Gdr 2332

[bczech]

Description

What changed?

Fixed todo in map_df
Related JIRA issue: GDR-2332

Why was it changed?

To fix todos

Checklist for sustainable code base

• I added tests for any code changed/added
• I added documentation for any code changed/added
• I made sure naming of any new functions is self-explanatory and consistent

Logistic checklist

• Package version bumped
• Changelog updated

Screenshots (optional)

[gemini-code-assist]

Summary of Changes

Hello @bczech, 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 several TODOs within the gDRcore package, primarily focusing on the map_df function and its related helpers. The changes aim to enhance the robustness and clarity of how treated conditions are mapped to reference controls, ensuring more accurate and reliable data processing. The refactoring improves code structure and maintainability, making the mapping logic more explicit and testable.

Highlights

• Refactored map_df function: The core map_df function has been significantly refactored to improve the logic for matching treated conditions to reference controls, particularly enhancing handling of partial matches and override_untrt_controls. This includes a new meta_score to prioritize matches based on metadata fields.
• New Internal Helper Function: A new internal helper function, .get_untreated_tag_count, has been introduced to encapsulate the logic for identifying and counting 'untreated' tags. This helper is now utilized by both .map_references and map_untreated.
• Improved map_references and map_untreated: The .map_references and map_untreated functions have been refactored to leverage the new helper function and improve data.table operations, leading to more concise and maintainable code.
• Documentation and Testing Updates: Extensive updates have been made to the documentation for map_df, .map_references, and map_untreated, including the removal of outdated examples and clarification of parameter details. Corresponding unit tests have been added and updated to ensure the correctness of the refactored logic.
• Package Version Bump: The package version has been bumped from 1.9.3 to 1.9.4, and the NEWS.md file has been updated to reflect these changes, specifically noting the fixes to TODOs in map_df.R.

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[gemini-code-assist]

Code Review

This pull request is a great improvement, successfully addressing several TODO items in map_df.R. The code has been significantly refactored for better clarity, performance, and maintainability. The introduction of the .get_untreated_tag_count helper function to eliminate duplicated code is a particularly nice touch. Additionally, the test suite has been substantially improved to cover the new logic and edge cases. My review includes a couple of suggestions to further enhance the code's maintainability and documentation.

[gladkia]

Looks great! Remove "<--" and update the docs, and IMO your PR is ready to merge.