Plot timeseries data contained in TIME_SERIES output from Stock Synthesis report file. Some values have optional uncertainty intervals.
SSplotTimeseries(replist, subplot, add = FALSE, areas = "all",
areacols = "default", areanames = "default", forecastplot = TRUE,
uncertainty = TRUE, bioscale = 1, minyr = -Inf, maxyr = Inf,
plot = TRUE, print = FALSE, plotdir = "default", verbose = TRUE,
btarg = "default", minbthresh = "default", xlab = "Year",
labels = NULL, pwidth = 6.5, pheight = 5, punits = "in",
res = 300, ptsize = 10, cex.main = 1)list created by SS_output
number controlling which subplot to create
add to existing plot? (not yet implemented)
optional subset of areas to plot for spatial models
vector of colors by area. Default uses rich.colors by Arni Magnusson
names for areas. Default is to use Area1, Area2,...
add points from forecast years
add intervals around quantities for which uncertainty is available
scaling for spawning biomass. Default = 1. Previously this was set to 0.5 for single-sex models, and 1.0 for all others, but now single-sex models are assumed to use the -1 option for Nsexes in the data file so the scaling is done automatically by SS.
optional input for minimum year to show in plots
optional input for maximum year to show in plots
plot to active plot device?
print to PNG files?
directory where PNG or PDF files will be written. by default it will be the directory where the model was run.
report progress to R GUI?
Target depletion to be used in plots showing depletion. May be omitted by setting to 0. "default" chooses value based on modeloutput.
Threshold depletion to be used in plots showing depletion. May be omitted by setting to 0. "default" assumes 0.25 unless btarg in model output is 0.25 in which case minbthresh = 0.125 (U.S. west coast flatfish).
x axis label for all plots
vector of labels for plots (titles and axis labels)
width of plot
height of plot
units for PNG file
resolution for PNG file
point size for PNG file
character expansion for plot titles