Usage
SSplotComparisons(summaryoutput,subplots=1:20,
plot=TRUE,print=FALSE,png=print,pdf=FALSE,
models="all",
endyrvec="default",
indexfleets=NULL,
indexUncertainty=FALSE,
indexQlabel = TRUE,
indexQdigits = 4,
indexSEvec="default",
indexPlotEach=FALSE,
labels=c("Year",
"Spawning biomass (mt)",
"Spawning depletion",
"Age-0 recruits (1,000s)",
"Recruitment deviations",
"Index",
"Log index",
"SPR ratio",
"Density",
"Management target",
"Minimum stock size threshold"),
col="default", shadecol="default",
pch="default", lty=1, lwd=2,
spacepoints = 10, staggerpoints = 1,
xlim="default", ylimAdj=1,
xaxs="r", yaxs="r",
type="o", uncertainty=TRUE, shadealpha=0.1,
legend=TRUE, legendlabels="default", legendloc="topright",
legendorder="default",legendncol=1,
btarg=0.4, minbthresh=0.25, sprtarg=1,
pwidth=7,pheight=7,punits="in",res=300,ptsize=12,cex.main=1,
plotdir=NULL,
densitynames=c("SPB_Virgin","R0"),
densityxlabs="default",
densityscalex=1,
densityscaley=1,
densityadjust=1,
densitysymbols = TRUE,
densitytails = TRUE,
fix0=TRUE,
new=TRUE,
add=FALSE,
par = list(mar = c(5, 4, 1, 1) + 0.1),
verbose=TRUE,
mcmcVec="default")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?
png
Has same result as print, included for consistency with
SS_plots.
pdf
Write output to PDF file? Can't be used in conjunction with
png or print.
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. By default it is set to the ending
year specified in 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.
indexQlabel
Add catchability to legend in plot of index fits (TRUE/FALSE)?
indexQdigits
Number of significant digits for catchability in legend
(if indexQlabel=TRUE)
indexSEvec
Optional replacement for the SE values in summaryoutput$indices to
deal with the issue of differing uncertainty by models described
above.
indexPlotEach
TRUE plots the observed index for each model with colors,
or FALSE just plots observed once in black dots.
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
spacepoints
Number of years between points shown on top of lines (for long
timeseries, points every year get mashed together)
staggerpoints
Number of years to stagger the first point
(if spacepoints > 1) for each line
(so that adjacent lines have points in different years)
ylimAdj
Multiplier for ylim parameter. Allows additional white space to fit
legend if necessary. Default=1.
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.
legendorder
Optional vector of model numbers that can be used to have the legend
display the model names in an order that is different than that
which is represented in the summary input object.
legendncol
Number of columns for the legend.
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)
sprtarg
Target value for SPR-ratio where line is drawn in the SPR plots and
phase plot.
pwidth
Width of plot written to PNG file
pheight
Height of plot written to PNG file
res
Resolution for PNG file
ptsize
Point size 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 (or subset of names) of parameters or derived
quantities contained in summaryoutput$pars$Label or
summaryoutput$quants$Label for which to make density plots
densityxlabs
Optional vector of x-axis labels to use in the density plots (must
be equal in length to the printed vector of quantities that match
the densitynames input)
densityscalex
Scalar for upper x-limit in density plots (values below 1 will cut
off the right tail to provide better contrast among narrower
distributions
densityscaley
Scalar for upper y-limit in density plots (values below 1 will cut
off top of highest peaks to provide better contrast among broader
distributions
densityadjust
Multiplier on bandwidth of kernel in density function used for
smoothing MCMC posteriors. See 'adjust' in ?density for details.
densitysymbols
Add symbols along lines in density plots. Quantiles are
c(0.025,0.1,0.25,0.5,0.75,0.9,0.975).
densitytails
Shade tails outside of 95% interval in density plots.
fix0
Always include 0 in the density plots?
new
Create new empty plot window
add
Allows single plot to be added to existing figure. This needs to be
combined with specific 'subplots' input to make sure only one thing
gets added.
par
list of graphics parameter values passed to the par function
verbose
Report progress to R GUI?
mcmcVec
Vector of TRUE/FALSE values (or single value) indicating whether
input values are from MCMC or to use normal distribution around MLE