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Create multi-figure sex ratio plots.

Source: R/make_multifig_sexratio.R
make_multifig_sexratio.Rd

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 plot titles. The default is cex.main=1.

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 for plot elements.

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.

See also

SS_plots(),SSplotSexRatio()

Author

Cole Monnahan. Adapted from make_multifig().