Sampling over many phylogenetic trees in brms

[dpascall]

@betanalpha

No. PP HMC doesn’t really handle the topology.

Because which topology is generated at the boundary when one of the edge lengths goes to 0 is random?

@betanalpha

But that presumes that the trees in the sample are representative. What typically happens is the sampler gets stuck in the neighborhood of the topology in which its initialized so the clades in the initial topology appears representative even when they’re not.

Standard practice in phylogenetics whereever I’ve done it is to initialise multiple runs (generally 4) from different random starting trees and only do any analysis when they’re sampling the same distribution, surely that alleviates the problem somewhat?