estimate.alpha: Function to estimate alpha
Description
optimize to maximize the
conditional expectation log likelihood in alpha. The interval is
set to [alpha_old/2, 2*alpha_old], supposing that the previous guess of
alpha_old is not far from reality.
Usage
estimate.alpha(phylo, conditional_law_X, sigma2, mu, shifts, alpha_old, max_selection.strength)
Arguments
conditional_law_X
result of function compute_E.OU
shifts
list of shifts on the tree
alpha_old
previous estimation of the selection strength
max_selection.strength
the maximal value of alpha authorized by
the user
Value
double : estimation of alpha
Details
This function uses functions compute_var_diff.OU
and compute_diff_exp.OU in the process. Carefull : only works if the
root is stationary, and shifts at nodes.