SSplotCatch: Plot catch related quantities.

In r4ss: R Code for Stock Synthesis

Plot catch related quantities.

Description

Plot catch related quantities from Stock Synthesis output. Plots include harvest rate, continuous F, landings, and discard fraction.

Usage

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
)

Arguments

replist	A list object created by SS_output().
subplots	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	Add to existing plot? (not yet implemented)
areas	Optional subset of areas to plot for spatial models
plot	Plot to active plot device?
print	Print to PNG files?
type	Type parameter passed to plot function. Default "l" is lines only. Other options include "o" for overplotting points on lines.
fleetlty	Vector of line type by fleet
fleetpch	Vector of plot character by fleet
fleetcols	Vector of colors by fleet
fleetnames	Optional replacement for fleenames used in data file, should include all fleets (not just those with catch)
lwd	Line width
areacols	Vector of colors by area. Default uses rich.colors by Arni Magnusson
areanames	Names for areas. Default is to use Area1, Area2,...
minyr	Optional input for minimum year to show in plots
maxyr	Optional input for maximum year to show in plots
annualcatch	Include plot of catch aggregated across seasons within each year
forecastplot	Add points from forecast years
plotdir	Directory where PNG or PDF files will be written. By default it will be the directory where the model was run.
showlegend	Put legend on plot
legendloc	Location of legend (see ?legend for more info)
order	Optional input to change the order of fleets in stacked plots.
xlab	x-label for all plots
labels	Vector of labels for plots (titles and axis labels)
catchasnumbers	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.
catchbars	Show catch by fleet as barplot instead of stacked polygons? (default=TRUE)
addmax	Add a point on the y-axis for the maximum catch (default=TRUE)
ymax	Optional input for ymax value (can be used to add or subtract white space at the top of the figure)
pwidth	Width of plot
pheight	Height of plot
punits	Units for PNG file
res	Resolution of plots printed to files. The default is res = 300.
ptsize	point size for PNG file
cex.main	Character expansion for plot titles
verbose	Report progress to R console?

Author(s)

Ian Taylor, Ian Stewart

See Also

SS_plots(), SS_output()

r4ss documentation built on May 28, 2022, 1:11 a.m.