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r4ss (version 1.44.0)

SSplotSexRatio: 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.

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()