spaccBetaPhylo: Phylogenetic Beta Diversity Accumulation

In spacc: Fast Spatial Species Accumulation Curves

Phylogenetic Beta Diversity Accumulation

Description

Compute spatial accumulation of phylogenetic beta diversity, partitioned into turnover and nestedness components. Measures how evolutionary composition changes as sites are accumulated spatially.

Usage

spaccBetaPhylo(
  x,
  coords,
  tree,
  n_seeds = 50L,
  method = "knn",
  index = c("sorensen", "jaccard"),
  distance = c("euclidean", "haversine"),
  parallel = TRUE,
  n_cores = NULL,
  progress = TRUE,
  seed = NULL
)

Arguments

x	A site-by-species matrix (presence/absence or abundance).
coords	A data.frame with columns x and y, or a spacc_dist object.
tree	A phylogenetic tree of class phylo (from ape), or a pairwise phylogenetic distance matrix.
n_seeds	Integer. Number of random starting points. Default 50.
method	Character. Accumulation method. Default "knn".
index	Character. Dissimilarity index: "sorensen" (default) or "jaccard".
distance	Character. Distance method. Default "euclidean".
parallel	Logical. Use parallel processing? Default TRUE.
n_cores	Integer. Number of cores.
progress	Logical. Show progress? Default TRUE.
seed	Integer. Random seed.

Details

Phylogenetic beta diversity quantifies evolutionary turnover across space. The PhyloSor index (phylogenetic Sorensen) is used: the fraction of branch length shared between two communities relative to total branch length. Partitioned into replacement (turnover) and loss (nestedness) components.

Value

An object of class spacc_beta with additional attribute beta_type = "phylogenetic".

References

Baselga, A. (2010). Partitioning the turnover and nestedness components of beta diversity. Global Ecology and Biogeography, 19, 134-143.

Chao, A., Chiu, C.H., Villeger, S., et al. (2023). Rarefaction and extrapolation with beta diversity under a framework of Hill numbers: the iNEXT.beta3D standardization. Ecological Monographs, 93, e1588.

See Also

spaccBeta(), spaccBetaFunc()

Examples

if (requireNamespace("ape", quietly = TRUE)) {
  tree <- ape::rtree(20)
  coords <- data.frame(x = runif(50), y = runif(50))
  species <- matrix(rbinom(50 * 20, 1, 0.3), nrow = 50)
  colnames(species) <- tree$tip.label

  beta_phylo <- spaccBetaPhylo(species, coords, tree)
  plot(beta_phylo)
}

spacc documentation built on June 20, 2026, 5:07 p.m.