Hi Nicholas.
The nodes in a "phylo" object are numbered 1:tree$Nnode+N, where N is
the number of tips in the tree & tree$Nnode is the number of nodes. That
means if your tree has 10 tips and 9 internal nodes, the node numbers
will be 11, 12, 13, ..., 19.
To use nodelabels(...,pie=XX) you can supply a matrix in which the rows
sum to one (as in the transpose of your example matrix). If the node
argument is left empty, then it is assumed that the rows are in node
order (i.e., 11, 12, ..., 19). This is the order returned by (for
example) ace. If you have a matrix in which the nodes are in a different
order, you can use nodelabels(...,node=YY,pie=XX) in which YY supplies
the node numbers (using the scheme above) for the rows of XX.
Note that as per recent discussion on this email list,
ace(...,type="discrete") should not be used for ancestral state
reconstruction except for the root node of the tree. I describe this in
some posts to my blog
(http://blog.phytools.org/2013/03/conditional-scaled-likelihoods-in-ace.html
and
http://blog.phytools.org/2013/03/a-little-more-on-ancestral-state.html).
The scaled likelihoods at internal nodes are conditional likelihoods for
the subtree, not marginal ancestral state reconstructions. I believe
that the help page for ace will be clarified in future versions of ape.
Good luck. 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 3/25/2013 12:09 PM, Nicholas Crouch wrote:
Hi,
Hoe does the function "nodelabels" match data to the phylogeny? Ancestral
reconstruction produces a vector with a sample output:
st
[,1] [,2] [,3] [,4] [,5]
[1,] 0.0001381085 0.007642601 0.01638118 0.001591162 0.001268793
[2,] 0.9998618915 0.992357399 0.98361882 0.998408838 0.998731207
The numbers across the top do no correlate with the node numbers on
the phylogeny: compare
nodelabels(pie=t(st))
with
nodelabels()
Would it be possible to create a list vector of the nodes in a
phylogeny with the corresponding values from an ancestral
reconstruction?
An example could be something like:
vector
Node 1
[1] 0.05
[2] 0.95
Node 2
[1] 0.3
[2] 0.7
Thanks
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