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Plot fit to discard fraction.

Source: R/SSplotDiscard.R
SSplotDiscard.Rd

Plot fit to discard fraction from Stock Synthesis output file.

Usage

SSplotDiscard(
  replist,
  subplots = 1:2,
  plot = TRUE,
  print = FALSE,
  plotdir = "default",
  fleets = "all",
  fleetnames = "default",
  datplot = FALSE,
  labels = c("Year", "Discard fraction", "Total discards", "for"),
  yhi = 1,
  ymax = NULL,
  col1 = "blue",
  col2 = "black",
  pwidth = 6.5,
  pheight = 5,
  punits = "in",
  res = 300,
  ptsize = 10,
  cex.main = 1,
  verbose = TRUE
)

Arguments

replist

A list object created by SS_output().

subplots

Vector of which plots to make (1 = data only, 2 = with fit). If plotdat = FALSE then subplot 1 is not created, regardless of choice of subplots.

plot

Plot to active plot device?

print

Print to PNG files?

plotdir

Directory where PNG files will be written.

fleets

Either the string "all", or a vector of numerical values, like c(1,3), listing fleets or surveys to be included in the plot.

fleetnames

Optional replacement for fleetnames used in data file.

datplot

Make data-only plot of discards? This can override the choice of subplots.

labels

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

yhi

Maximum y-value which will always be included in the plot (all data included regardless). Default = 1 so that discard fractions are always plotted on a 0-1 range, but total discard amounts which are greater than this value will exceed it.

ymax

Optional maximum y-value to include (useful if upper tails on discard amounts are very high)

col1

First color to use in plot (for expected values)

col2

Second color to use in plot (for observations and intervals)

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).

cex.main

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

verbose

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

See also

SS_plots()

Author

Ian G. Taylor, Ian J. Stewart, Robbie L. Emmet