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(dir = "c:/path/", repfile = "Report.sso",
xlab="Parameter value",ylab="Density",
postfile = "posteriors.sso", showpost = TRUE, showprior = TRUE,
showmle = TRUE, showinit = TRUE, showrecdev = TRUE, priorinit = TRUE,
priorfinal = TRUE, showlegend = TRUE, fitrange = FALSE, xaxs="i",
xlim=NULL, ylim=NULL, verbose = TRUE, nrows = 3, ncols = 3,
new = TRUE, pdf = FALSE, pwidth = 7, pheight = 7, punits="in",
ptsize = 12, returntable = FALSE, strings = c(), exact = FALSE,
newheaders=NULL, burn = 0, thin = 1,
ctlfile = "control.ss_new")

`dir`	Directory where all files are located.
`repfile`	Name of report file. Default="Report.sso".
`xlab`	Label on horizontal axis.
`ylab`	Label on vertical axis.
`postfile`	Name of MCMC posteriors file (not required). Default="posteriors.sso".
`showpost`	Show posterior distribution as bar graph? Default=TRUE.
`showprior`	Show prior distribution as black line? Default=TRUE.
`showmle`	Show MLE estimate and asymptotic variance estimate with blue lines? Default=TRUE.
`showinit`	Show initial value as red triangle? Default=TRUE.
`showrecdev`	Include recdevs in the plot? Default=TRUE.
`priorinit`	TRUE/FALSE for prior probability at initial value (not implemented).
`priorfinal`	TRUE/FALSE for prior probability at final value (not implemented).
`showlegend`	Show the legend? Default=TRUE.
`fitrange`	Fit range tightly around MLE & posterior distributions, instead of full parameter range? Default=FALSE.
`xaxs`	Parameter input for x-axis. See `?par` for more info. Default="i".
`xlim`	Optional x-axis limits to be applied to all plots. Otherwise, limits are based on the model results. Default=NULL.
`ylim`	Optional y-axis limits to be applied to all plots. Otherwise, limits are based on the model results. Default=NULL.
`verbose`	Controls amount of text output (maybe). Default=TRUE.
`nrows`	How many rows in multi-figure plot. Default=3.
`ncols`	How many columns in multi-figure plot. Default=3.
`new`	Open new window for plotting? Default=TRUE.
`pdf`	Write to PDF file instead of R GUI? Default=FALSE.
`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_R0" and "SR_steep" if they are both estimated quantities in this model). Default=c().
`exact`	Should strings input match parameter names exactly? Otherwise substrings are allowed. Default=FALSE.
`newheaders`	Optional vector of headers for each panel to replace the parameter names. Default=NULL.
`burn`	Additional burn-in applied to MCMC posteriors. Default=0.
`thin`	Additional thinning applied to MCMC posteriors. Default=1.
`ctlfile`	Specify control file to get min and max recdev values (otherwise assumed to be -5 and 5). Default="control.ss_new".

Ian Taylor

## 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)