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Plot sex-ratio data and fits for two sex models

Source: R/SSplotSexRatio.R
SSplotSexRatio.Rd

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

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.

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 for plot elements.

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.

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".

ptsize

Point size for plotted text in plots printed to files (see help("png") in R for details).

res

Resolution of plots printed to files. The default is res = 300.

plotdir

Directory where PNG files will be written.

cex.main

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

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

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

mainTitle

Logical indicating if a title should be included at the top (not yet implemented for all plots).

...

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()

Author

Cole Monnahan, Ian Taylor