Package index • arfun

Package

arfun arfun-package: arfun: Ancestral Reconstruction of the Fundamental Niche

From occurrence points and a shared accessible area to the data blocks consumed by the joint models.

prepare_niche_data(): Prepare niche data for Stan
prepare_phylo_data(): Prepare phylogenetic data for evolutionary models
prepare_phylo_niche_data(): Prepare joint phylogenetic niche data for evolutionary models
shared_background_sample(): Draw one shared background sample for a clade

The math-scale log-posterior, its compiled C++ backend, multistart optimization and boundary diagnostics for poorly identified niches.

niche_logpost(): Joint phylo-niche log-posterior on the unconstrained scale
niche_logpost_xptr(): Compiled C++ objective for the phylo-niche log-posterior
niche_logpost_eval_xptr(): Evaluate the compiled phylo-niche log-posterior
niche_theta_layout(): Parameter layout of the phylo-niche objective
niche_empirical(): Empirical per-species niche moments
niche_start_ranges(): Data-driven start ranges for the phylo-niche objective
niche_multistart(): Multi-start MAP optimization of the joint phylo-niche posterior
niche_boundary_report(): Per-species boundary diagnostics at a fitted point
niche_warmstart(): Per-species warm-start for the joint phylo-niche objective

Stan models and posterior extraction for niche evolution.

compile_model(): Compile a Stan model for the fundamental niche
model_path(): Get path to a Stan model file
fit_niche(): Fit a Bayesian presence-only niche model
fit_evolution(): Fit an evolutionary model for niche parameters
extract_pars(): Extract niche parameters from a fitted presence-only model
extract_evolution_pars(): Extract evolutionary parameters from a fitted model
stan_only(): Keep only the fields a Stan model declares
niche_overlap(): Compare niche overlap between two ancestral states

Project niches to geography and simulate virtual clades for reverse-engineering benchmarks.

probability_detection(): Probability of detection under the ellipsoidal niche model
virtual_species_occurrences(): Sample occurrence points for a virtual species
simulate_niche_evolution(): Simulate niche evolution along a phylogeny
project_single_niche(): Generate suitability raster for a single niche state
project_ancestral_niche(): Project supplied niche states to geographic space