mcmc.nuisance: Summarize nuisance MCMC output

In r4ss: R Code for Stock Synthesis

Summarize nuisance MCMC output

Description

Summarize nuisance MCMC output (used in combination with mcmc.out() for key parameters).

Usage

mcmc.nuisance(
  directory = "c:/mydirectory/",
  run = "mymodel/",
  file = "posteriors.sso",
  file2 = "derived_posteriors.sso",
  bothfiles = FALSE,
  printstats = FALSE,
  burn = 0,
  header = TRUE,
  thin = 1,
  trace = 0,
  labelstrings = "all",
  columnnumbers = "all",
  sep = ""
)

Arguments

directory	Directory where all results are located, one level above directory for particular run.
run	Directory with files from a particular run.
file	Filename either with full path or relative to working directory. Contents of the file that is referenced here should contain posterior samples for nuisance parameters, e.g., posteriors.sso or something written by SSgetMCMC.
file2	Optional second file containing posterior samples for nuisance parameters. This could be derived_posteriors.sso.
bothfiles	TRUE/FALSE indicator on whether to read file2 in addition to file1.
printstats	Return all the statistics for a closer look.
burn	Optional burn-in value to apply on top of the option in the starter file and SSgetMCMC().
header	Data file with header?
thin	Optional thinning value to apply on top of the option in the starter file, in the mcsave runtime command, and in SSgetMCMC().
trace	Plot trace for param # (to help sort out problem parameters).
labelstrings	Vector of strings that partially match the labels of the parameters you want to consider.
columnnumbers	Vector of column numbers indicating the columns you want to consider.
sep	Separator for data file passed to the read.table function.

Author(s)

Ian Stewart

See Also

mcmc.out(), SSgetMCMC()

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