spaccPhylo: Spatial Phylogenetic Diversity Accumulation

In spacc: Fast Spatial Species Accumulation Curves

Spatial Phylogenetic Diversity Accumulation

Description

Compute spatial accumulation of phylogenetic diversity metrics (MPD, MNTD, PD).

Usage

spaccPhylo(
  x,
  coords,
  tree,
  metric = c("mpd", "mntd"),
  n_seeds = 50L,
  method = "knn",
  distance = c("euclidean", "haversine"),
  parallel = TRUE,
  n_cores = NULL,
  progress = TRUE,
  seed = NULL,
  map = FALSE
)

Arguments

x	A site-by-species matrix.
coords	A data.frame with columns x and y, or a spacc_dist object.
tree	A phylogenetic tree of class phylo (from ape package), or a pairwise phylogenetic distance matrix.
metric	Character vector. Metrics to compute: "mpd": Mean Pairwise Distance "mntd": Mean Nearest Taxon Distance "pd": Faith's Phylogenetic Diversity (requires tree, not distance matrix) "rao": Rao's quadratic entropy (abundance-weighted mean pairwise phylogenetic distance). Pass abundance data for weighting; with presence/absence it reduces to the equal-weight form.
n_seeds	Integer. Number of random starting points. Default 50.
method	Character. Accumulation method. Default "knn".
distance	Character. Site distance method: "euclidean" or "haversine".
parallel	Logical. Use parallel processing? Default TRUE.
n_cores	Integer. Number of cores.
progress	Logical. Show progress? Default TRUE.
seed	Integer. Random seed.
map	Logical. If TRUE, run accumulation from every site as seed and store per-site final values for spatial mapping. Enables as_sf() and plot(type = "map"). Default FALSE.

Details

Phylogenetic diversity metrics incorporate evolutionary relationships:

• MPD (Mean Pairwise Distance): Average phylogenetic distance between all pairs of species. Sensitive to tree-wide patterns.

• MNTD (Mean Nearest Taxon Distance): Average distance to closest relative. Sensitive to terminal clustering.

• PD (Faith's Phylogenetic Diversity): Total branch length connecting species. Requires full tree object.

Value

An object of class spacc_phylo containing:

curves	Named list of matrices, one per metric (n_seeds x n_sites)
metric	Metrics computed
coords, n_seeds, n_sites, method	Parameters used

References

Faith, D.P. (1992). Conservation evaluation and phylogenetic diversity. Biological Conservation, 61, 1-10.

Webb, C.O. (2000). Exploring the phylogenetic structure of ecological communities: an example for rain forest trees. American Naturalist, 156, 145-155.

See Also

picante::mpd(), picante::mntd(), picante::pd()

Examples

if (requireNamespace("ape", quietly = TRUE)) {
  # Create random tree
  tree <- ape::rtree(30)

  coords <- data.frame(x = runif(50), y = runif(50))
  species <- matrix(rbinom(50 * 30, 1, 0.3), nrow = 50)
  colnames(species) <- tree$tip.label

  phylo <- spaccPhylo(species, coords, tree, metric = c("mpd", "mntd"))
  plot(phylo)
}

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