Plot selectivity

Description

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

Usage

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SSplotSelex(replist, infotable = NULL, fleets = "all",
  fleetnames = "default", sizefactors = c("Lsel"), agefactors = c("Asel",
  "Asel2"), years = "endyr", season = 1, sexes = "all",
  selexlines = 1:6, 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, showmain = TRUE,
  plotdir = "default", verbose = TRUE)

Arguments

replist

List created by SS_output

infotable

Optional table of information controlling appearance of plot and legend. Is produced as output and can be modified and entered as input.

fleets

Optional vector to subset fleets for which to make plots

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 = Sel*Ret, 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)?

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

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.

pwidth

width of plot

pheight

height of plot

punits

units for PNG file

res

resolution for PNG file

ptsize

point size for PNG file

cex.main

character expansion for plot titles

showmain

Include main title at top of plot?

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?

Author(s)

Ian Stewart, Ian Taylor

See Also

SS_plots, SS_output

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