uniqueness: Phylogenetic/functional uniqueness of species.

In BAT: Biodiversity Assessment Tools

Phylogenetic/functional uniqueness of species.

Description

Dissimilarity between each species and the single closest in a community.

Usage

uniqueness(comm, tree, distance, relative = FALSE)

Arguments

comm	A sites x species matrix, with either abundance or incidence data. If missing, the uniqueness 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.
relative	A boolean (T/F) indicating whether uniqueness should be relative to the maximum distance between any two species in the tree or distance matrix.

Details

This is equivalent to the originality measure of Mouillot et al. (2013).

Value

A matrix of sites x species values.

References

Mouillot, D., Graham, N.A., Villeger, S., Mason, N.W. & Bellwood, D.R. (2013) A functional approach reveals community responses to disturbances. Trends in Ecology and Evolution, 28: 167-177.

Examples

comm <- matrix(c(1,2,0,0,0,1,1,0,0,0,0,2,2,0,0,0,0,1,0,1), nrow = 4, byrow = TRUE)
distance <- dist(c(1:5), method="euclidean")
tree <- hclust(distance, method="average")

uniqueness(tree = tree)
uniqueness(distance = distance)
uniqueness(comm, tree)

BAT documentation built on Oct. 11, 2023, 1:07 a.m.