dispersion: Phylogenetic/functional dispersion of species or individuals.

Description

Average dissimilarity between any two species or individuals randomly chosen in a community.

Usage

dispersion(
  comm,
  tree,
  distance,
  func = "originality",
  abund = TRUE,
  relative = TRUE
)

Arguments

comm

A sites x species matrix, with either abundance or incidence data. If missing, the dispersion using the full tree or distance matrix is calculated.

tree

An hclust or phylo object representing a phylogenetic or functional tree. One of tree or distance must be provided.

distance

A dist object representing the phylogenetic or functional distance between species.

func

Calculate dispersion using originality (default), uniqueness or contribution.

abund

A boolean (T/F) indicating whether dispersion should be calculated using individuals (T) or species (F).

relative

A boolean (T/F) indicating whether dispersion should be relative to the maximum distance between any two species in the tree or distance matrix.

Value

A vector of values per site (or a single value if no comm is given).

Details

If abundance data is used and a tree is given, dispersion is the quadratic entropy of Rao (1982). If abundance data is not used but a tree is given, dispersion is the phylogenetic dispersion measure of Webb et al. (2002).

References

Rao, C.R. (1982) Diversity and dissimilarity coefficients: a unified approach. Theoretical Population Biology, 21: 24-43.

Webb, C.O., Ackerly, D.D., McPeek, M.A. & Donoghue, M.J. (2002) Phylogenies and community ecology. Annual Review of Ecology and Systematics, 33: 475-505.

Examples

Run this code

# NOT RUN {
comm <- matrix(c(1,2,0,0,0,1,1,0,0,0,0,2,2,0,0,0,0,1,1,1), nrow = 4, byrow = TRUE)
distance <- dist(c(1:5), method="euclidean")
tree <- hclust(distance, method="average")
dispersion(tree = tree)
dispersion(distance = distance)
dispersion(comm, tree)
dispersion(comm, tree, abund = FALSE)
dispersion(comm, tree, abund = FALSE, relative = FALSE)
# }

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