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

In r4ss: R Code for Stock Synthesis

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

Brown, L.; Cai, T. Tony; DasGupta, A. (2001). Interval Estimation for a Binomial Proportion. Statistical Science. 16(2): 101-133. http://www.jstor.org/stable/2676784.

See Also

SS_plots(), make_multifig_sexratio()

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