comdist {picante} | R Documentation |
Calculates MPD (mean pairwise distance) separating taxa in two communities, a measure of phylogenetic beta diversity
comdist(comm, dis, abundance.weighted = FALSE, exclude.conspecifics = FALSE)
comm |
Community data matrix |
dis |
Interspecific distance matrix |
abundance.weighted |
Should mean pairwise distances separating species in two communities be weighted by species abundances? (default = FALSE) |
exclude.conspecifics |
Should conspecific taxa in different communities be excluded from MPD calculations? (default = FALSE) |
This function calculates a measure of phylogenetic beta diversity: the expected phylogenetic distance separating two individuals or taxa drawn randomly from different communities.
Distance object of MPD values separating each pair of communities.
Steven Kembel <skembel@uoregon.edu>
C.O. Webb, D.D. Ackerly, and S.W. Kembel. 2008. Phylocom: software for the analysis of phylogenetic community structure and trait evolution. Bioinformatics 18:2098-2100.
data(phylocom) comdist(phylocom$sample, cophenetic(phylocom$phylo), abundance.weighted=TRUE)