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,
mainTitle = FALSE,
mar = NULL
)A list object created by SS_output().
number controlling which subplot to create
Numbering of subplots is as follows, where the spawning biomass plots
(7 to 10) are provided first when this function is called by SS_plots():
1 Total biomass (mt) with forecast
2 Total biomass by area (spatial models only)
3 Total biomass (mt) at beginning of spawning season with forecast
4 Summary biomass (mt) with forecast
5 Summary biomass (mt) by area (spatial models only)
6 Summary biomass (mt) at beginning of season 1 with forecast
7 Spawning output with forecast with ~95% asymptotic intervals
8 Spawning output by area (spatial models only)
9 Relative spawning output with forecast with ~95% asymptotic intervals
10 Relative spawning output by area (spatial models only)
11 Age-0 recruits (1,000s) with forecast with ~95% asymptotic intervals
12 Age-0 recruits by area (spatial models only)
13 Fraction of recruits by area (spatial models only)
14 Age-0 recruits (1,000s) by birth season with forecast
15 Fraction of total Age-0 recruits by birth season with forecast
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 of plots printed to files.
The default is res = 300.
point size for PNG file
character expansion for plot titles
Logical indicating if a title should be included at the top (not yet implemented for all plots)
Either NULL to allow the default (which depends on whether the main title is included or not) or a numerical vector of the form c(bottom, left, top, right) which gives the number of lines of margin to be specified on the four sides of the plot, which is passed to par().