mcmc.out: Summarize, analyze and plot key MCMC output.

In r4ss: R Code for Stock Synthesis

Summarize, analyze and plot key MCMC output.

Description

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

Usage

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
)

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.
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

Value

directory, because this function is used for its plotting side effects

Author(s)

Ian Stewart, Allan Hicks (modifications)

See Also

mcmc.nuisance(), SSgetMCMC()

Examples

## Not run: 
mcmc.df <- SSgetMCMC(
  dir = "mcmcRun", writecsv = T,
  keystrings = c("NatM", "R0", "steep", "Q_extraSD"),
  nuisancestrings = c("Objective_function", "SSB_", "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)

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