Plot catch related quantities from Stock Synthesis output. Plots include harvest rate, continuous F, landings, and discard fraction.
SSplotCatch(
replist,
subplots = 1:16,
add = FALSE,
areas = 1,
plot = TRUE,
print = FALSE,
type = "l",
fleetlty = 1,
fleetpch = 1,
fleetcols = "default",
fleetnames = "default",
lwd = 3,
areacols = "default",
areanames = "default",
minyr = -Inf,
maxyr = Inf,
annualcatch = TRUE,
forecastplot = FALSE,
plotdir = "default",
showlegend = TRUE,
legendloc = "topleft",
order = "default",
xlab = "Year",
labels = c("Harvest rate/Year", "Continuous F", "Landings", "Total catch",
"Predicted discards", "Discard fraction", "(mt)", "(numbers x1000)",
"Observed and expected", "aggregated across seasons"),
catchasnumbers = NULL,
catchbars = TRUE,
addmax = TRUE,
ymax = NULL,
pwidth = 6.5,
pheight = 5,
punits = "in",
res = 300,
ptsize = 10,
cex.main = 1,
verbose = TRUE
)A list object created by SS_output().
Vector controlling which subplots to create Numbering of subplots is as follows,
Basic plots for all models
1 landings
2 landings stacked
3 observed and expected landings (if different)
9 harvest rate
Plots for models with discards
4 total catch (including discards)
5 total catch (including discards) stacked
6 discards
7 discards stacked plot (depends on multiple fleets)
8 discard fraction
16 landings + dead discards
Plots for seasonal models
10 landings aggregated across seasons
11 landings aggregated across seasons stacked
12 total catch (if discards present) aggregated across seasons
13 total catch (if discards present) aggregated across seasons stacked
14 discards aggregated across seasons
15 discards aggregated across seasons stacked
Add to existing plot? (not yet implemented)
Optional subset of areas to plot for spatial models
Plot to active plot device?
Print to PNG files?
Type parameter passed to plot function. Default "l" is lines only. Other options include "o" for overplotting points on lines.
Vector of line type by fleet
Vector of plot character by fleet
Vector of colors by fleet
Optional replacement for fleenames used in data file, should include all fleets (not just those with catch)
Line width
Vector of colors by area. Default uses rich.colors by Arni Magnusson
Names for areas. Default is to use Area1, Area2,...
Optional input for minimum year to show in plots
Optional input for maximum year to show in plots
Include plot of catch aggregated across seasons within each year
Add points from forecast years
Directory where PNG or PDF files will be written. By default it will be the directory where the model was run.
Put legend on plot
Location of legend (see ?legend for more info)
Optional input to change the order of fleets in stacked plots.
x-label for all plots
Vector of labels for plots (titles and axis labels)
Is catch in numbers instead of biomass? Should be set automatically if set to NULL. If fleets include a mix of biomass and numbers, then catch plots should be interpreted carefully.
Show catch by fleet as barplot instead of stacked polygons? (default=TRUE)
Add a point on the y-axis for the maximum catch (default=TRUE)
Optional input for ymax value (can be used to add or subtract white space at the top of the figure)
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
Report progress to R console?