Re: [R-sig-phylo] Assigning node ages to a tree, revisited
Roger, If you like, go ahead and send me off-list your code and tree file. The function does not do a lot of error checking, so it is probably hanging on tip or node names; an incorrect tree structure can flummox it, too. If it is working ,it shouldn't take more than a few seconds. Best, Gene On 7/14/11 12:15 AM, Scott Chamberlain myrmecocys...@gmail.com wrote: Hi Roger, Can you provide a reproducible example (perhaps a subset of your tree and their tip and node ages if the tree is very large)? I don't know what the problem could be without the data, but perhaps Gene knows? Scott On Wednesday, July 13, 2011 at 10:57 PM, Roger Close wrote: Hello all, I wish to transform branch lengths on a tree according to ages of terminal taxa and internal node ages; to this end I have tried to implement the script written by Gene Hunt mentioned in a recent post to this list (http://www.mail-archive.com/r-sig-phylo@r-project.org/msg01005.html; script available at https://gist.github.com/938313). However, when attempting to run the command scalePhylo(tr, tip.ages, node.mins), it crunches away for hours on my computer (a 2010 MacBook Pro Core i7, which is quite fast). Clearly there's something wrong. I'm afraid I don't know enough about R to debug a script. I thought I'd send this to the list in case someone other than Gene Hunt or Scott Chamberlain has had a go at using this script. Thanks in advance, Roger -- 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 ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Re: [R-sig-phylo] Assigning node ages to a tree, revisited
Hi all, As a side note to this discussion: ape has now the function compute.brtime (though it considers only node ages), available on ape's SVN in R/compute.brtime.R. Cheers, Emmanuel Scott Chamberlain wrote on 14/07/2011 11:15: Hi Roger, Can you provide a reproducible example (perhaps a subset of your tree and their tip and node ages if the tree is very large)? I don't know what the problem could be without the data, but perhaps Gene knows? Scott On Wednesday, July 13, 2011 at 10:57 PM, Roger Close wrote: Hello all, I wish to transform branch lengths on a tree according to ages of terminal taxa and internal node ages; to this end I have tried to implement the script written by Gene Hunt mentioned in a recent post to this list (http://www.mail-archive.com/r-sig-phylo@r-project.org/msg01005.html; script available at https://gist.github.com/938313). However, when attempting to run the command scalePhylo(tr, tip.ages, node.mins), it crunches away for hours on my computer (a 2010 MacBook Pro Core i7, which is quite fast). Clearly there's something wrong. I'm afraid I don't know enough about R to debug a script. I thought I'd send this to the list in case someone other than Gene Hunt or Scott Chamberlain has had a go at using this script. Thanks in advance, Roger [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Emmanuel Paradis IRD, Jakarta, Indonesia http://ape.mpl.ird.fr/ ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Re: [R-sig-phylo] Assigning node ages to a tree, revisited
Hi Roger, Can you provide a reproducible example (perhaps a subset of your tree and their tip and node ages if the tree is very large)? I don't know what the problem could be without the data, but perhaps Gene knows? Scott On Wednesday, July 13, 2011 at 10:57 PM, Roger Close wrote: Hello all, I wish to transform branch lengths on a tree according to ages of terminal taxa and internal node ages; to this end I have tried to implement the script written by Gene Hunt mentioned in a recent post to this list (http://www.mail-archive.com/r-sig-phylo@r-project.org/msg01005.html; script available at https://gist.github.com/938313). However, when attempting to run the command scalePhylo(tr, tip.ages, node.mins), it crunches away for hours on my computer (a 2010 MacBook Pro Core i7, which is quite fast). Clearly there's something wrong. I'm afraid I don't know enough about R to debug a script. I thought I'd send this to the list in case someone other than Gene Hunt or Scott Chamberlain has had a go at using this script. Thanks in advance, Roger [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
