jags.basic <- function(data, inits=NULL, parameters.to.save, model.file,
n.chains, n.adapt=NULL, n.iter, n.burnin=0, n.thin=1,
modules=c('glm'), factories=NULL, parallel=FALSE,
n.cores=NULL, DIC=TRUE, seed=NULL, save.model=FALSE, verbose=TRUE){
# Check input data
inps <- process_input(data, parameters.to.save, inits,
n.chains, n.adapt, n.iter, n.burnin, n.thin, n.cores,
DIC, !verbose, parallel, seed)
# Run JAGS via rjags
rjags_out <- run_rjags(inps$data, inps$inits, inps$params, model.file,
inps$mcmc.info, modules, factories, DIC, parallel, !verbose)
# Report time
if(verbose) cat('MCMC took', rjags_out$elapsed.mins, 'minutes.\n')
# Create output object
if(save.model){
samples <- order_samples(rjags_out$samples, inps$params)
output <- list(samples = samples, model = rjags_out$m)
output$n.cores <- inps$mcmc.info$n.cores
class(output) <- 'jagsUIbasic'
} else{
output <- rjags_out$samples
}
return(output)
}
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