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Changelog

Source: NEWS.md

arfun 0.3.1.9000

  • niche_multistart() gains ncores for parallel start optimization via parallel::mclapply (the compiled objective is read-only during evaluation, so forked workers share it safely).

arfun 0.3.1

  • Fix: niche_warmstart()$per_species now returns mu2 (the second centroid coordinate) alongside mu1, sigma1, sigma2, rho.

arfun 0.3.0

  • niche_logpost(): exact log-posterior on the mathematical (unconstrained) scale, matching the four Stan parameterizations.
  • Compiled C++ objective via niche_logpost_xptr() + ucminfcpp::ucminf_xptr for fast MAP estimation.
  • niche_multistart(): Sobol/LHS multistart MAP with boundary diagnostics (niche_boundary_report()).
  • niche_warmstart(): per-species independent fits via xnicher assembled into a joint-model start point.
  • prepare_phylo_niche_data(): mask_species keeps weakly identified species in the phylogenetic prior while excluding them from the likelihood (mask-and-predict validation).
  • simulate_niche_evolution(): BM/OU/null niche simulation on a tree.
  • shared_background_sample(): a single shared background sample for all species, as required by the J&S likelihood under a common accessible area M.
  • Vignette: virtual species evolving inside a real One Earth bioregion.
  • All Stan models accept N_occ = 0 (masked species); they still emit predicted niche parameters in generated quantities.