Description Usage Arguments Author(s) Examples
Make multifigure plots of prior, posterior, and estimated asymptotic parameter distributions. MCMC not required to make function work.
1 2 3 4 5 6 7 8 9  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 
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 
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 xaxis. See 
xlim 
Optional xaxis limits to be applied to all plots. Otherwise, limits are based on the model results. 
ylim 
Optional yaxis 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 multifigure plot. 
ncols 
How many columns in multifigure 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

pheight 
Default height width of plots printed to files in units of

punits 
Units for 
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
1 2 3 4 5 6 7  ## 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)

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