R: Compute moments of params_old

compute_mean_variance.simple {PhylogeneticEM} | R Documentation

## Compute moments of params_old

### Description

`compute_mean_variance.simple` computes the quantities needed to compute mean and variance matrix with parameters params_old.

### Usage

    compute_mean_variance.simple(phylo, times_shared, distances_phylo,
      process = c("BM", "OU", "rBM", "scOU"), params_old,
      masque_data = c(rep(TRUE, attr(params_old, "p_dim") *
      length(phylo$tip.label)), rep(FALSE, attr(params_old, "p_dim") *
      phylo$Nnode)), sim = NULL, U_tree = NULL, ...)

### Arguments

`phylo` | Input tree.
`times_shared` | (matrix) : times of shared ancestry, result of function `compute_times_ca`
`distances_phylo` | (matrix) : phylogenetic distance, result of function `compute_dist_phy`
`process` | a two letter string indicating the process to consider
`params_old` | a list of parameters to be used in the computations

### Details

This function is used by functions `compute_E.simple` and `compute_log_likelihood.simple`.

### Value

sim (list) : result of function `simulate` with the appropriate parameters

Sigma matrix of variance covariance, result of function `compute_variance_covariance`

Sigma_YY_chol_inv invert of Cholesky matrix of Sigma_YY: (Sigma_YY)^(-1) = tcrossprod(Sigma_YY_chol_inv)

[Package PhylogeneticEM version 1.1.0 Index]