Run MCMC using rtmbstan

Usage

do_mcmc(obj, chains, cores, iter, thin, bounds = Inf, laplace = FALSE, ...)

Arguments

obj: Object built from ADFUN via RTMB
chains: Number of chains to run
cores: Number of cores to use
iter: Number of MCMC iterations to run
thin: Thinning rate
bounds: Uniform bounds to constrain parameter bounds
laplace: Whether or not to do laplace approximation for random effects and MCMC for fixed effects
...: Additional arguments for tmbstan (e.g., adapt_delta)

Value

MCMC list object from rtmbstan

Examples

if (FALSE) { # \dontrun{
obj <- RTMB::MakeADFun(cmb(SPoRC_rtmb, data), parameters = parameters, map = mapping)
mcmc <- do_mcmc(obj = obj,
                chains = 4,
                cores = 4,
                iter = 10000,
                thin = 10,
                bounds = 1.5,
                laplace = FALSE,
                adapt_delta = 0.99)
saveRDS(mcmc, here('output', 'MCMC_Model_23.5.rds'))
} # }