make_multifig_sexratio: Create multi-figure sex ratio plots.

In r4ss: R Code for Stock Synthesis

Create multi-figure sex ratio plots.

Description

Modified version of make_multifig() for multi-figure plots of sex ratio data with crude confidence intervals (+/i 1 se) and fits from Stock Synthesis output.

Usage

make_multifig_sexratio(
  dbase,
  sexratio.option = 2,
  CI = 0.75,
  sampsizeround = 1,
  maxrows = 6,
  maxcols = 6,
  rows = 1,
  cols = 1,
  fixdims = TRUE,
  main = "",
  cex.main = 1,
  xlab = "",
  ylab = "Fraction female",
  horiz_lab = "default",
  xbuffer = c(0.1, 0.1),
  ybuffer = "default",
  yupper = NULL,
  datonly = FALSE,
  showsampsize = TRUE,
  showeffN = TRUE,
  axis1 = NULL,
  axis2 = NULL,
  ptscex = 1,
  ptscol = gray(0.5),
  linescol = 4,
  lty = 1,
  lwd = 2,
  nlegends = 3,
  legtext = list("yr", "sampsize", "effN"),
  legx = "default",
  legy = "default",
  legadjx = "default",
  legadjy = "default",
  legsize = c(1.2, 1),
  legfont = c(2, 1),
  ipage = 0,
  multifig_oma = c(5, 5, 5, 2) + 0.1,
  ...
)

Arguments

dbase	element of list created by SS_output() passed from SSplotSexRatio()
sexratio.option	code to choose among (1) female:male ratio or (2) fraction females out of the total (the default)
CI	confidence interval for uncertainty
sampsizeround	rounding level for sample size values
maxrows	maximum (or fixed) number or rows of panels in the plot
maxcols	maximum (or fixed) number or columns of panels in the plot
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 elements in yr input.
main	title of plot
cex.main	character expansion for title
xlab	x-axis label
ylab	y-axis label
horiz_lab	axis labels set horizontal all the time (TRUE), never (FALSE) or only when relatively short ("default")
xbuffer	extra space around points on the left and right as fraction of total width of plot
ybuffer	extra space around points on the bottom and top as fraction of total height of plot. "default" will cause c(0,.15) for sexratio.option=1 and c(.15, .3) for sexratio.option=2.
yupper	upper limit on ymax (applied before addition of ybuffer)
datonly	make plots of data without fits?
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
ptscex	character expansion factor for points (default=1)
ptscol	color for points/bars
linescol	color for fitted model
lty	line type
lwd	line width
nlegends	number of lines of text to add as legends in each plot
legtext	text in legend, a list of length=nlegends. values may be any of 1. "yr", 2. "sampsize", 3. "effN", or a vector of length = ptsx.
legx	vector of length=nlegends of x-values of legends (default is first one on left, all after on right)
legy	vector of length=nlegends of y-values of legends (default is top for all plots)
legadjx	left/right adjustment of legends around legx
legadjy	left/right adjustment of legends around legy
legsize	font size for legends. default=c(1.2,1.0) (larger for year and normal for others)
legfont	font type for legends, same as "font" under ?par
ipage	which page of plots when covering more than will fit within maxrows by maxcols.
multifig_oma	vector of outer margins. Can be input to SS_plots and will be passed to this function via the ... argument.
...	additional arguments (NOT YET IMPLEMENTED).

Details

The SE of the sex ratio is crude and calculated as follows. First, assume a multinomial which as MLEs of proportions. Then use the delta method of the ratio F/M, using the MLE as the expected values and analytical variances and covariance between F and M. After some algebra this calculation reduces to: SE(F/M)= sqrt((f/m)^2*( (1-f)/(f*N) + (1-m)/(m*N) +2/N )). Confidence intervals created from these should be considered very crude and would not necessarily be appropriate for future alternative compositional likelihoods.

This function was derived from make_multifig and hence has a lot of overlap in functionality and arguments.

Author(s)

Cole Monnahan. Adapted from make_multifig().

See Also

SS_plots(),SSplotSexRatio()

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