R: Penalty function type Baraud Giraud Huet.

penalty_BaraudGiraudHuet_likelihood {PhylogeneticEM} | R Documentation

## Penalty function type Baraud Giraud Huet.

### Description

`penalty_BaraudGiraudHuet_likelihood` is the penalty defined by : pen' = ntaxa * log(1 + pen/(ntaxa - K)) with pen = C * (ntaxa - K)/(ntaxa - K - 1) * EDkhi[K + 1; ntaxa - K - 1; exp(-Delta_K)/(K + 1)] and Delta = log(model_complexity) + log(K + 1) such that sum(exp(-Delta_K)) < infty.

### Usage

    penalty_BaraudGiraudHuet_likelihood(K, model_complexity, ntaxa, C = 1.1)

### Arguments

`K` | the dimension of the model.
`model_complexity` | the complexity of the set of models with dimension K.
`ntaxa` | the number of tips.
`C` | a constant, C > 1. Default is C = 1.1 (as suggested in Baraud Giraud Huet (2009))

### Details

See Baraud Giraud Huet (2009, 2011). Must be applied to log-likelihood criterion. Function pen is computed using function `penalty` from package `LINselect`.

### Value

value of the penalty.

### See Also

`penalty_BirgeMassart_shape1`, `penalty_BirgeMassart_shape2`

[Package PhylogeneticEM version 1.1.0 Index]