SSplotIndices: Plot indices of abundance and associated quantities.
In r4ss: R code for Stock Synthesis

Description Usage Arguments Author(s) See Also

Plot indices of abundance and associated quantities.

SSplotIndices(replist,subplots=1:9,
  plot=TRUE,print=FALSE,
  fleets="all",fleetnames="default",
  smooth=TRUE,add=FALSE,datplot=FALSE,
  labels=c("Year",         
    "Index",               
    "Observed index",      
    "Expected index",      
    "Log index",           
    "Log observed index",  
    "Log expected index",  
    "Standardized index",  
    "Catchability (Q)",    
    "Time-varying catchability",
    "Vulnerable biomass",
    "Catchability vs. vulnerable biomass"),
  col1="default", col2="default", col3="blue", col4="red",
  pch1=1, pch2=16, cex=1,
  legend=TRUE, legendloc="topright", seasnames=NULL,
  pwidth=7,pheight=7,punits="in",res=300,ptsize=12,cex.main=1,
  addmain=TRUE, plotdir="default",
  minyr = NULL, maxyr = NULL, verbose=TRUE)

`replist`	list created by `SS_output`
`subplots`	vector controlling which subplots to create
`plot`	plot to active plot device?
`print`	print to PNG files?
`fleets`	optional vector to subset fleets for which plots will be made
`fleetnames`	optional replacement for fleenames used in data file
`smooth`	add smoothed line to plots of observed vs. expected sample sizes
`add`	add to existing plot (not yet implemented)
`datplot`	make plot of data only?
`labels`	vector of labels for plots (titles and axis labels)
`col1`	vector of colors for points in each season for time series plot. Default is red for single season models and a rainbow using the rich.colors.short function for multiple seasons.
`col2`	vector of colors for points in each season for obs. vs. exp. plot. Default is blue for single season models and a rainbow using the rich.colors.short function for multiple seasons.
`col3`	color of line showing expected index in time series plot. Default is blue.
`col4`	color of smoother shown in obs. vs. exp. plots. Default is red.
`pch1`	single value or vector of plotting characters (pch parameter) for time-series plots of index fit. Default=1.
`pch2`	single value or vector of plotting characters (pch parameter) for sample size plots of index fit. Default=16.
`cex`	character expansion factor for points showing observed values. Default=1.
`legend`	add a legend to seasonal colors (only for seasonal models)
`legendloc`	add a legend to seasonal colors (default is "topright")
`seasnames`	optional vector of names for each season to replace defaults if a legend is used
`pwidth`	width of plot written to PNG file
`pheight`	height of plot written to PNG file
`punits`	units for PNG file
`res`	resolution for PNG file
`ptsize`	ptsize for PNG file
`cex.main`	character expansion for plot titles
`addmain`	switch which allows the plot title to be left off
`plotdir`	directory where PNG files will be written. by default it will be the directory where the model was run.
`minyr`	First year to show in plot (for zooming in on a subset of values)
`maxyr`	Last year to show in plot (for zooming in on a subset of values)
`verbose`	report progress to R GUI?