posterior: Sample posterior of TMB models in SAMtool
In SAMtool: Stock Assessment Methods Toolkit

posterior

R Documentation

Sample posterior of TMB models in SAMtool

Description

A convenient wrapper function (posterior) to sample the posterior using MCMC in rstan and returns a stanfit object for diagnostics. Use RCMstan to update the RCM and the enclosed operating model with MCMC samples..

Usage

posterior(x, ...)

## S4 method for signature 'RCModel'
posterior(
  x,
  priors_only = FALSE,
  laplace = FALSE,
  chains = 2,
  iter = 2000,
  warmup = floor(iter/2),
  thin = 5,
  seed = 34,
  init = "last.par.best",
  cores = chains,
  ...
)

## S4 method for signature 'Assessment'
posterior(x, priors_only = FALSE, ...)

RCMstan(RCModel, stanfit, sim, cores = 1, silent = FALSE)

Arguments

`x`	An object of class Assessment or RCModel.
`...`	Additional arguments to pass to `rstan::sampling` via `tmbstan::tmbstan`.
`priors_only`	Logical, whether to set the likelihood to zero and sample the priors only.
`laplace`	Logical, whether to do the Laplace approximation for random parameters.
`chains`	The numer of MCMC chains.
`iter`	The number of iterations for each chain, including warmup.
`warmup`	The number of burnin iterations
`thin`	The frequency at which iterations are kept (e.g., `5` saves every fifth iteration)
`seed`	Seed for random number generator during the MCMC.
`init`	The initial values of parameters for starting the MCMC chain. See `tmbstan::tmbstan`.
`cores`	The number of cores for running in parallel, e.g., one core per MCMC chain. Used in `RCMstan` for reconstructing the population.
`RCModel`	An object of class `RCModel`
`stanfit`	An object of class `stanfit` returned by `posterior`.
`sim`	A matrix of `RCModel@OM@nsim` rows and 2 columns that specifies the samples used to update the operating model. The first column specifies the chain and the second columns specifies the MCMC iteration.
`silent`	Logical to indicate if progress messages should be printed to console.