Scott, I have written a function to transform branch lengths on a tree according to age constraints in the terminal taxa and (optionally) the nodes (attached). If your phylo object is tr, the command
scalePhylo(tr, tip.ages, node.mins) will return a phylo object with new branch lengths scaled to the age constraints. Ages are positive numbers (e.g., in Ma). If all your taxa are extant, set tip.ages to be a vector of zeroes. The argument node.mins can have NA entries for nodes without constraints. I developed this for paleontological trees so the tip ages usually constrain branch lengths as well. This may not work exactly as you would like for trees of extant species with only some of the nodes constrained (some internal nodes can be pushed up to the recent). You may also want to look at Graeme Lloyd's function for doing this, which handles zero-length branches in a more elegant way: http://www.graemetlloyd.com/methdpf.html. Again, this was designed for paleontological applications, so it might not get you exactly what you need. The code may be a useful starting point, though. Best, Gene On 3/11/11 10:01 AM, "Scott Chamberlain" <myrmecocys...@gmail.com> wrote: Hello, We have trees for which we have estimated node ages for many nodes (but not all nodes in any one tree). We would like to assign node ages to the trees, and then later transform branch lengths according to node ages. How does one assign node ages in R? Thanks, Scott Chamberlain [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Gene Hunt Curator, Department of Paleobiology National Museum of Natural History Smithsonian Institution [NHB, MRC 121] P.O. Box 37012 Washington DC 20013-7012 Phone: 202-633-1331 Fax: 202-786-2832 http://paleobiology.si.edu/staff/individuals/hunt.cfm
Tree-node-ages.R
Description: Tree-node-ages.R
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