SSgetMCMC: Read MCMC output.

In r4ss: R Code for Stock Synthesis

Read MCMC output.

Description

Reads the MCMC output (in the posteriors.sso and derived_posteriors.sso files) from a model.

Usage

SSgetMCMC(
  dir = NULL,
  verbose = TRUE,
  writecsv = FALSE,
  postname = "posteriors.sso",
  derpostname = "derived_posteriors.sso",
  csv1 = "keyposteriors.csv",
  csv2 = "nuisanceposteriors.csv",
  keystrings = c("NatM", "R0", "steep", "RecrDev_2008", "Q_extraSD"),
  nuisancestrings = c("Objective_function", "SSB_", "InitAge", "RecrDev"),
  burnin = 0,
  thin = 1
)

Arguments

dir	Directory containing MCMC output.
verbose	TRUE/FALSE switch to get more or less information about the progress of the function.
writecsv	Write key parameters and certainty nuisance quantities to a CSV file.
postname	Name of file with parameter posteriors (default matches "posteriors.sso" used by SS, but the user could change the name)
derpostname	Name of file with parameter posteriors (default matches "derived_posteriors.sso" used by SS, but the user could change the name)
csv1	First CSV file for key parameters.
csv2	Second CSV file for nuisance quantities.
keystrings	Vector of strings that partially match parameter names to write to the file csv1. This file intended to feed into mcmc.out().
nuisancestrings	Vector of strings that partially match derived quantity names to write to the file csv2. This file intended to feed into mcmc.nuisance().
burnin	Optional burn-in value to apply on top of the option in the starter file.
thin	Optional thinning value to apply on top of the option in the starter file and in the -mcsave runtime command.

Author(s)

Ian Taylor

See Also

mcmc.out(), mcmc.nuisance(), SSplotPars()

r4ss documentation built on May 28, 2022, 1:11 a.m.