contribution {BAT}R Documentation

Contribution of species or individuals to total phylogenetic/functional diversity.

Description

Contribution of each species or individual to the total PD or FD of a number of communities.

Usage

contribution(comm, tree, abund = TRUE, relative = TRUE)

Arguments

comm

A sites x species matrix, with either abundance or incidence data. If missing, the contribution of all species to the full tree 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.

abund

A boolean (T/F) indicating whether contribution should be weighted by abundance of each species.

relative

A boolean (T/F) indicating whether contribution should be relative to total PD or FD (proportional contribution per individual or species). If FALSE, the sum of contributions for each site is equal to total PD/FD, if TRUE it is 1.

Details

Contribution is equivalent to the evolutionary distinctiveness index (ED) of Isaac et al. (2007) if done by species and to the abundance weighted evolutionary distinctiveness (AED) of Cadotte et al. (2010) if done by individual.

Value

A matrix of sites x species values (or values per species if no comm is given).

References

Isaac, N.J.B., Turvey, S.T., Collen, B., Waterman, C. & Baillie, J.E.M. (2007) Mammals on the EDGE: conservation priorities based on threat and phylogeny. PLoS One, 2: e296.

Cadotte, M.W., Davies, T.J., Regetz, J., Kembel, S.W., Cleland, E. & Oakley, T.H. (2010) Phylogenetic diversity metrics for ecological communities: integrating species richness, abundance and evolutionary history. Ecology Letters, 13: 96-105.

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)
tree <- hclust(dist(c(1:5), method="euclidean"), method="average")
contribution(tree = tree)
contribution(comm, tree)
contribution(comm, tree, FALSE)
contribution(comm, tree, abund = FALSE, relative = FALSE)

[Package BAT version 2.6.0 Index]