originality: Phylogenetic/functional originality of species or...

In BAT: Biodiversity Assessment Tools

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 = FALSE, relative = FALSE)

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	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.
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.

Details

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

Value

A matrix of sites x species values.

References

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

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)

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

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