spacc 0.8.3

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()).

spacc 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.

spacc 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.

spacc 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.

spacc 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.

spacc 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

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

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