Hi Scott- There are lots of indices to quantify tree shape differences, both in terms of topology (Colless etc) and temporal differences (e.g., Pybus and Harvey's gamma). MNTD and MPD will largely capture the temporal dimension of your trees and will be highly correlated with gamma. For example, if you have long terminal branches in your tree and with very short internal branches, gamma will be negative and both MPD and MNTD will be large.
I don't think there is a right or wrong answer here and any index might be appropriate, but you will have to think hard about what exactly you want to quantify (e.g, topological imbalance or asymmetry versus branching time differences) and why. It might be good to think about standardized metrics, to control for differences in the number of taxa in trees. You may want to use several indices in concert. ~Dan Rabosky On Mar 17, 2011, at 8:45 AM, Scott Chamberlain wrote: > Hello, > > > I am curious if it is appropriate to calculate mntd (mean nearest taxon > distance) and mpd (mean pairwise distance) in the picante package on trees > themselves, that is, without community data. > > We are trying to think of informative metrics that can tell us something > about tree shape among lots of different trees. Using mntd and mpd we give > the functions a tree and just a vector of all 1's for the community data so > that each species is equally abundant. > > Does this approach make sense? Are there better metrics to use given that we > are just dealing with trees without community data? > > (I am aware of Sackin's, Colless', beta splitting, gamma, etc.) > > > > Here is a reproducible example of what I am doing: > require(picante) > require(ape) > > tree <- rcoal(10) > abund <- rep(1, 10) > names(abund) <- tree$tip.label > mpd_ <- mpd(rbind(abund, abund), # can't have just one vector/community > apparently > cophenetic(tree))[1] # just one of the two numbers needed as they are the same > > > > Sincerely, > Scott Chamberlain > Rice University, EEB Dept. > > > > [[alternative HTML version deleted]] > > _______________________________________________ > R-sig-phylo mailing list > R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
