SSgetMCMC {r4ss}

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()