PhylogeneticEM (version 1.0.0)

equivalent_shifts_values: Find values given edges. OU stationary case. Ultrametric tree.

Description

equivalent_shifts_values computes the values of the shifts given all thepossible allocations computed by function equivalent_shifts_edges.

Usage

equivalent_shifts_values(phylo, eq_shifts_edges, T_tree_ac, vect_Y, p)

Arguments

phylo

a phylogenetic tree, class phylo.

eq_shifts_edges

matrix (optional) result of function equivalent_shifts_edges.

T_tree_ac

matrix of incidence of the tree, result of function incidence.matrix, actualized with coeficients computed by function incidence_matrix_actualization_factors.

shifts

a list of positions and values of original shifts.

beta_0

value of the original optimal value at the root.

Value

Named list, with "shifts_values" a matrix of shifts values corresponding to the shifts positions in eq_shifts_edges; and "betas_0" a vector of corresponding root optimal values.

Details

This function uses the linear representation of the problem. It fist compute the mean at the tips given by the orgininal shifts positions and values, and then uses function qr.solve to find back the values of the shifts, givent their various positions, and the means at the tips. Function compute_actualization_factors is used to compute the actualization factor that multipies the shifts values at the tips. Carefull, only work for ULTRAMETRIC trees.