Hi Cecile, Thanks for the input - it looks like this function does perform the tree rescaling, and in about 1/4 of the time, so this could help speed up the code!
However, the function doesn't seem to return a covariance matrix. Is there a way to get the cophenetic matrix with the out put of this function? Otherwise I'm stuck using cophenetic again... Max Max On Fri, Dec 15, 2017 at 4:36 PM, Cecile Ane <cecile....@wisc.edu> wrote: > In the package phylolm, the function "transf.branch.lengths” might do what > you need. It has an option model=“EB” for early burst. > Cécile > > > On Dec 15, 2017, at 3:27 PM, Max Farrell <maxwellfarr...@gmail.com> > wrote: > > > > I have been using the rescale function from geiger for a link prediction > > model I recently helped develop (https://arxiv.org/abs/1707.08354). I'm > now > > running this model on a much larger dataset and part of the code is > > computing cophenetic(rescale(phy)) with 'EB' rescaling many many times. > > > > We're finding that calling cophenetic() is the rate limiting step, and if > > we can avoid this function we expect to speed up our code by up to 4 > times. > > This would be very useful as our simulation has been running for over 50 > > days now... > > > > I was wondering if there is a way to do EB transformations on a > > phylogenetic distance matrix directly so as to avoid using the cophenetic > > function? > > > > Any help or insights would be greatly appreciated! > > > > [[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-ph...@r-project.org/ > > _______________________________________________ > 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-ph...@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/
