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 - Rfirstname.lastname@example.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://email@example.com/