DTA likelihood — DTA_likelihood • StructCoalescent

Computes the likelihood of a structured phylogenetic tree under the Discrete Trait Analysis (DTA) model

Usage

DTA_likelihood(
  strphylo,
  fit_mig_mat = FitMigMatC(bit_mig_mat, coal_rate),
  bit_mig_mat = BitMigMatC(fit_mig_mat, coal_rate),
  coal_rate
)

Arguments

strphylo: Structured dated phylogeny
fit_mig_mat: Matrix of forwards-in-time migration rates between pairs of demes
bit_mig_mat: Matrix of backwards-in-time migration rates between pairs of demes
coal_rate: Vector of coalescent rate in each deme (1 / effective population size)

Value

List containing log-likelihood and likelihood of the structured phylogenetic tree