make_multifig: Create multi-figure plots.

In r4ss: R Code for Stock Synthesis

Create multi-figure plots.

Description

Function created as an alternative to lattice package for multi-figure plots of composition data and fits from Stock Synthesis output.

Usage

make_multifig(
  ptsx,
  ptsy,
  yr,
  linesx = 0,
  linesy = 0,
  ptsSD = 0,
  sampsize = 0,
  effN = 0,
  showsampsize = TRUE,
  showeffN = TRUE,
  sampsize_label = "N=",
  effN_label = "effN=",
  sampsizeround = 1,
  maxrows = 6,
  maxcols = 6,
  rows = 1,
  cols = 1,
  fixdims = TRUE,
  main = "",
  cex.main = 1,
  xlab = "",
  ylab = "",
  size = 1,
  cexZ1 = 1.5,
  bublegend = TRUE,
  maxsize = NULL,
  do.sqrt = TRUE,
  minnbubble = 8,
  allopen = TRUE,
  xbuffer = c(0.1, 0.1),
  ybuffer = c(0, 0.15),
  yupper = NULL,
  ymin0 = TRUE,
  xlas = 0,
  ylas = NULL,
  axis1 = NULL,
  axis2 = NULL,
  axis1labs = NULL,
  linepos = 1,
  type = "o",
  polygons = TRUE,
  bars = FALSE,
  barwidth = "default",
  ptscex = 1,
  ptscol = 1,
  ptscol2 = 1,
  colvec = c(rgb(1, 0, 0, 0.7), rgb(0, 0, 1, 0.7), rgb(0.1, 0.1, 0.1, 0.7)),
  linescol = c(rgb(0, 0.8, 0, 0.7), rgb(1, 0, 0, 0.7), rgb(0, 0, 1, 0.7)),
  lty = 1,
  lwd = 2,
  pch = 1,
  nlegends = 3,
  legtext = list("yr", "sampsize", "effN"),
  legx = "default",
  legy = "default",
  legadjx = "default",
  legadjy = "default",
  legsize = c(1.2, 1),
  legfont = c(2, 1),
  venusmars = TRUE,
  sampsizeline = FALSE,
  effNline = FALSE,
  sampsizemean = NULL,
  effNmean = NULL,
  ipage = 0,
  scalebins = FALSE,
  sexvec = NULL,
  multifig_colpolygon = grey(c(0.6, 0.8, 0.7), alpha = 0.7),
  multifig_oma = NULL,
  ...
)

Arguments

ptsx	vector of x values for points or bars
ptsy	vector of y values for points or bars of same length as ptsx
yr	vector of category values (years) of same length as ptsx
linesx	optional vector of x values for lines
linesy	optional vector of y values for lines
ptsSD	optional vector of standard deviations used to plot error bars on top of each point under the assumption of normally distributed error
sampsize	optional sample size vector of same length as ptsx
effN	optional effective sample size vector of same length as ptsx
showsampsize	show sample size values on plot?
showeffN	show effective sample size values on plot?
sampsize_label	label on sampsize
effN_label	label on effN
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
size	vector of bubbles sizes if making a bubble plot
cexZ1	Character expansion (cex) for point associated with value of 1.
bublegend	Add legend with example bubble sizes to bubble plots.
maxsize	maximum size of bubbles
do.sqrt	scale bubbles based on sqrt of size vector. see ?bubble3 for more info.
minnbubble	number of unique x values before adding buffer. see ?bubble3 for more info.
allopen	should all bubbles be open? see ?bubble3 for more info.
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
yupper	upper limit on ymax (applied before addition of ybuffer)
ymin0	fix minimum y-value at 0?
xlas	label style (las) input for x-axis. Default 0 has horizontal labels, input 2 would provide vertical lables.
ylas	label style (las) input for y-axis. Default NULL has horizontal labels when all labels have fewer than 6 characters and vertical otherwise. Input 0 would force vertical labels, and 1 would force horizontal.
axis1	optional position of bottom axis values
axis2	optional position of left size axis values
axis1labs	optional vector of labels for axis1 (either NULL or needs to match length of axis1)
linepos	should lines be added on top of points (linepos=1) or behind (linepos=2)? A value of linepos = 0 will result in no line.
type	type of line/points used for observed values (see 'type' in ?plot for details) on top of a grey polygon. Default is "o" for overplotting points on lines.
polygons	should polygons be added to the (turning off is required for sex-ratio plot)
bars	should the ptsx/ptsy values be bars instead of points (TRUE/FALSE) NOT CURRENTLY FUNCTIONAL
barwidth	width of bars in barplot, default method chooses based on quick and dirty formula also, current method of plot(...type='h') could be replaced with better approach
ptscex	character expansion factor for points (default=1)
ptscol	color for points/bars
ptscol2	color for negative value points in bubble plots
colvec	Vector of length 3 with colors for females, males, unsexed fish
linescol	color for lines
lty	line type
lwd	line width
pch	point character type
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
venusmars	Label females and males with venus and mars symbols?
sampsizeline	show line for input sample sizes on top of conditional age-at-length plots (TRUE/FALSE/scalar, still in development)
effNline	show line for effective sample sizes on top of conditional age-at-length plots (TRUE/FALSE/scalar, still in development)
sampsizemean	mean input sample size value (used when sampsizeline=TRUE)
effNmean	mean effective sample size value (used when effNline=TRUE)
ipage	which page of plots when covering more than will fit within maxrows by maxcols.
scalebins	Rescale expected and observed proportions by dividing by bin width for models where bins have different widths? Caution!: May not work correctly in all cases.
sexvec	vector of sex codes if more than one present (otherwise NULL)
multifig_colpolygon	vector of polygon fill colors of length 3 (for females, males, and unsexed fish). Can be input to SS_plots and will be passed to this function via the ... argument.
multifig_oma	vector of outer margins. Can be input to SS_plots and will be passed to this function via the ... argument.
...	additional arguments passed to par.

Author(s)

Ian Taylor

See Also

SS_plots(),SSplotComps()

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