Usage
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")
Arguments
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".