Phylogenetic Beta Diversity Accumulation

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.

Value

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

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.

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.

Examples

# \donttest{
library(ape)
tree <- 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)
# }