Computes Deviance Information Criterion from the MCMC object returned by ancThresh.
threshDIC(tree, x, mcmc, burnin=NULL, sequence=NULL, method="pD")A vector containing the mean deviance and deviance for the parameter means, the effective number of parameters, and the DIC.
phylogenetic tree.
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.
list object returned by ancThresh.
number of generations (not samples) to exclude as burn in; if not supplied then 20% of generations are excluded.
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 for computing the effective number of parameters (options are "pD" and "pV").
Liam Revell liam.revell@umb.edu
This function computes the Deviance Information Criterion from the MCMC object returned by ancThresh.
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.
ancThresh