Thanks much Dan and Steve.
Scott
On Thursday, March 17, 2011 at 11:05 AM, Dan Rabosky wrote:
>
> 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]]
> >
> > _______________________________________________
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> > R-sig-phylo@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
>
>
>
>
>
>
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