Thanks Liam for the quick answer.
The exemple you made up is nice, I will work on, and try to transfer that on my
case
Not sure that it would be possible.
Benjamin
Le Mercredi 4 Juin 2014 16:10 GMT, "Liam J. Revell" <liam.rev...@umb.edu> a
écrit:
> Hi Gilles.
>
> which.edge returns the rows of phy$edge containing the edges to the mrca
> of the taxa in group. If the group is monophyletic, this will be all the
> edges in the group descended from that mrca. If the group is
> non-monophyletic, it will be only the edges leading from the mrca of
> group to the tips. Key to keep in mind is that which.edge computes the
> indices from phy$edge, not the node numbers themselves!
>
> So, for instance:
>
> require(phytools)
> set.seed(1)
> tree<-pbtree(n=26,tip.label=LETTERS)
> plotTree(tree,node.numbers=T)
> group<-c("E","F","G","H") ## should be monophyletic
> ii<-which.edge(tree,group)
> tree$edge[ii,] ## should be the edges tipward of the mrca of group
> ## visualize this:
> plotSimmap(paintBranches(tree,tree$edge[ii,2],state="2"),
> colors=setNames(c("blue","red"),1:2),lwd=3,node.numbers=T)
> group<-c("C","D","F","E") ## should be non-monophyletic
> ii<-which.edge(tree,group)
> tree$edge[ii,] ## should be the edges tipward of the mrca of group
> ## visualize this:
> plotSimmap(paintBranches(tree,tree$edge[ii,2],state="2"),
> colors=setNames(c("blue","red"),1:2),lwd=3,node.numbers=T)
>
> All the best, Liam
>
> Liam J. Revell, Assistant Professor of Biology
> University of Massachusetts Boston
> web: http://faculty.umb.edu/liam.revell/
> email: liam.rev...@umb.edu
> blog: http://blog.phytools.org
>
> On 6/4/2014 11:41 AM, Gilles Benjamin Leduc wrote:
> > Hello,
> >
> > I am looking the correct way to use the function which.edge {ape} and to
> > understand what it returns…
> >
> > which.edge(phy, group)
> >
> > so I use as phy an object I get like that:
> > as.phylo(dendroIcscan)
> >
> > summary(as.phylo(dendroIcscan))
> >
> > Phylogenetic tree: as.phylo(dendroIcscan)
> >
> > Number of tips: 169
> > Number of nodes: 168
> > Branch lengths:
> > mean: 0.1140614
> > variance: 0.006095345
> > distribution summary:
> > Min. 1st Qu. Median 3rd Qu. Max.
> > 0.005061 0.047450 0.093750 0.175000 0.361100
> > No root edge.
> > First ten tip labels: B-40-2x-T
> > B-41-2x-T
> > B-43-2x-T
> > B-47-2x-T
> > B-52-2x-T
> > B-72-3x-T
> > B-73-2x-A
> > B-75-4x-T
> > B-83-4x-A
> > B-84-4x-NA
> > No node labels.
> >
> >
> > and as group, I get an object:
> > ColPloIcscan
> > [1] 2 2 2 2 2 3 2 4 4 4 4 4 4 2 4 2 2 4 2 4 2 4 2 4 2 4 2 4 2 3 2 3 2 4
> > 2 3 2 4 2 4 3 3 4 2 4 2 4 2 4 3 4 2 4 2 4 2 4 2 3 4 4 2 3 4 2 4 3 3 2 4 2 4
> > 2 4 4 4 4 2 4 2 4 4 3 4 4 4
> > [87] 2 3 4 2 4 4 2 4 2 2 3 2 4 2 4 2 4 2 4 4 2 2 4 3 4 4 4 4 4 4 4 4 4 4
> > 4 2 2 3 2 2 4 3 4 2 4 4 2 2 4 3 4 2 4 4 2 4 3 2 3 2 4 2 4 2 4 4 4 2 2 2 4 2
> > 2 4 2 4 2 2 4 4 4 4 2
> >
> > with everything in the same order than in the phylogenetic tree.
> >
> > As there is no exemple, I try around with several commande :
> >> which.edge(as.phylo(dendroIcscan), ColPloIcscan)
> > [1] 10 50 68 69 71 72 73 74 79 80 110 120 121 122
> >> which.edge(as.phylo(dendroIcscan), ColPloIcscan==2)
> > [1] 9 10 50 68 69 70
> >> which.edge(as.phylo(dendroIcscan), ColPloIcscan==3)
> > [1] 9 10 50 68 69 70
> >> which.edge(as.phylo(dendroIcscan), ColPloIcscan==4)
> > [1] 8 9 10 50 68 69 70
> >
> >
> > There is no exemple, and it doesn't make sens in itself… who could help me
> > with that?
> >
> > Benjamin
> >
> > _______________________________________________
> > R-sig-phylo mailing list - R-sig-phylo@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
> > Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
> >
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