Re: [R-sig-phylo] Rescaling a cophenetic matrix based on the Early Burst Model?

Dear Max, there is a function called coph in phangorn. The function is hidden in the name space, so you have to use phangorn:::coph. It returns a dist object instead of a matrix and computing time is roughly O(n^2) instead of O(n^3). > library(phangorn)> tree <- rtree(1) > system.time(cm1 <-

Re: [R-sig-phylo] Rescaling a cophenetic matrix based on the Early Burst Model?

Not in phylolm, because it’s faster to avoid manipulating this large matrix, if possible (and it is indeed possible for many purposes). If you can rephrase your calculations to use branching times (distance from a node to its descendant tips) or using the nodes’ distance to the root, then you

Re: [R-sig-phylo] Rescaling a cophenetic matrix based on the Early Burst Model?

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 wrote: > > I have been using the rescale function from geiger for a link prediction >

[R-sig-phylo] Rescaling a cophenetic matrix based on the Early Burst Model?

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