R: Function to estimate alpha

estimate.alpha {PhylogeneticEM} | 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.

### Value

double : estimation of alpha

[Package PhylogeneticEM version 1.1.0 Index]