selection.index 2.0.0

Breaking changes

• 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).

Major changes

• 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.

New features

• 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.