Collect MCMC chains into a multiPhylo object — collect

Reconstructs phylo trees from raw edge-list chains, applies burn-in removal and iteration truncation, then pools all chains into a single multiPhylo object.

Usage

collect_chains(edge_list_all, phy_init, burnin = 0, max_iter = Inf)

Arguments

edge_list_all: List of chains, each a list of 2-column integer edge matrices.
phy_init: The initial phylo object whose tip labels and metadata are used to reconstruct full phylo objects.
burnin: Integer; number of initial samples to discard from each chain.
max_iter: Numeric; maximum iteration to retain (samples beyond this are dropped).

Value

A multiPhylo object containing the pooled post-burn-in trees.