Hi Gustavo, I'm paleotree's author and maintainer. Just to be clear that I understand your problem, I believe you are saying that when you use timeSliceTree, you are getting an error that the internal call to dist.nodes is failing? Is that right?
The first thought I have is that maybe the solution here is to avoid dist.nodes, as it is somewhat overkill. I use dist.nodes in that code, which I wrote in 2011, to get the distance of tips and nodes from the root. A better solution may now exist in another R package. I'd have to investigate (although maybe someone on the list can suggest one). The second thought I have is that there might be alternative functions that do something lie timeSliceTree in another R package. Off the top of my head, I recall that Nick Matzke had a similar, 'chainsaw' function, which you can find here and appears not to call dist.nodes: https://stat.ethz.ch/pipermail/r-sig-phylo/2011-July/001483.html Again, maybe someone on the list knows of a good alternative function. I'll try to give this more thought, but for now, maybe see if you can use Nick's function succesfully. Overall though, I've discovered the use of truly gigantic trees can often run into unexpected problems. Cheers, -Dave On Fri, Oct 16, 2015 at 12:47 PM, Gustavo Burin Ferreira <ariete...@gmail.com> wrote: > Dear list, > > I'm trying to perform a time travel in simulated phylogenies with both > extant and extinct species using the timeSliceTree function form the > paleotree package. My aim is to have the molecular phylogenies derived from > the complete phylogeny (attached) in different points in time. > > However, when I try that with big trees (bigger than 20000 tips total), I > get an error of integer overflow coming from the dist.nodes function. After > slightly tweaking the dist.nodes function (changing nm from integer to > numeric/double), I get the following message: > > Error in dist.nodes(tree) (from #7) : > long vectors (argument 7) are not supported in .Fortran > > Since I don't know much about C or Fortran, I couldn't find a way of solving > this by myself, so any help will be greatly appreciated. > > I'm sending one tree attached for example. > > Thank you very much in advance! > > Best, > > Gustavo Burin Ferreira, Msc. > Instituto de Biociências > Universidade de São Paulo > Tel: (11) 98525-8948 > > _______________________________________________ > 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/ -- David W. Bapst, PhD Adjunct Asst. Professor, Geology and Geol. Eng. South Dakota School of Mines and Technology 501 E. St. Joseph Rapid City, SD 57701 http://webpages.sdsmt.edu/~dbapst/ http://cran.r-project.org/web/packages/paleotree/index.html _______________________________________________ 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/
