R: Create multi-figure sex ratio plots.

make_multifig_sexratio {r4ss}

R Documentation

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)