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).
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, ...)a phylogenetic tree, class phylo.
data at the tips.
: number of shifts wanted
(matrix) : phylogenetic distance, result of function
compute_dist_phy
number of shifts used in the EM algorithm
params_init the list of initial parameters to be used, in the right format.
Function robustbase::nlrob is used for the robust fit.