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Plot catch related quantities.

Source: R/SSplotCatch.R
SSplotCatch.Rd

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 = NULL,
  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", "(t)", "(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 fleetnames used in data file.

lwd

Line width for plot elements.

areacols

Optional vector of colors for each area if model has multiple areas. NULL value will be replaced by a default set of areas.

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 files will be written.

showlegend

Put legend on plot

legendloc

Location of legend. Either a string like "topleft" or a vector of two numeric values representing the fraction of the maximum in the x and y dimensions, respectively. See help("legend") for more info on the string options.

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

Default width of plots printed to files in units of punits.

pheight

Height of plots printed to png files in units of punits. Default is designed to allow two plots per page, with pheight_tall used for plots that work best with a taller format and a single plot per page.

punits

Units for pwidth and pheight. Can be "px" (pixels), "in" (inches), "cm" (centimeters), or "mm" (millimeters). The default is punits="in".

res

Resolution of plots printed to files. The default is res = 300.

ptsize

Point size for plotted text in plots printed to files (see help("png") in R for details).

cex.main

Character expansion for plot titles. The default is cex.main=1.

verbose

A logical value specifying if output should be printed to the screen.

See also

SS_plots(), SS_output()

Author

Ian Taylor, Ian Stewart