dispersion {BAT} R Documentation

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 A phylo or hclust object (used only for PD or FD) or alternatively a species x traits matrix or data.frame to build a functional tree. 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.

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).

Value

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

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

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)

[Package BAT version 2.7.1 Index]