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 <- co
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 co
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
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
> model I recently helped devel
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 fin
