SSgetMCMC: Read MCMC output.
In r4ss: R code for Stock Synthesis

Description Usage Arguments Author(s) See Also

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

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)

`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.