PhylogeneticEM (version 1.0.0)

compute_log_likelihood.simple: Log Likelihood

Description

compute_log_likelihood.simple computes the log-likelihood of the data in the simple case where the inverse of the variance matrix is given.

Usage

compute_log_likelihood.simple(phylo, Y_data_vec, sim, Sigma, Sigma_YY_chol_inv, miss = rep(FALSE, dim(sim)[1] * length(phylo$tip.label)), masque_data = c(rep(TRUE, dim(sim)[1] * length(phylo$tip.label)), rep(FALSE, dim(sim)[1] * phylo$Nnode)), ...)

Arguments

phylo

Input tree.

sim

(list) : result of function simulate

Sigma

: variance-covariance matrix, result of function compute_variance_covariance

Y_data

: vector indicating the data at the tips

Sigma_YY_inv

: invert of the variance-covariance matrix of the data

Value

log likelihood of the data

Details

This function takes parameters sim, Sigma and Sigma_YY_inv from compute_mean_variance.simple. It uses functions extract.variance_covariance, extract.covariance_parents, and extract_simulate_internal to extract the needed quantities from these objects.