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Plot Dynamic B0

Source: R/SSplotDynamicB0.R
SSplotDynamicB0.Rd

Plots the spawning output with and without fishing mortality

Usage

SSplotDynamicB0(
  replist,
  ylab = "Spawning biomass (t)",
  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 (t)" which is replaced by replist[["SpawnOutputLabel"]] 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.

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.

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().

See also

SSplotTimeseries()

Author

Ian G. Taylor