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Plot yield and surplus production.

Source: R/SSplotYield.R
SSplotYield.Rd

Plot yield and surplus production from Stock Synthesis output. Surplus production is based on Walters et al. (2008).

Usage

SSplotYield(
  replist,
  subplots = 1:5,
  refpoints = c("MSY", "Btgt", "SPR", "Current"),
  add = FALSE,
  plot = TRUE,
  print = FALSE,
  labels = c("Fraction unfished", "Equilibrium yield (t)", "Total biomass (t)",
    "Surplus production (t)", "Yield per recruit (kg)", "Spawning output"),
  col = "blue",
  col2 = "black",
  lty = 1,
  lwd = 2,
  cex.main = 1,
  pwidth = 6.5,
  pheight = 5,
  punits = "in",
  res = 300,
  ptsize = 10,
  plotdir = "default",
  verbose = TRUE
)

Arguments

replist

A list object created by SS_output().

subplots

vector controlling which subplots to create Numbering of subplots is as follows:

  • 1 yield curve

  • 2 yield curve with reference points

  • 3 surplus production vs. total biomass plots (Walters et al. 2008)

  • 4 surplus production vs. spawning biomass plots (Forrest et al. 2023)

  • 5 yield per recruit plot

refpoints

character vector of which reference points to display in subplot 2, from the options 'MSY', 'Btgt', and 'SPR'.

add

add to existing plot? (not yet implemented)

plot

Plot to active plot device?

print

Print to PNG files?

labels

Vector of labels for plots (titles and axis labels).

col

line color for equilibrium plot

col2

line color for dynamic surplus production plot

lty

line type (only applied to equilibrium yield plot at this time)

lwd

Line width for plot elements.

cex.main

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

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).

plotdir

Directory where PNG files will be written.

verbose

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

References

Walters, Hilborn, and Christensen, 2008, Surplus production dynamics in declining and recovering fish populations. Can. J. Fish. Aquat. Sci. 65: 2536-2551. https://doi.org/10.1139/F08-170.

Forrest, Kronlund, Cleary, and Grinnell. 2023. An evidence-based approach for selecting a limit reference point for Pacific herring (Clupea pallasii) stocks in British Columbia, Canada. Can. J. Fish. Aquat. Sci. 80: 1071-1083. https://doi.org/10.1139/cjfas-2022-0168.

See also

SS_plots(), SS_output()

Author

Ian Stewart, Ian Taylor