mcmc.nuisance: Summarize nuisance MCMC output
In r4ss: R code for Stock Synthesis

Description Usage Arguments Author(s) See Also

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

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 = "")

`directory`	Directory where all results are located, one level above directory for particular run.
`run`	Directory with files from a particular run.
`file`	File containing posterior samples for nuisance parameters. This could be posteriors.sso or something written by the function `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.