originality {BAT} | R Documentation |
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)