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]]
> 
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