R: Initialization of the shifts using Lasso.

init.EM.lasso {PhylogeneticEM} | R Documentation

## Initialization of the shifts using Lasso.

### Description

`init.EM.lasso` does the following regression : ||Y_data-T.delta||_(Sigma_YY^(-1)) + lambda |delta|_1 using the function `glmnet::glmnet` of package `glmnet`, through function `lasso_regression_K_fixed`. T is the incidence matrix of the tree, and delta the vectorial representation of the shifts (see functions `incidence.matrix` and `shifts.list_to_vector` for further details).

### Usage

    init.EM.lasso(phylo, Y_data, Y_data_imp = Y_data,
      Y_data_vec_known = as.vector(Y_data), process,
      times_shared = compute_times_ca(phylo), distances_phylo, nbr_of_shifts,
      K_lag_init = 0, use_sigma = TRUE, params_sigma = NULL,
      variance.init = diag(1, p, p), random.init = FALSE,
      value.root.init = rep(0, p), exp.root.init = rep(1, p),
      var.root.init = diag(1, p, p), edges.init = NULL,
      values.init = matrix(0, p, length(edges.init)), relativeTimes.init = NULL,
      selection.strength.init = 1, optimal.value.init = rep(0, p),
      T_tree = incidence.matrix(phylo), subtree.list = NULL, miss = FALSE,
      sBM_variance = FALSE, stationary.root.init = FALSE,
      impute_init_Rphylopars = FALSE, masque_data, independent = FALSE, ...)

### Arguments

`Y_data` | data at the tips.
`times_shared` | (matrix) : times of shared ancestry, result of function `compute_times_ca`.
`distances_phylo` | (matrix) : phylogenetic distance, result of function `compute_dist_phy`
`nbr_of_shifts` | number of shifts used in the EM algorithm

### Details

A Cholesky decomposition of function Sigma_YY^(-1) is used. lambda is chosen so that delta has the right number of non zero components.

### Value

params_init the list of initial parameters to be used, in the right format.

[Package PhylogeneticEM version 1.1.0 Index]