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Plot Spawning Potential Ratio (SPR) quantities.

Source: R/SSplotSPR.R
SSplotSPR.Rd

Plot time series of SPR, 1-SPR, the chosen SPR ratio and the phase plot.

Usage

SSplotSPR(
  replist,
  add = FALSE,
  plot = TRUE,
  print = FALSE,
  uncertainty = TRUE,
  subplots = 1:4,
  forecastplot = FALSE,
  col1 = "black",
  col2 = "blue",
  col3 = "green3",
  col4 = "red",
  sprtarg = "default",
  btarg = "default",
  minbthresh = "default",
  labels = c("Year", "SPR", "1-SPR", "Relative fishing intensity",
    "Relative spawning output"),
  pwidth = 6.5,
  pheight = 5,
  pheight_tall = 5,
  punits = "in",
  res = 300,
  ptsize = 10,
  cex.main = 1,
  plotdir = "default",
  verbose = TRUE
)

Arguments

replist

A list object created by SS_output().

add

add to existing plot (not yet implemented)

plot

Plot to active plot device?

print

Print to PNG files?

uncertainty

include plots showing uncertainty?

subplots

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

  1. timeseries of SPR,

  2. timeseries of 1 - SPR,

  3. timeseries of SPR ratio (as specified in the starter file), and

  4. phase plot of Biomass ratio vs SPR ratio (as specified in the starter file).

forecastplot

Include forecast years in plot?

col1

first color used

col2

second color used

col3

third color used

col4

fourth color used

sprtarg

F/SPR proxy target. "default" chooses based on model output, where models which have SPR_report_basis = 0 or 1 specified in the starter file will use the SPR target specified in the forecast file. Models which have SPR_report_basis = 2 will use SPR at MSY for the SPR target and models which have the SPR_report_basis = 3 will use SPR at Btarget for the SPR target in these plots. Zero or negative values of sprtarg input here will cause no horizontal line to be plotted.

btarg

target depletion to be used in plots showing depletion. May be omitted by setting to NA. "default" chooses based on model output.

minbthresh

minimum biomass threshold to be used in plots showing depletion. May be omitted by setting to NA. "default" chooses based on model output.

labels

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

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.

pheight_tall

Height of tall plots printed to png files in units of punits, where the tall plots are a subset of the plots which typically work best in a taller format.

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.

plotdir

Directory where PNG files will be written.

verbose

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

See also

SS_plots(), SS_output()

Author

Ian Stewart, Ian Taylor