Hi! I re-did chainsaw at some point, now there is chainsaw2. However, googling that gets you horror movies, so here is a link with example code:
https://groups.google.com/d/msg/biogeobears/Jy9uYckOL7s/XuNZ0B3jAwAJ (the discussion there points out a rare case where this crashes, but for most trees it should work fine) Cheers, Nick On Fri, Oct 16, 2015 at 2:17 PM, David Bapst <dwba...@gmail.com> wrote: > 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/ [[alternative HTML version deleted]] _______________________________________________ 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/
