[R-sig-phylo] question about pic3

Liam J. Revell liam.revell at umb.edu
Fri Nov 11 20:29:14 CET 2011


BTW:

 > library(picante)
 > K<-phylosig(tr1,x)

should actually be:

 > library(phytools)
 > K<-phylosig(tr1,x)

Best, Liam

-- 
Liam J. Revell
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.revell at umb.edu
blog: http://phytools.blogspot.com

On 11/11/2011 12:26 PM, Liam J. Revell wrote:
> Hi David.
>
> No, pic3 & phylosignal from the picante library do not appear to work
> with polytomies; however you can use mult2di from the ape package to
> resolve polytomies in the tree using multiple methods (default is random):
>
> library(picante)
> tr2<-multi2di(tr1)
> picX<-pic3(x,tr2)
> # or
> K<-phylosignal(x,tr2)
>
> Note that K from phylosignal will be unaffected by the specific
> resolution of the tree (ie., random=TRUE or random=FALSE, in which
> polytomies are resolved in the order in which they appear); the specific
> values of individual contrasts will be affected, but regression of
> contrasts will not be.
>
> Also, in a bit of self promotion, I will also note that phylosig in the
> phytools package can compute K for trees with polytomies with no problem
> because it does not use contrasts:
>
> library(picante)
> K<-phylosig(tr1,x)
>
> All the best, Liam
>



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