SSv3_plotpars {r4ss} | R Documentation |
Make multi-figure plots of prior, posterior, and estimated asymptotic parameter distributions. MCMC not required to make function work.
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")
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". |
Ian Taylor
## 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)