Changelog • selection.index

selection.index (development version)

CRAN release: 2026-03-08

Fixed numerical stability in ppg_esim tests where eigen() could return complex values on certain hardware architectures (e.g., macOS ARM64).
Added automated documentation spell-checking via the spelling package in a dedicated GitHub Actions workflow.
Expanded the GitHub Actions CI matrix to 17 runners, mirroring all official CRAN check flavors.

CRAN release: 2026-02-28

All primary user-facing functions have transitioned from dot-notation to snake_case notation for better clarity and to avoid S3 method dispatch conflicts.
- phen.varcov() is now phen_varcov()
- gen.varcov() is now gen_varcov()
- weight.mat() is now weight_mat()
- gen.advance() is now gen_advance()
The base combinatorial selection functions have been replaced with the dedicated lpsi() function (Linear Phenotypic Selection Index).

The variance-covariance calculation engine, system solvers, and combinatorial index builders are now fully powered by Rcpp and RcppEigen.
Index evaluations for large trait configurations are now exponentially faster due to primitive matrix operations.

Introduced new suites for evaluating linear genomic selection indices (lgsi()) and combining genomic/phenotypic data (ppg_lgsi()).
Introduced new modules for tracking continuous index performance across multiple stages of breeding trials (mlpsi(), mlgsi()).
Implemented specialized solvers to maximize genetic advance while specifically constraining genetic gain for restrictive/undesired traits to zero (rlpsi(), dg_lpsi()).
Adopted Eigen-decomposition based selection methods for phenotypic (esim()) and genomic (gesim()) evaluations.
Added specialized infrastructure for evaluating linear marker selection indices (lmsi()).
Added new comprehensive toolsets to actively simulate and visualize multi-cycle genetic advance over time under varied selection index intensities and environmental variances (simulate_selection_cycles()).
Created a complete pkgdown official website.
Added a complete vignette suite detailing the mathematical foundation and code usage for all new marker, genomic, multi-stage, constrained, and stochastic features.

CRAN release: 2026-01-26

CRAN release: 2023-09-19

add new function meanPerformance() for calculating the mean performance in randomized block design data
remove some typos from the documentation

CRAN release: 2022-06-13

removed two functions sel.index() and sel.score.rank() for easy implementation of comb.indices()

CRAN release: 2021-09-25

CRAN release: 2021-07-26

CRAN release: 2021-06-03

Added a new function rcomb.indices() for calculated possible selection indices excluding single character or particular index from all possible selection indices

CRAN release: 2021-04-23

Bug fixes in phen.varcov()
Added a new function comb.indices() for calculating possible selection indices with the group/pairs of traits/characters
removed function: rank.index()

CRAN release: 2021-04-06