mismatch between {emmeans}\s and model_parameters()'s adjusted p-values

[strengejacke]

Fixes #1103

[gemini-code-assist]

Summary of Changes

Hello @strengejacke, 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 addresses a critical bug where model_parameters() produced incorrect Tukey-adjusted p-values for emmeans objects, leading to inconsistencies with direct emmeans output. The changes ensure that p-value adjustments, particularly Tukey's, are accurately applied, improving the reliability of statistical results and maintaining consistency across different functions. The update also includes minor code refactoring for readability and expanded test coverage.

Highlights

• P-value Adjustment Fix: Resolved a discrepancy in Tukey p-value adjustments when using model_parameters() with emmeans objects, ensuring consistency with direct emmeans output.
• Tukey Adjustment Logic: Adjusted the calculation of nmeans for Tukey adjustment to ensure correct application based on the number of means being compared.
• Correction Factor Enhancement: Enhanced the logic for determining the correction factor in p-value adjustments, particularly for grouped emmeans results.
• Test Coverage: Introduced new test cases to validate the accuracy of Tukey p-value adjustments for emmeans objects, improving robustness.
• Package Version Update: Incremented the package version to reflect these bug fixes and improvements.

Changelog

• DESCRIPTION
  • Updated the package version from 0.28.3.3 to 0.28.3.4.
• NEWS.md
  • Added a changelog entry for fixing issues with Tukey-p-value adjustment for emmeans objects.
• R/format_p_adjust.R
  • Refactored code for improved readability and consistency in switch statements.
  • Corrected the nmeans calculation for Tukey adjustment.
  • Introduced a new correction factor calculation for grouped emmeans objects.
  • Improved formatting for warning messages and function calls.
• tests/testthat/test-p_adjust.R
  • Added new test cases for emmeans objects with Tukey p-value adjustment.
  • Refactored existing test code for better readability and consistent formatting.

Activity

• Addressed and fixed issue mismatch between {emmeans}\s and model_parameters()'s adjusted p-values #1103, which reported a mismatch in adjusted p-values between {emmeans} and model_parameters().

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[gemini-code-assist]

Code Review

This pull request addresses a mismatch in adjusted p-values between emmeans and model_parameters(). The core of the fix is in the Tukey p-value adjustment logic, where the nmeans parameter for stats::ptukey is now correctly calculated. The method for determining the number of comparisons (rank_adjust) has also been improved with a fallback mechanism. The changes are well-supported by new unit tests that validate the fix against emmeans output. Additionally, the pull request includes several formatting improvements that enhance code readability by breaking up long lines, which is a welcome change. Overall, this is a solid contribution that fixes an important bug and improves code quality.

[strengejacke]

@gemini-code-assist review

[gemini-code-assist]

Code Review

This pull request addresses a mismatch in adjusted p-values between {emmeans} and model_parameters(). The core of the fix involves correcting the nmeans argument for Tukey p-value adjustments and adding new tests to ensure correctness. The changes are well-implemented and improve the reliability of p-value adjustments. I have one suggestion to remove a redundant line of code to improve maintainability.

[Copilot]

Pull request overview

This PR addresses #1103 by aligning model_parameters() p-value adjustment behavior with emmeans, focusing on Tukey adjustments for emmeans contrast objects.

Changes:

• Updated Tukey p-value adjustment logic used by .p_adjust() for emmeans outputs.
• Expanded test coverage to assert model_parameters() p-values match emmeans’ own adjusted p.value across additional Tukey scenarios.
• Bumped package version and added a NEWS entry for the Tukey/emmeans adjustment fix.

Reviewed changes

Copilot reviewed 4 out of 4 changed files in this pull request and generated 2 comments.

File	Description
tests/testthat/test-p_adjust.R	Adds regression tests ensuring model_parameters() matches emmeans adjusted p-values (incl. additional Tukey cases).
R/format_p_adjust.R	Adjusts Tukey adjustment computation and rank/correction logic used during p-value adjustment.
NEWS.md	Documents the Tukey/emmeans p-value adjustment fix.
DESCRIPTION	Version bump from 0.28.3.3 to 0.28.3.4.

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