SSv3_plotpars {r4ss}R Documentation

Plot distributions of priors, posteriors, and estimates.

Description

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

Usage

SSv3_plotpars(dir = "c:/path/", repfile = "Report.sso",
postfile = "posteriors.sso", showpost = T, showprior = T,
showmle = T, showinit = T, showrecdev = T, priorinit = T,
priorfinal = T, showlegend = T, fitrange = F, xaxs="i",
verbose = T, nrows = 3, ncols = 3, new = T, pdf = F,
pwidth = 7, pheight = 7, punits="in", ptsize = 12,
returntable = F, strings = c(), burn = 0, thin = 1,
ctlfile = "control.ss_new")

Arguments

dir Directory where all files are located.
repfile Name of report file. Default="Report.sso".
postfile Name of MCMC posteriors file (not required). Default="posteriors.sso".
showpost Show posterior distribution as bar graph? Default=T.
showprior Show prior distribution as black line? Default=T.
showmle Show MLE estimate and asymptotic variance estimate with blue lines? Default=T.
showinit Show initial value as red triangle? Default=T.
showrecdev Include recdevs in the plot? Default=T.
priorinit T/F for prior probability at initial value (not implemented).
priorfinal T/F for prior probability at final value (not implemented).
showlegend Show the legend? Default=T.
fitrange Fit range tightly around MLE & posterior distributions, instead of full parameter range? Default=F.
xaxs Parameter input for x-axis. See ?par for more info. Default="i".
verbose Controls amount of text output (maybe). Default=T.
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=T.
pdf Write to PDF file instead of R GUI? Default=F.
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=F.
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().
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".

Author(s)

Ian Taylor

Examples

## Not run: 
pars <- SSv3_plotpars(dir='c:/SS/Simple/')

# strings can be partial match
pars <- SSv3_plotpars(dir='c:/SS/Simple/',strings=c("steep"))
## End(Not run)

[Package r4ss version 1.04 Index]