Monday, December 10, 2012

New version of threshDIC

I just posted a new version of threshDIC for computing the Deviance Information Criterion from the object returned by ancThresh. The previous version (of threshDIC not ancThresh) just plain doesn't work. I made some mistakes on key calculations that are now fixed.

DIC is in some ways analogous to the Akaike Information Criterion (AIC), but provides the advantage that it can be used on the results of an MCMC chain - and thus doesn't not require that we can analytically or numerically solve for the maximum of the likelihood function.

The deviance is just -2 × the log-likelihood; and DIC requires that we calculate to versions of this - the mean deviance across samples (Dbar), and deviance at the mean parameter values from the posterior sample (Dhat. We penalize our IC by computing the effective number of parameters of the model (pD or pV, depending on the method we want to use).

Here's a quick demo for the dataset and tree I used earlier:
> require(phytools)
> threshDIC(tree,X,mcmc,sequence=c("not","mod","high"))
    Dbar      Dhat        pD       DIC
-21.29781 -68.07082  46.77302  25.47521

Just like with AIC, we should generally prefer the model with the lowest DIC - although DIC differences of less than 5-10 are difficult to interpret.

The new function is here, but I would advise downloading the latest version of phytools (phytools 0.2-15) and installing from source if you want to use this function:
> install.packages("phytools_0.2-15.tar.gz",type="source", repos=NULL)

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