logllk_location {ddtlcm}

Compute log likelihood of parameters

Description

Compute the marginal log likelihood of the parameters on the leaves of a tree

Usage

logllk_location(
  tree_phylo4d,
  Sigma_by_group,
  item_membership_list,
  dist_mat = NULL,
  tol = 1e-07
)

Arguments

tree_phylo4d

a "phylo4d" object

Sigma_by_group

a vector of diffusion variances of G groups

item_membership_list

a list of G elements, where the g-th element contains the column indices of data corresponding to items in major group g

dist_mat

a tree-structured covariance matrix from a given tree. Default is NULL. If given a matrix, then computation of the covariance matrix will be skipped to save time. This is useful in the Metropolis-Hasting algorithm when the previous proposal is not accepted.

tol

a small number to prevent underflow when computing eigenvalues

Value

A list of two elements: a numeric loglikelihood, a covariance matrix of the input tree

See Also

Other likelihood functions: logllk_ddt(), logllk_ddt_lcm(), logllk_div_time_one(), logllk_div_time_two(), logllk_lcm(), logllk_tree_topology()