Changes in version 2.0.0 (2026-07-05)                  

New features

  - Sparse node-time solver (clsSolver = "sparse"), now the default. The
    temporally-constrained least-squares step that estimates
    internal-node times is now solved with a sparse tree-Laplacian
    Goldfarb–Idnani dual active-set instead of forming and solving a
    dense quadratic program. Each step applies L⁻¹ to one constraint
    column (an O(n) sparse solve) and updates a small dense Schur
    factor. End-to-end this is roughly 6× faster than the dense solver
    on a real 1,000-tip relaxed-clock fit and ~15× at 2,000 tips, while
    returning numerically identical estimates (tMRCA/rate agree with the
    dense solver to ~1e-8 or better).
    
    Because it is a dual method, it also converges on degenerate
    constraint sets — many linearly-dependent binding constraints,
    common on large, non-clock-like trees — by exchanging constraints,
    where the earlier primal active-set had to fall back to the dense
    quadprog solver (e.g. ~14× faster than that fallback at 4,000 tips).
    
    The dense solver is available as clsSolver = "quadprog", and "mgcv"
    is unchanged. The sparse path requires the Matrix package (a
    recommended package shipped with R) and falls back to "quadprog"
    automatically if it is unavailable or fails, so a result is always
    produced.
    
    See notes/sparse-active-set.md for details.

Dependencies

  - limSolve is no longer required (it is being discontinued on CRAN).
    The dense constrained-least-squares solver now uses quadprog (moved
    to Imports); limSolve has been dropped from Depends.

Bug fixes

  - dater() now forwards its clsSolver argument to the internal fitting
    routine (previously the top-level clsSolver argument was ignored).