Hi Liam,
it works perfectly! Thankyou very much!
And....it is elegant...
> Hi Paolo.
>
> I think this code fragment from my phytools function anc.trend does what
> you want (here, I have made it into its own function), although it might
> not be the most elegant way to do it:
>
> vcvPhylo<-function(phy,anc.nodes=T){
> if(anc.nodes){
> D<-dist.nodes(phy)
> ntips<-length(phy$tip.label)
> Cii<-D[ntips+1,]
> C<-D; C[,]<-0
> for(i in 1:nrow(D)) for(j in 1:ncol(D))
> C[i,j]<-(Cii[i]+Cii[j]-D[i,j])/2
>
> dimnames(C)[[1]][1:length(phy$tip)]<-dimnames(C)[[2]][1:length(phy$tip)]<-phy$tip.label
> C<-C[c(1:ntips,(ntips+2):nrow(C)),c(1:ntips,(ntips+2):ncol(C))]
> return(C)
> } else return(vcv.phylo(phy))
> }
>
> All the best, Liam
>
> --
> Liam J. Revell
> University of Massachusetts Boston
> web: http://faculty.umb.edu/liam.revell/
> email: liam.rev...@umb.edu
> blog: http://phytools.blogspot.com
>
> On 11/21/2011 12:09 PM, ppi...@uniroma3.it wrote:
> > Hi all,
> > Having a tree (NOT ultrametric in my case) I would
> > like to extract the phylogenetic covariance matrix
> > including both tips and nodes (like dist.nodes for
> > patristic distances).
> > vcv returns the cov matric just for tips.
> > Someone has a fast way?
> >
> > Thankyou very much
> >
> > Paolo
> >
> > _______________________________________________
> > R-sig-phylo mailing list
> > R-sig-phylo@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
> >
>
>
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