estimate.alpha: Function to estimate alpha
In PhylogeneticEM: Automatic Shift Detection using a Phylogenetic EM

estimate.alpha

R Documentation

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

`phylo`	Input tree.
`conditional_law_X`	result of function `compute_E.OU`
`sigma2`	variance of params
`mu`	mean of the root state
`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

Details

This function uses functions compute_var_diff.OU and compute_diff_exp.OU in the process. Careful : only works if the root is stationary, and shifts at nodes.