SSplotSelex: Plot selectivity
In r4ss: R code for Stock Synthesis

Description Usage Arguments Author(s) See Also

Plot selectivity, including retention and other quantities, with additional plots for time-varying selectivity.

SSplotSelex(replist, infotable = NULL, fleets = "all",
fleetnames = "default", sizefactors = c("Lsel"),
agefactors = c("Asel"), years = "endyr", season = 1,
sexes="all", selexlines = 1:5, subplot = 1:25,
skipAgeSelex10 = TRUE,
plot = TRUE, print = FALSE, add = FALSE,
labels=c("Length (cm)",
  "Age (yr)",     
  "Year",         
  "Selectivity",  
  "Retention",    
  "Discard mortality"),
col1 = "red", col2 = "blue",
lwd = 2, fleetcols = "default", fleetpch = "default",
fleetlty = "default", spacepoints = 5,
staggerpoints = 1, legendloc = "bottomright", 
pwidth = 7, pheight = 7, punits = "in", res = 300, ptsize = 12,
cex.main = 1, plotdir = "default", verbose = TRUE)

`replist`	List created by `SS_output`
`fleets`	Optional vector to subset fleets for which to make plots
`infotable`	Optional table of information controlling appearance of plot and legend. Is produced as output and can be modified and entered as input.
`fleetnames`	Optional replacement for fleenames used in data file
`sizefactors`	Which elements of the factors column of SIZE_SELEX should be included in plot of selectivity across multiple fleets?
`agefactors`	Which elements of the factors column of AGE_SELEX should be included in plot of selectivity across multiple fleets?
`years`	Which years for selectivity are shown in multi-line plot (default = last year of model).
`season`	Which season (if seasonal model) for selectivity shown in multi-line plot (default = 1).
`sexes`	Optional vector to subset genders for which to make plots (1=females, 2=males)
`selexlines`	Vector to select which lines get plotted. values are 1. Selectivity, 2. Retention, 3. Discard mortality, 4. Keep = SelRet, 5. Dead = Sel(Ret+(1-Ret)*Mort).
`subplot`	Vector controlling which subplots to create
`skipAgeSelex10`	Exclude plots for age selectivity type 10 (selectivity = 1.0 for all ages beginning at age 1)?
`lwd`	Line widths for plots
`fleetcols`	Optional vector of colors for each fleet (in multi-fleet plots)
`fleetpch`	Optional vector of plot characters for each fleet (in multi-fleet plots)
`fleetlty`	Optional vector of line types for each fleet (in multi-fleet plots)
`spacepoints`	number of years between points shown on top of lines (for long timeseries, points every year get mashed together)
`staggerpoints`	number of years to stagger the first point (if `spacepoints > 1`) for each line (so that adjacent lines have points in different years)
`legendloc`	location of legend. See ?legend for more info.
`plot`	Plot to active plot device?
`print`	Print to PNG files?
`add`	Add to existing plot (not yet implemented)
`labels`	vector of labels for plots (titles and axis labels)
`col1`	color for female growth curve
`col2`	color for male growth curve
`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
`plotdir`	directory where PNG files will be written. by default it will be the directory where the model was run.
`verbose`	report progress to R GUI?