Usage
SSplotComparisons(summaryoutput,subplots=1:10,
plot=TRUE,print=FALSE,
models="all",
endyrvec=NULL,
indexfleets="default",
indexUncertainty=FALSE,
indexSEvec="default",
labels=c("Year", #1
"Spawning biomass (mt)", #2
"Spawning depletion", #3
"Age-0 recruits (1,000s)", #4
"Recruitment deviations", #5
"Index", #6
"Log index", #7
"Density"), #8
col="default", shadecol="default",
pch="default", lty=1, lwd=2,
xlim="default", xaxs="r", yaxs="r",
type="o", uncertainty=TRUE, shadealpha=0.1,
legend=TRUE, legendlabels="default", legendloc="topright",
btarg=0.4, minbthresh=0.25,
pwidth=7,pheight=7,punits="in",res=300,ptsize=12,cex.main=1,
plotdir="workingdirectory",
densitynames=c("SPB_Virgin","SPB_2011","Bratio_2011","SR_R0","TotYield_MSY"),
densityxlabs=c("B0","Spawning Biomass in 2011","depletion in 2011","log(R0)","MSY"),
densityscale=1,
new=TRUE,
verbose=TRUE)Arguments
summaryoutput
list created by SSsummarize
subplots
Vector of subplots to be created.
plot
plot to active plot device?
print
send plots to PNG files in directory specified by plotdir
models
optional subset of the models described in summaryoutput.
Either "all" or a vector of numbers indicating columns in summary
tables.
endyrvec
optional single year or vector of years representing the final year
of values to show for each model
indexfleets
vector of fleets for each model for which to compare indices of
abundance. Only necessary if any model has more than one index.
indexUncertainty
show uncertainty intervals on index data? Default=FALSE because if
models have any extra standard deviations added, these intervals may
differ across models.
indexSEvec
optional replacement for the SE values in summaryoutput$indices to
deal with the issue of differing uncertainty by models described
above.
labels
vector of labels for plots (titles and axis labels)
col
optional vector of colors to be used for lines. Input 'default'
makes use of rich.colors.short function.
shadecol
optional vector of colors to be used for shading uncertainty
intervals. Input 'default' makes use of rich.colors.short
function with alpha transparency.
pch
optional vector of plot character values
lty
optional vector of line types
lwd
optional vector of line widths
xaxs
choice of xaxs parameter (see ?par for more info)
yaxs
choice of yaxs parameter (see ?par for more info)
type
type parameter passed to points (default 'o' overplots points on top
of lines)
uncertainty
show plots with uncertainty intervals
shadealpha
transparency parameter used to make default shadecol values (see
?rgb for more info)
legendlabels
optional vector of labels to include in legend. Default is 'model1','model2',etc.
legendloc
location of legend. See ?legend for more info.
btarg
target biomass value at which to show a line (set to 0 to remove)
minbthresh
minimum biomass threshhold at which to show a line (set to 0 to remove)
pwidth
width of plot written to PNG file
pheight
height of plot written to PNG file
res
resolution for PNG file
ptsize
ptsize for PNG file
cex.main
character expansion for plot titles
plotdir
directory where PNG or PDF files will be written. By default it will
be the directory where the model was run.
densitynames
vector of names of parameters or derived quantities contained in
summaryoutput$pars$Label or summaryoutput$quants$Label for which to
make density plots
densityxlabs
vector of x-axis labels to use in the density plots (must be equal
in length to densitynames)
densityscale
scalar for upper y-limit in density plots (values below 1 will cut
of top of highest peaks to provide better contrast among broader
distributions
new
create new empty plot window (Windows only)
verbose
report progress to R GUI?