SSplotPars: Plot distributions of priors, posteriors, and estimates.
In r4ss: R Code for Stock Synthesis

Description Usage Arguments Author(s) Examples

Make multi-figure plots of prior, posterior, and estimated asymptotic parameter distributions. MCMC not required to make function work.

SSplotPars(replist, xlab = "Parameter value", ylab = "Density",
  showmle = TRUE, showpost = TRUE, showprior = TRUE,
  showinit = TRUE, showdev = FALSE, showlegend = TRUE,
  fitrange = FALSE, xaxs = "i", xlim = NULL, ylim = NULL,
  verbose = TRUE, nrows = 3, ncols = 3, ltyvec = c(1, 1, 3, 4),
  colvec = c("blue", "red", "black", "gray60", rgb(0, 0, 0, 0.5)),
  new = TRUE, add = FALSE, pdf = FALSE, pwidth = 6.5,
  pheight = 5, punits = "in", ptsize = 10, returntable = FALSE,
  strings = c(), exact = FALSE, newheaders = NULL)

`replist`	List produced by `SS_output`.
`xlab`	Label on horizontal axis.
`ylab`	Label on vertical axis.
`showmle`	Show MLE estimate and asymptotic variance estimate with blue lines?
`showpost`	Show posterior distribution as bar graph if MCMC results are available in `replist`?
`showprior`	Show prior distribution as black line?
`showinit`	Show initial value as red triangle?
`showdev`	Include devs in the plot?
`showlegend`	Show the legend?
`fitrange`	Fit range tightly around MLE & posterior distributions, instead of full parameter range?
`xaxs`	Parameter input for x-axis. See `?par` for more info.
`xlim`	Optional x-axis limits to be applied to all plots. Otherwise, limits are based on the model results.
`ylim`	Optional y-axis limits to be applied to all plots. Otherwise, limits are based on the model results.
`verbose`	Controls amount of text output (maybe).
`nrows`	How many rows in multi-figure plot.
`ncols`	How many columns in multi-figure plot.
`ltyvec`	Vector of line types used for lines showing MLE and prior distributions and the median of the posterior distribution.
`colvec`	Vector of colors used for lines and polygons showing MLE, initial value, prior, posterior, and median of the posterior.
`new`	Open new window for plotting?
`add`	Add to existing plot?
`pdf`	Write to PDF file instead of R GUI?
`pwidth`	Default width of plots printed to files in units of `punits`. Default=7.
`pheight`	Default height width of plots printed to files in units of `punits`. Default=7.
`punits`	Units for `pwidth` and `pheight`. Can be "px" (pixels), "in" (inches), "cm" or "mm". Default="in".
`ptsize`	Point size for plotted text in plots printed to files (see help("png") in R for details). Default=12.
`returntable`	Return table of parameter info? Default=FALSE.
`strings`	Subset parameters included in the plot using substring from parameter names (i.e. "SR" will get "SR_LN(R0)" and "SR_steep" if they are both estimated quantities in this model).
`exact`	Should strings input match parameter names exactly? Otherwise substrings are allowed.
`newheaders`	Optional vector of headers for each panel to replace the parameter names.

Ian G. Taylor, Cole C. Monnahan

## Not run: 
pars <- SSplotPars(dir='c:/SS/Simple/')

# strings can be partial match
pars <- SSplotPars(dir='c:/SS/Simple/',strings=c("steep"))

## End(Not run)