penalty_BaraudGiraudHuet_likelihood: Penalty function type Baraud Giraud Huet.

In PhylogeneticEM: Automatic Shift Detection using a Phylogenetic EM

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

PhylogeneticEM documentation built on Aug. 31, 2022, 9:16 a.m.