
R/hdi.R	Updates roxygen text (MCSE/ESS guidance) and reformats several functions.
R/equivalence_test.R	Updates roxygen wording (89% -> 95%) and reformats methods for readability.
R/ci.R	Updates roxygen examples and reformats several functions for readability.

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[gemini-code-assist]

Code Review

This pull request aims to remove the default 89% CI and standardize on 95%. The changes primarily involve updating documentation and examples to reflect this, along with some code reformatting for style consistency. The changes are generally good and align with the PR's goal. I've identified a few minor issues: two function definitions that are now inconsistent with the project's style guide, and a couple of broken code blocks in a vignette file that will likely prevent it from rendering correctly. Applying the suggested fixes will improve code consistency and resolve the vignette rendering issues.

[mattansb]

These snapshottssssssss.....

@DominiqueMakowski wdyt?

[strengejacke]

These snapshottssssssss.....

@etiennebacher is investigating possible related issues here:
easystats/modelbased#602

Not sure what's wrong with snapshot testing

[bwiernik]

Where in the book does Kruschke actually suggest this though? I've searched for all of the cases of 95% and 90% in the 2014/2015 edition and as far as I can find, he doesn't actually suggest using a width other than 95% anywhere. He discusses the stability of the tails in the section on ESS/MSCE (p 184 – 186), but even there he doesn't suggest using a narrower interval at all.

[mattansb]

@DominiqueMakowski do you know? I think you originally wrote that section.

[mattansb]

Pinging...