Phylogenetic Diversity Profile

Compute phylogenetic Hill numbers (Chao et al. 2010) across a continuous range of diversity orders (q), producing a phylogenetic diversity profile.

Usage

diversityProfilePhylo(
  x,
  tree,
  q = seq(0, 3, by = 0.1),
  type = c("both", "per_site", "regional"),
  coords = NULL
)

Arguments

x: A site-by-species matrix (abundance data). Column names must match tip labels in the phylogeny.
tree: An ape::phylo object. Tips must include all species in x.
q: Numeric vector. Orders of diversity. Default seq(0, 3, by = 0.1).
type: Character. What to compute: "per_site", "regional", or "both" (default).
coords: Optional data.frame with x and y for spatial mapping.

Value

An object of class spacc_profile with $profile_type = "phylogenetic".

Details

Phylogenetic Hill numbers (Chao et al. 2010) weight branches by their evolutionary distance. At q=0 this approximates normalized Faith's PD. Higher q values increasingly emphasize common lineages.

References

Chao, A., Chiu, C.H. & Jost, L. (2010). Phylogenetic diversity measures based on Hill numbers. Philosophical Transactions of the Royal Society B, 365, 3599-3609.

Examples

# \donttest{
if (requireNamespace("ape", quietly = TRUE)) {
  species <- matrix(rpois(20 * 10, 2), nrow = 20,
                    dimnames = list(NULL, paste0("sp", 1:10)))
  tree <- ape::rcoal(10, tip.label = paste0("sp", 1:10))
  prof <- diversityProfilePhylo(species, tree)
  print(prof)
}
# }