threshDIC: Deviance Information Criterion from the threshold model

In phytools: Phylogenetic Tools for Comparative Biology (and Other Things)

Deviance Information Criterion from the threshold model

Description

Computes Deviance Information Criterion from the MCMC object returned by ancThresh.

Usage

threshDIC(tree, x, mcmc, burnin=NULL, sequence=NULL, method="pD")

Arguments

tree	phylogenetic tree.
x	a named vector containing discrete character states; or a matrix containing the tip species, in rows, and probabilities of being in each state, in columns.
mcmc	list object returned by ancThresh.
burnin	number of generations (not samples) to exclude as burn in; if not supplied then 20% of generations are excluded.
sequence	assumed ordering of the discrete character state. If not supplied and x is a vector then numerical-alphabetical order is assumed; if not supplied and x is a matrix, then the column order of x is used.
method	method for computing the effective number of parameters (options are "pD" and "pV").

Details

This function computes the Deviance Information Criterion from the MCMC object returned by ancThresh.

Value

A vector containing the mean deviance and deviance for the parameter means, the effective number of parameters, and the DIC.

Author(s)

Liam Revell [e-mail]

References

Revell, L. J. (2014) Ancestral character estimation under the threshold model from quantitative genetics. Evolution, 68, 743-759.

Revell, L. J. (2024) phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ, 12, e16505.

Spiegelhalter, D. J., N. G. Best, B. P. Carlin, and A. Van Der Linde (2002) Bayesian measures of model complexity and fit. Journal of the Royal Statistical Society Series B: Statistical Methodology, 64, 583-639.

See Also

ancThresh

phytools documentation built on June 22, 2024, 10:39 a.m.