SSplotSpawnrecruit: Plot spawner-recruit curve.

In r4ss: R Code for Stock Synthesis

Plot spawner-recruit curve.

Description

Plot spawner-recruit curve based on output from Stock Synthesis model.

Usage

SSplotSpawnrecruit(
  replist,
  subplot = 1:3,
  add = FALSE,
  plot = TRUE,
  print = FALSE,
  xlim = NULL,
  ylim = NULL,
  labels = c("Spawning biomass (mt)", "Recruitment (1,000s)", "Spawning output",
    expression(paste("Spawning output (relative to ", italic(B)[0], ")")),
    expression(paste("Recruitment (relative to  ", italic(R)[0], ")")),
    "Log recruitment deviation"),
  bioscale = "default",
  plotdir = "default",
  pwidth = 6.5,
  pheight = 6.5,
  punits = "in",
  res = 300,
  ptsize = 10,
  verbose = TRUE,
  colvec = c("blue", "black", "black", gray(0, 0.7)),
  ltyvec = c(1, 2, 1, NA),
  ptcol = "default",
  legend = TRUE,
  legendloc = NULL,
  minyr = "default",
  textmindev = 0.5,
  relative = FALSE,
  expected = TRUE,
  estimated = TRUE,
  bias_adjusted = TRUE,
  show_env = TRUE,
  virg = TRUE,
  init = TRUE,
  forecast = FALSE
)

Arguments

replist	A list object created by SS_output().
subplot	vector of which subplots to show. 1=plot without labels, 2=plot with year labels.
add	add to existing plot?
plot	plot to active plot device?
print	print to PNG files?
xlim	optional control of x range
ylim	optional control of y range
labels	vector containing x-axis label for models with spawning biomass in metric tons, y-axis label, and alternative x-axis for models with a fecundity relationship making spawning output not equal to spawning biomass.
bioscale	multiplier on spawning biomass, set to 0.5 for single-sex models
plotdir	directory where PNG files will be written. by default it will be the directory where the model was run.
pwidth	Default width of plots printed to files in units of punits. The default is pwidth=6.5.
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).
verbose	report progress to R GUI?
colvec	vector of length 4 with colors for 3 lines and 1 set of points (where the 4th value for the points is the color of the circle around the background color provided by ptcol
ltyvec	vector of length 4 with line types for the 3 lines and 1 set of points, where the points are disconnected (lty=NA) by default
ptcol	vector or single value for the color of the points, "default" will by replaced by a vector of colors of length equal to nrow(replist[["recruit"]])
legend	add a legend to the figure?
legendloc	location of legend. By default it is chosen as the first value in the set of "topleft", "topright", "bottomright" that results in no overlap with the points in the plot, but the user can override this with their choice of location. See ?legend for more info on the options.
minyr	minimum year of recruitment deviation to show in plot
textmindev	minimum recruitment deviation for label to be added so only extreme devs are labeled (labels are added to first and last years as well). Default=0.7.
relative	scale both axes so that B0 and R0 are at 1 to show spawning output and recruitment relative to the equilibrium
expected	show line for expected recruitment (stock-recruit curve)
estimated	show points for estimated recruitment values (including deviations)
bias_adjusted	show lines for bias adjusted expected recruitment
show_env	add line for expected recruitment with environmental variability
virg	add point for equilibrium conditions (x=B0,y=R0)
init	add point for initial conditions (x=B1,y=R1), only appears if this point differs from virgin values
forecast	include forecast years in the curve?

Author(s)

Ian Stewart, Ian Taylor

See Also

SS_plots(), SS_output()

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