Generate the tmrca of every node

[Dhihram]

I have utilized parboot to find tmrca and HPD 05% of my tree. Can parboot also extract the interval of every node in my tree?

[emvolz]

Yes, it is possible. The output of parboot should contain a list called $trees.
Each element of $trees is itself a treedater fit. If you are interested in a particular node (e.g. 'x' ), iterate over these trees, find the distance from the root (ape::node.depth.edgelength) and add to the estimated tmrca of the total tree.
Example:

sapply( pb$trees, function(tr) tr$timeOfMRCA + node.depth.edgelength(tr)[x] )  |> quantile(prob=c(.025,.975))

[Dhihram]

Thank you very much.

[Dhihram]

Btw, Is it right to say the quantile as HPD? Or is it CI?

[emvolz]

I would call it a CI

[Dhihram]

Thank you very much