mcmc.out: Summarize, analyze and plot key MCMC output.
In r4ss: R Code for Stock Synthesis

Description Usage Arguments Author(s) See Also Examples

Makes four panel plot showing trace plots, moving average, autocorrelations, and densities for chosen parameters from MCMC output.

mcmc.out(directory = "c:/mydirectory/", run = "mymodel/",
  file = "keyposteriors.csv", namefile = "postplotnames.sso",
  names = FALSE, headernames = TRUE, numparams = 1, closeall = TRUE,
  burn = 0, thin = 1, scatter = FALSE, surface = FALSE, surf1 = 1,
  surf2 = 2, stats = FALSE, plots = TRUE, header = TRUE, sep = ",",
  print = FALSE, new = T, colNames = NULL)

`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 key parameters. This could be written by the function `SSgetMCMC`.
`namefile`	The (optional) file name of the dimension and names of posteriors.
`names`	Read in names file (T) or use generic naming (F).
`headernames`	Use the names in the header of `file`?
`numparams`	The number of parameters to analyze.
`closeall`	By default close all open devices.
`burn`	Optional burn-in value to apply on top of the option in the starter file and `SSgetMCMC`.
`thin`	Optional thinning value to apply on top of the option in the starter file, in the `-mcsave` runtime command, and in `SSgetMCMC`.
`scatter`	Can add a scatter-plot of all params at end, default is none.
`surface`	Add a surface plot of 2-way correlations.
`surf1`	The first parameter for the surface plot.
`surf2`	The second parameter for the surface plot.
`stats`	Print stats if desired.
`plots`	Show plots or not.
`header`	Data file with header?
`sep`	Separator for data file passed to the `read.table` function.
`print`	Send to screen unless asked to print.
`new`	Logical whether or not to open a new plot window before plotting
`colNames`	Specific names of the `file` to extract and work with. `NULL` keeps all columns

Ian Stewart, Allan Hicks (modifications)

mcmc.nuisance, SSgetMCMC

  ## Not run: 
      mcmc.df <- SSgetMCMC(dir="mcmcRun", writecsv=T,
                  keystrings = c("NatM", "R0", "steep", "Q_extraSD"),
                  nuisancestrings = c("Objective_function", "SPB_", "InitAge", "RecrDev"))
      mcmc.out("mcmcRun",run="",numparams=4,closeall=F)

  #Or for more control
      par(mar=c(5,3.5,0,0.5),oma=c(0,2.5,0.2,0))
      mcmc.out("mcmcRun",run="",numparams=1,closeall=F,new=F,colNames=c("NatM_p_1_Fem_GP_1"))
      mtext("M (natural mortality)",side=2,outer=T,line=1.5,cex=1.1)
  
## End(Not run)