SSgetMCMC: Read MCMC output.

Description Usage Arguments Author(s) See Also

View source: R/SSgetMCMC.R

Description

Reads the MCMC output (in the posteriors.sso and derived_posteriors.sso files) from one or more models.

Usage

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SSgetMCMC(dir = NULL, verbose = TRUE, writecsv = FALSE,
  csv1 = "keyposteriors.csv", csv2 = "nuisanceposteriors.csv",
  keystrings = c("NatM", "R0", "steep", "RecrDev_2008", "Q_extraSD"),
  nuisancestrings = c("Objective_function", "SPB_", "InitAge", "RecrDev"),
  modelnames = "default", burnin = 0, thin = 1)

Arguments

dir

A string (or vector of strings) of the directory (or directories) with 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.

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.

modelnames

Either "default" or a vector of names to use in naming elements of list that is output by the function. Default is "model1", "model2", etc.

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 29, 2017, 2:24 p.m.