| uniqueness {BAT} | R Documentation |
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)