evenness(),
diversityProfile(), spatialEigenvectors()/spatialPartition(),
wavefront(), and compareModels()).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.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.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.sum_i sum_j p_i p_j d_ij.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.spacc_diversity object inheriting spacc, so the standard
summary(), plot(), as.data.frame(), and predict() methods apply.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() gains an order argument for supplying an explicit accumulation
sequence, bypassing distance computation and seed sampling.
seq_len(nrow(x)).cpp_order_parallel(), which reuses the random-accumulation
worker with caller-supplied orderings.spaccHill() - Spatial accumulation with Hill numbers (q = 0, 1, 2)
spaccBeta() - Beta diversity accumulation with partitioning
spaccCoverage() - Track sample coverage during accumulationinterpolateCoverage() - Interpolate richness at target coverage levelsspaccPhylo() - Phylogenetic diversity accumulation
spaccFunc() - Functional diversity accumulation
spaccMetrics() - Extract accumulation metrics per site
slope_10, slope_25: Initial accumulation slopeshalf_richness, richness_Npct: Sites to reach richness thresholdsauc: Area under accumulation curveas_sf() - Convert metrics to sf for spatial analysisplot(type = "heatmap")support parameter in spacc() for areaOfEffect integration
spacc(species, coords, support = "France")aoe_result objectsinclude_halo = FALSE for hard/political boundariescpp_knn_parallel_seeds() - kNN with explicit seed indicesInitial release.
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 seedgaussian: Probabilistic selection weighted by distancecone: Directional expansion within angular constraintcollector: Sites in data orderwavefront() - Expanding radius accumulationdistanceDecay() - Distance-decay relationshipscoleman() - Coleman expected accumulationmao_tau() - Mao Tau (exact) expected accumulationcollector() - Collector's curve (data order)spatialRarefaction() - Spatially-constrained rarefactionextrapolate() - Fit asymptotic models (Michaelis-Menten, Lomolino, etc.)compare() - Statistical comparison between curvesrarefy() - Rarefaction to common effortsubsample() - Subsample sites spatially