SSplotDynamicB0: Plot Dynamic B0

In r4ss: R Code for Stock Synthesis

Plot Dynamic B0

Description

Plots the spawning output with and without fishing mortality

Usage

SSplotDynamicB0(
  replist,
  ylab = "Spawning biomass (mt)",
  equilibrium = TRUE,
  forecast = FALSE,
  yrs = "all",
  plot = TRUE,
  print = FALSE,
  plotdir = "default",
  verbose = TRUE,
  uncertainty = TRUE,
  legend = TRUE,
  legendlabels = c("equilibrium", "without fishing", "with fishing"),
  legendloc = "bottom",
  col = c("blue", "red"),
  lty = 1,
  lwd = 2,
  add = FALSE,
  pwidth = 6.5,
  pheight = 5,
  punits = "in",
  res = 300,
  ptsize = 10,
  mainTitle = FALSE,
  mar = NULL
)

Arguments

replist	A list object created by SS_output().
ylab	Y-axis label. Default is "Spawning biomass (mt)" which is replaced by "Spawning output" for models with replist[["SpawnOutputUnits"]] == "numbers"
equilibrium	Show equilibrium in plot? Applies whether "yrs" is specified or not.
forecast	Show forecast years in plot? Only applies if yrs = "all".
yrs	Which years to include. Default "all" will show startyr to endyr + 1 modified by the arguments forecast.
plot	Plot to active plot device?
print	Print to PNG files?
plotdir	Directory where PNG files will be written. By default it will be the directory where the model was run.
verbose	A logical value specifying if output should be printed to the screen.
uncertainty	Show 95% uncertainty intervals around point estimates? These intervals will only appear when uncertainty in the dynamic B0 estimates is available via the control file settings for "read specs for more stddev reporting".
legend	Add a legend?
legendlabels	Character vector with labels for the unfished equilibrium point (if equilibrium = TRUE) and the two lines showing spawning biomass or output without and with fishing.
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.
col	Optional vector of colors to be used for the two lines (single value will apply to both lines).
lty	Optional vector of line types to be used for the two lines (single value will apply to both lines).
lwd	Optional vector of line widths to be used for the two lines (single value will apply to both lines).
add	add to existing plot
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).
mainTitle	Logical indicating if a title should be included at the top (not yet implemented for all plots)
mar	Either NULL to allow the default (which depends on whether the main title is included or not) or a numerical vector of the form c(bottom, left, top, right) which gives the number of lines of margin to be specified on the four sides of the plot, which is passed to par().

Author(s)

Ian G. Taylor

See Also

SSplotTimeseries()

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