picante (version 0.7-1)

comdist: Calculates inter-community mean pairwise distance

Description

Calculates MPD (mean pairwise distance) separating taxa in two communities, a measure of phylogenetic beta diversity

Usage

comdist(comm, dis, abundance.weighted = FALSE, exclude.conspecifics = FALSE)

Arguments

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)

Value

• Distance object of MPD values separating each pair of communities.

Details

This function calculates a measure of phylogenetic beta diversity: the expected phylogenetic distance separating two individuals or taxa drawn randomly from different communities.

References

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.

See Also

mpd, ses.mpd

Examples

data(phylocom)
comdist(phylocom$sample, cophenetic(phylocom$phylo), abundance.weighted=TRUE)