MultiTypeTree Probability Density

Computes the transition kernel for a MultiTypeTree NodeRetype operator for a full structured phylogeny

Usage

MTT_transition_kernel(
  ED,
  bit_rates,
  node_indices = NodeIndicesC(ED),
  eigen_vals = eigen(bit_rates)$values,
  eigen_vecs = eigen(bit_rates)$vectors,
  inverse_vecs = solve(eigen_vecs)
)

Arguments

ED

Extended data representation of phylogenetic tree and initial migration history

node_indices

Vector of row indices corresponding to which row of ED corresponds to each node label

bit_mig_mat

Matrix of initial backwards-in-time migration rates for the MCMC chain

st_labels

Reduced extended data structure consisting of the rows of ED corresponding to coalescent nodes in the selected subtree only (local likelihood only)

Value

List consisting of the log.likelihood and likelihood of the structured genealogy