threshDIC: Deviance Information Criterion from the threshold model

Description Usage Arguments Value Author(s) References See Also

Description

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

Usage

1
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 percent 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").

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 liam.revell@umb.edu

References

Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217-223.

Revell, L. J. (2014) Ancestral character estimation under the threshold model from quantitative genetics. Evolution, bold68, 743-759.

See Also

ancThresh



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