Changes in version 0.8.3 (2026-06-20) Documentation - Expanded all seven vignettes from brief overviews into full worked guides (quickstart, diversity, rarefaction/standardization, community assembly, spatial analysis, extrapolation, richness estimation). Each now covers the underlying model, simulation with known ground truth, fitting, uncertainty, prediction/comparison, and practical guidance, and exercises the full exported API (including evenness(), diversityProfile(), spatialEigenvectors()/spatialPartition(), wavefront(), and compareModels()). Changes in version 0.8.2 Improvements - spaccDiversity() objects gain a dedicated plot() method with a metric-neutral default y-axis label ("Cumulative diversity") and a ylab/title argument, so custom-metric curves are no longer labelled as species counts. Changes in version 0.8.1 Improvements - spaccPhylo() and spaccFunc() now accept non-integer abundances (e.g. cover or biomass) for Rao's Q and FDis weighting. The phylogenetic and functional accumulation backends use double-precision community matrices instead of truncating to integers. Presence-based metrics (MPD/MNTD/PD/FRic) are unaffected. Changes in version 0.8.0 New Features Rao's Quadratic Entropy (v0.8.0) - spaccPhylo() and spaccFunc() gain a "rao" metric: abundance-weighted mean pairwise distance (phylogenetic cophenetic distance, or Euclidean trait distance), accumulated along the spatial curve. - spaccPhylo() no longer binarises its input, so abundance data now weights Rao; presence metrics (MPD/MNTD/PD) are unchanged. - Exact-math recovery tests against the Rao definition sum_i sum_j p_i p_j d_ij. Custom Diversity Metrics (v0.8.0) - spaccDiversity() accumulates any user-supplied index along a spatial ordering: at each step the cumulative community is passed to a function that returns a scalar. Supports knn, kncn, random, radius, and collector orderings, abundance or incidence input, and extra arguments. - Returns a spacc_diversity object inheriting spacc, so the standard summary(), plot(), as.data.frame(), and predict() methods apply. Arbitrary-Order Rarefaction (v0.8.0) - rarefy() now accepts any q >= 0 (q = 0, 1, 2 keep their exact estimators; other orders report the Hill number of order q) instead of silently falling back to richness. Changes in version 0.7.1 New Features User-Defined Accumulation Order (v0.7.1) - spacc() gains an order argument for supplying an explicit accumulation sequence, bypassing distance computation and seed sampling. - Accepts a single ordering vector, a list of vectors, or a matrix with one ordering per row (each row treated like a seed for uncertainty bounds). - Each ordering must be a permutation of seq_len(nrow(x)). - Backed by cpp_order_parallel(), which reuses the random-accumulation worker with caller-supplied orderings. Changes in version 0.7.0 New Features Hill Numbers (v0.2.0) - spaccHill() - Spatial accumulation with Hill numbers (q = 0, 1, 2) - q = 0: Species richness - q = 1: Exponential Shannon entropy (effective common species) - q = 2: Inverse Simpson (effective dominant species) - Extends iNEXT framework to spatial accumulation Spatial Beta Diversity (v0.3.0) - spaccBeta() - Beta diversity accumulation with partitioning - Total beta diversity (Sorensen or Jaccard) - Turnover component (species replacement) - Nestedness component (species loss) - Based on Baselga (2010) framework Coverage-Based Rarefaction (v0.4.0) - spaccCoverage() - Track sample coverage during accumulation - interpolateCoverage() - Interpolate richness at target coverage levels - Implements Chao & Jost (2012) Good-Turing coverage estimator Phylogenetic/Functional Diversity (v0.5.0) - spaccPhylo() - Phylogenetic diversity accumulation - MPD: Mean Pairwise Distance - MNTD: Mean Nearest Taxon Distance - spaccFunc() - Functional diversity accumulation - FDis: Functional Dispersion - FRic: Functional Richness (approximation) Per-Site Metrics & Heatmaps (v0.6.0) - spaccMetrics() - Extract accumulation metrics per site - slope_10, slope_25: Initial accumulation slopes - half_richness, richness_Npct: Sites to reach richness thresholds - auc: Area under accumulation curve - as_sf() - Convert metrics to sf for spatial analysis - Heatmap plotting via plot(type = "heatmap") Spatial Support Integration (v0.7.0) - New support parameter in spacc() for areaOfEffect integration - Accepts country names: spacc(species, coords, support = "France") - Accepts sf polygons or pre-computed aoe_result objects - Seeds sampled from core sites only (inside support) - Accumulation expands into halo sites (buffer zone) by default - include_halo = FALSE for hard/political boundaries - Eliminates edge effects at arbitrary administrative boundaries Internal Changes - New C++ implementations: hill.cpp, beta.cpp, coverage.cpp, phylo.cpp, metrics.cpp - cpp_knn_parallel_seeds() - kNN with explicit seed indices - Added sf, areaOfEffect, ape, iNEXT, betapart to Suggests Changes in version 0.1.0 Initial release. Features Core Spatial Accumulation Methods - spacc() - Main function with multiple spatial sampling methods: - knn: k-Nearest Neighbor (always visit closest unvisited) - kncn: k-Nearest Centroid Neighbor (visit closest to centroid) - random: Random order (null model) - radius: Expand by distance from seed - gaussian: Probabilistic selection weighted by distance - cone: Directional expansion within angular constraint - collector: Sites in data order Additional Accumulation Methods - wavefront() - Expanding radius accumulation - distanceDecay() - Distance-decay relationships Analytical Methods (No Simulation) - coleman() - Coleman expected accumulation - mao_tau() - Mao Tau (exact) expected accumulation - collector() - Collector's curve (data order) - spatialRarefaction() - Spatially-constrained rarefaction Analysis Functions - extrapolate() - Fit asymptotic models (Michaelis-Menten, Lomolino, etc.) - compare() - Statistical comparison between curves - rarefy() - Rarefaction to common effort - subsample() - Subsample sites spatially Infrastructure - C++ backend via Rcpp for performance - Parallel processing via RcppParallel - Haversine distance support for geographic coordinates