You could try it using the function fastHeight in phytools. fastHeight(tree,sp1,sp1) +fastHeight(tree,sp2,sp2) - fastHeight(tree,sp1,sp2)
Have not tried it with a tree of this size! Liam J. Revell, Associate Professor of Biology University of Massachusetts Boston web: http://faculty.umb.edu/liam.revell email: [email protected] blog: http://blog.phytools.org --- Sent from my Windows Phone ________________________________ From: Jonathan Greenberg<mailto:[email protected]> Sent: �10/�2/�2015 6:14 PM To: [email protected]<mailto:[email protected]> Subject: [R-sig-phylo] Distance between two species from a 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 (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]]
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