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xsdm 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.

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.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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