Thanks! Liam, what would be the intrepretation of your function if branch lengths are not included? Just how many "segments" it takes to get between species? As a generality, the larger this number, the more distantly related two species might be? Or without lengths can I not make any generalizations?
--j P.S. This function worked great on that big tree. On Fri, Oct 2, 2015 at 8:06 PM Joseph W. Brown <[email protected]> wrote: > There are no branch lengths in the OpenTree synthetic tree (yet). > Joseph. > ________________________________________ > > Joseph W. Brown > Post-doctoral Researcher, Smith Laboratory > University of Michigan > Department of Ecology & Evolutionary Biology > Room 2071, Kraus Natural Sciences Building > Ann Arbor MI 48109-1079 > [email protected] > > On 2 Oct, 2015, at 17:12, Jonathan Greenberg <[email protected]> wrote: > > Folks: > > Pardon the newbish question, I'm an outsider joining the world of > phylogenetic analysis. Given a large newick tree e.g. from the new open > tree of life: > > http://files.opentreeoflife.org/trees/v3subtrees/chloroplastida.tre.gz > <https://urldefense.proofpoint.com/v2/url?u=http-3A__files.opentreeoflife.org_trees_v3subtrees_chloroplastida.tre.gz&d=AwMFAg&c=8hUWFZcy2Z-Za5rBPlktOQ&r=rVZB6fYleVUDfV0TxTbBZKqFxQKdA_ifFsqsiwLwxio&m=D2gcT4_WJlt0zVaULXs8lCrMTpWpkKRXwBWy7MVXq9I&s=vaQnh80A72P-Q_9k048juaiepUbudvuDFS_N-azw8bM&e=> > > (304959 tips) > > I want to calculate a pairwise distance between a small subset of species. > The tricks I've seen so far using the ape package do no work on a tree of > that size: > > MyTree <- read.tree("pathto/chloroplastida.tre") > pairwise_distance <- cophenetic(MyTree) > > Error in double(nm * nm) : vector size cannot be NA > In addition: Warning message: > In nm * nm : NAs produced by integer overflow > > pairwise_distance <- cophenetic(MyTree)["Abies concolor","Pinus jeffreyi"] > > Error in double(nm * nm) : vector size cannot be NA > In addition: Warning message: > In nm * nm : NAs produced by integer overflow > > This is due to the matrix having more cells than allowed > by .Machine$integer.max > > My question is thus: I want to determine either single species to single > species distances without having an algorithm attempt to calculate the > distance for all possible species (which is what ape is doing). Is there a > package/trick to accomplish this? Thanks! > > --j > > [[alternative HTML version deleted]] > > _______________________________________________ > R-sig-phylo mailing list - [email protected] > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at > http://www.mail-archive.com/[email protected]/ > > [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/[email protected]/
