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Neclow
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Feb 13, 2026
Neclow
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- Expose sackin, leaf_depth_variance, and b2 balance index functions in the R package via extendr bindings
- Add tests: manual values from Rust test suite + comparisons against treestats package
- Document treestats CRAN install step in development guide (not on conda-forge)
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Pull request overview
This PR exposes three tree balance index functions (sackin, leaf_depth_variance, and b2) from the Rust phylo2vec library to the R package through extendr bindings. These indices are statistical measures used to characterize tree topology shape and balance, with sackin and leaf_depth_variance measuring imbalance (higher = more imbalanced) and b2 measuring balance (higher = more balanced).
Changes:
- Added R bindings for sackin, leaf_depth_variance, and b2 balance indices
- Comprehensive test coverage with manual test cases from Rust suite and cross-validation against treestats package
- Documentation update to development guide about installing treestats from CRAN
Reviewed changes
Copilot reviewed 11 out of 11 changed files in this pull request and generated 1 comment.
Show a summary per file
| File | Description |
|---|---|
| r-phylo2vec/src/rust/src/lib.rs | Added extendr wrapper functions and exports for the three balance indices (sackin, leaf_depth_variance, b2) |
| r-phylo2vec/R/extendr-wrappers.R | Added R function wrappers with roxygen2 documentation for the three balance indices; added default parameter for cophenetic_distances |
| r-phylo2vec/tests/testthat/test_stats.R | Added comprehensive tests including manual test cases with known values and comparison tests against treestats package |
| r-phylo2vec/man/sackin.Rd | Generated documentation for sackin function |
| r-phylo2vec/man/leaf_depth_variance.Rd | Generated documentation for leaf_depth_variance function |
| r-phylo2vec/man/b2.Rd | Generated documentation for b2 function |
| r-phylo2vec/man/get_common_ancestor.Rd | Updated parameter documentation (removed duplicate vector param, fixed tree param) |
| r-phylo2vec/man/cophenetic_distances.Rd | Cleaned up duplicate documentation and standardized parameter descriptions |
| r-phylo2vec/R/stats.R | Removed duplicate cophenetic_distances function definition |
| r-phylo2vec/NAMESPACE | Added exports for the three new balance index functions |
| docs/development.md | Documented manual installation of treestats package from CRAN for R testing |
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