R: Initialization the selection strength alpha using robust...

init.alpha.gamma.estimation {PhylogeneticEM} | R Documentation

## Initialization the selection strength alpha using robust estimation

### Description

`init.alpha.estimation` fits (Y_i-Y_j)^2 ~ gamma^2(1-exp(-alpha*d_ij)) for all couples of tips (i,j) that have the same mean, i.e than are not separated by a shift. Shifts are initialized thanks to a lasso (function `init.EM.lasso`).

### Usage

    init.alpha.gamma.estimation(phylo, Y_data, nbr_of_shifts, times_shared,
      distances_phylo, T_tree, subtree.list, max_triplet_number, alpha_known,
      method.init.alpha.estimation, tol, h_tree, miss, masque_data, independent,
      ...)

### Arguments

`phylo` | a phylogenetic tree, class `phylo`.
`Y_data` | data at the tips.
`nbr_of_shifts` | : number of shifts wanted
`distances_phylo` | (matrix) : phylogenetic distance, result of function `compute_dist_phy`
`nbr_of_shifts` | number of shifts used in the EM algorithm

### Details

Function `robustbase::nlrob` is used for the robust fit.

### Value

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

[Package PhylogeneticEM version 1.1.0 Index]