extendMPT {TreeBUGS}

Extend MCMC Sampling for MPT Model

Description

Adds more MCMC samples to the fitted MPT model.

Usage

extendMPT(fittedModel, n.iter = 10000, n.adapt = 1000, n.burnin = 0, ...)

Arguments

fittedModel

a fitted traitMPT or betaMPT

n.iter

Number of iterations per chain (including burnin samples). See run.jags for details.

n.adapt

number of adaption samples to adjust MCMC sampler in JAGS. The sampler will be more efficient if it is tuned well. However, MCMC sampling will still give correct results even if the warning appears: "Adaptation incomplete." (this just means that sampling efficiency could be better).

n.burnin

Number of samples for burnin (samples will not be stored and removed from n.iter)

...

further arguments passed to extend.jags (see arguments listed in: run.jags).

When drawing more samples, JAGS requires an additional adaptation phase, in which the MCMC sampling procedure is adjusted. Note that the MCMC sampling will still give correct results even if the warning appears: "Adaptation incomplete." (this just means that sampling efficiency is not optimal).