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]