R: Plot sex-ratio data and fits for two sex models

SSplotSexRatio {r4ss}

R Documentation

Plot sex-ratio data and fits for two sex models

Description

Plot sex-ratio data and fits from Stock Synthesis output. Multi-figure plots depend on make_multifig. The confidence intervals around the observed points are based on a Jeffreys interval calculated from the adjusted input sample size (with a floor of 1).

Usage

SSplotSexRatio(
  replist,
  kind = "AGE",
  sexratio.option = 2,
  CI = 0.75,
  plot = TRUE,
  print = FALSE,
  fleets = "all",
  fleetnames = "default",
  yupper = 4,
  datonly = FALSE,
  linescol = rgb(0.6, 0, 0.9, 0.7),
  lwd = 2,
  showsampsize = TRUE,
  showeffN = TRUE,
  axis1 = NULL,
  axis2 = NULL,
  pwidth = 6.5,
  pheight = 5,
  punits = "in",
  ptsize = 10,
  res = 300,
  plotdir = "default",
  cex.main = 1,
  labels = c("Length (cm)", "Age (yr)", "Sex ratio (females:males)", "Fraction female"),
  maxrows = 6,
  maxcols = 6,
  rows = 1,
  cols = 1,
  fixdims = TRUE,
  verbose = TRUE,
  mainTitle = FALSE,
  ...
)

Arguments

`replist`	A list object created by `SS_output()`.
`kind`	indicator of type of plot can be "LEN", "SIZE", "AGE", "cond", "GSTAGE", "L@A", or "W@A".
`sexratio.option`	code to choose among (1) female:male ratio or (2) fraction females out of the total
`CI`	confidence interval for uncertainty
`plot`	plot to active plot device?
`print`	print to PNG files?
`fleets`	optional vector to subset fleets for which plots will be made
`fleetnames`	optional vector of fleet names to put in the labels
`yupper`	upper limit on ymax (only applies for sexratio.option == 1)
`datonly`	make plots of data without fits?
`linescol`	Color for line showing expected value (default is purple).
`lwd`	line width
`showsampsize`	add sample sizes to plot
`showeffN`	add effective sample sizes to plot
`axis1`	position of bottom axis values
`axis2`	position of left size axis values
`pwidth`	default width of plots printed to files in units of `punits`. Default=7.
`pheight`	default height width of plots printed to files in units of `punits`. Default=7.
`punits`	units for `pwidth` and `pheight`. Can be "px" (pixels), "in" (inches), "cm" or "mm". Default="in".
`ptsize`	point size for plotted text in plots printed to files (see help("png") in R for details). Default=12.
`res`	Resolution of plots printed to files. The default is `res = 300`.
`plotdir`	directory where PNG files will be written. by default it will be the directory where the model was run.
`cex.main`	character expansion parameter for plot titles
`labels`	vector of labels for plots (titles and axis labels)
`maxrows`	maximum (or fixed) number or rows of panels in the plot
`maxcols`	maximum (or fixed) number or columns of panels in the plot plots
`rows`	number or rows to return to as default for next plots to come or for single plots
`cols`	number or cols to return to as default for next plots to come or for single plots
`fixdims`	fix the dimensions at maxrows by maxcols or resize based on number of years of data
`verbose`	return updates of function progress to the R GUI?
`mainTitle`	Logical indicating if a title for the plot should be produced
`...`	additional arguments that will be passed to the plotting.

Author(s)

Cole Monnahan, Ian Taylor

References