R: Log Likelihood

compute_log_likelihood.simple {PhylogeneticEM} | R Documentation

## 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

### 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.

### Value

log likelihood of the data

[Package PhylogeneticEM version 1.1.0 Index]