checkIsConverged: checkConvergence - Check the convergence of a mcmc.list...
In tmcd82070/evoab: Evidence of Absence (EoA)

Description Usage Arguments Details Value Author(s) References See Also Examples

Run various diagnostic procedures in the coda package to check convergence of a set of mcmc chains.

1	checkIsConverged(obj, criterion = 1.1, quiet = FALSE)

`obj`	An mcmc.list object from the `rjags` package. These are output by the `coda.samples` function. This mcmc.list must contain 2 or more chains.
`quiet`	Whether to print any output on screen.

This routine runs the Gelman and Rubin (1992) diagnostic for a set of MCMC chains by calling gelman.diag in the coda package.

A list with the following components

converged: If the uppper limits of the 'potential scale reduction factors' associated with all parameters are less than criterion, the chain is declared converged and this is TRUE. Otherwise, this component of the returns is FALSE.
Rhats: the 'potential scale reduction factors' or Rhats associated with all parameters.

Trent McDonald

Gelman, A and Rubin, DB (1992) Inference from iterative simulation using multiple sequences, Statistical Science, 7, 457-511.

gelman.diag, checkIsConverged

## Not run: 
jags = jags.model(file="someJAGSFile.txt",
   data=someJAGS.data, inits=someJAGS.inits,
   n.chains=3,n.adapt=100)
update(jags, n.iter=1000)
out = coda.samples(jags,
   variable.names=c("someParameter"),
   n.iter=1000,
   thin=2)

conf <- chechIsConverged(out)

## End(Not run)