Hi Amy.
Yes, if you wanted to export ancestral character values as node labels,
you can.
For instance:
temp<-ace(x,tree)
tree$node.label<-round(temp$ace,5) # for instance
write.tree(tree,file="")
You could also loop this over the set of trees in a multiPhylo object.
I hope this helps. - 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 2/8/2012 1:59 PM, Amy Boddy wrote:
Hello,
I was wondering if somebody could help me with a problem I am having in
APE. I want to reconstruct the ancestral states of some continuous
characters for over 600 mammalian species. I was able to reconstruct the
ancestral states with the ace function:>ace_body = ace(data$LogBody, tree,
type="continuous" and then plot them on my tree:
nodelabels(round(ace_body$ace, digits=1))
However, my problem is that my data tree is very large, so plotting is a
bit messy. My tree file does not have the internal nodes labeled, and I
know that they are assigned a number to them (ex. if i have 600 species,
the nodes are numbered starting with 601, 602 etc). So my question is, what
is the best way to export this information? Is there a function to write
this tree with the node labels (i.e. the ancestral reconstructions?)?
Any input would be helpful and very much appreciated.
Thank you!
-Amy
[[alternative HTML version deleted]]
_______________________________________________
R-sig-phylo mailing list
R-sig-phylo@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
_______________________________________________
R-sig-phylo mailing list
R-sig-phylo@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
