BAT (version 2.1.1)

originality: Phylogenetic/functional originality of species or individuals.

Description

Average dissimilarity between a species or individual and all others in a community.

Usage

originality(comm, tree, distance, abund = TRUE, relative = TRUE)

Arguments

comm

A sites x species matrix, with either abundance or incidence data. If missing, the originality 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.

abund

A boolean (T/F) indicating whether originality should be calculated per individual (T) or species (F).

relative

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

Value

A matrix of sites x species values.

Details

This is the originality measure of Pavoine et al. (2005) without replacement.

References

Pavoine, S., Ollier, S. & Dufour, A.-B. (2005) Is the originality of a species measurable? Ecology Letters, 8: 579-586.

Examples

# 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")
originality(tree = tree)
originality(distance = distance)
originality(comm, tree)
originality(comm, tree, abund = FALSE)
originality(comm, tree, abund = FALSE, relative = FALSE)
# }