Changes in version 1.0.1                        

Bug fixes

  - vsp() now selects presence/absence cells by cell index with uniform
    sampling (via sample.int()) instead of sample(cell_indices, prob =
    ...). This fixes the base-R sample() footgun when a pool has a
    single eligible cell, and removes suitability weighting from the
    spatial draw (suitability already enters the presence/absence
    outcome via rbinom()), which also avoids an error when an absence
    pool's weights are all zero.

                        Changes in version 1.0.0                        

First public release.

Highlights

  - End-to-end C++ likelihood chain. The optimization hot path
    (loglik_math, loglik_bio, log_prob_detect, math_to_bio,
    create_param_vector_masked, like_neg_ltsgr) is now driven entirely
    by C++ kernels via thin R wrappers. The pure-R reference
    implementations are preserved as non-exported *_r functions in
    R/internals.R and used by the test suite to assert numerical parity
    at tol = 1e-6.
  - optimize_likelihood() and profile_likelihood() drive
    ucminfcpp::ucminfcpp_xptr() with a pure-C++ XPtr factory
    (make_loglik_math_xptr_cpp), so there are no R callbacks in the
    inner loop.
  - Parameter masking is fully integrated: any subset of the canonical
    parameter vector can be fixed during optimization, and the remaining
    free parameters are optimized end-to-end on the math scale.
  - Profile-likelihood name propagation fix. profile_likelihood() now
    preserves free-parameter names across the ucminf boundary, so
    profile rows are reliably labelled with the parameter being held
    fixed.

API changes

  - New canonical exported names (with thin C++ wrappers):
    
    | exported | non-exported reference | | --- | --- | | loglik_math |
    xsdm:::loglik_math_r | | loglik_bio | xsdm:::loglik_bio_r | |
    log_prob_detect | xsdm:::log_prob_detect_r | | math_to_bio |
    xsdm:::math_to_bio_r | | create_param_vector_masked |
    xsdm:::create_param_vector_masked_r | | like_neg_ltsgr |
    xsdm:::like_neg_ltsgr_r | | dist_between_params |
    xsdm:::dist_between_params_r |

  - like_neg_ltsgr_cpp is no longer exported; it remains as an
    unexported back-compat alias (xsdm:::like_neg_ltsgr_cpp) that
    forwards to like_neg_ltsgr. New code should call like_neg_ltsgr
    directly.

  - dist_between_params() is now backed by a pure-C++ implementation in
    src/dist_between_params.cpp that builds the pairing cost matrix and
    solves the linear sum assignment problem via a clean-room Hungarian
    / Kuhn--Munkres routine (O(n^3) potentials variant from Kuhn 1955,
    Munkres 1957, Jonker & Volgenant 1987). No code is taken from the
    clue package, avoiding the GPL-2 / AGPL-3 licence mismatch. The
    pure-R reference xsdm:::dist_between_params_r continues to call
    clue::solve_LSAP() and is used by the parity tests in
    tests/testthat/test-dist_between_params_r_vs_cpp.R. The legacy
    brute-force reference distance_between_params() is also preserved
    (non-exported) as xsdm:::distance_between_params_r.

Validation & robustness

  - optimize_likelihood(), start_parms(), and get_start_parms_() now
    reject num_starts < 3 early with an informative checkmate error,
    rather than crashing inside sobol::sobol_design() (which segfaults
    at nseq = 0 and returns a malformed vector at nseq = 1).
  - start_parms() runtime: sobol::sobol_design output is defensively
    coerced to a data.frame, protecting against future behaviour
    changes.
  - dist_between_params() (and the xsdm:::dist_between_params_r
    reference) now accept a +/-Inf value in a sig* or pd coordinate of a
    free math-scale parameter vector, matching the rule already applied
    to the mask argument. This is the boundary-model case where a shape
    parameter saturates (e.g. sigrtil -> Inf): the distance is still
    well defined because sig* are compared on the inverse scale (1 / Inf
    = 0). Previously such a vector was rejected with "Must be finite",
    which forced callers to catch the error and record a missing (NA)
    distance. NA anywhere, and Inf in any non-sig*/non-pd coordinate,
    are still rejected.

Build & packaging

  - terra and tibble moved from Suggests: to Imports:. Both are used
    unconditionally in mainline package code (env_data_array(),
    habitat_suitability(), start_parms(), vsp()).
  - src/*.hpp headers renamed to src/*.h to satisfy R CMD check's
    "Subdirectory 'src' contains" warning.
  - New R-CMD-check.yaml GitHub workflow runs R CMD check --as-cran on
    Ubuntu (release / devel / oldrel-1 / oldrel-2), Windows, and macOS.
  - Test suite: 1006 tests, full suite ~9s, all green; parity tests live
    under tests/testthat/test-*_r_vs_cpp.R.

Internals

  - All non-exported helpers (check_env_array, logit, permutations,
    auto_plot_lims_, etc.) consolidated in R/internals.R.
  - profile_likelihood() cleanly stops when the requested parameter is
    outside the masked design.