Changelog

Source: NEWS.md

spacc 0.7.0 (development)

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

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spacc 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