SSplotSelex {r4ss}

Plot selectivity

Description

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

Usage

SSplotSelex(
  replist,
  infotable = NULL,
  fleets = "all",
  fleetnames = "default",
  sizefactors = c("Lsel"),
  agefactors = c("Asel", "Asel2"),
  years = "endyr",
  minyr = -Inf,
  maxyr = Inf,
  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,
  spacepoints = 5,
  staggerpoints = 1,
  legendloc = "bottomright",
  pwidth = 6.5,
  pheight = 5,
  punits = "in",
  res = 300,
  ptsize = 10,
  cex.main = 1,
  mainTitle = TRUE,
  showmain = lifecycle::deprecated(),
  mar = NULL,
  plotdir = "default",
  verbose = TRUE
)

Arguments

replist

A list object 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).

minyr

optional input for minimum year to show in plots

maxyr

optional input for maximum year to show in plots

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.

subplot

Vector controlling which subplots to create. Numbering of subplots is as follows,

Plots with all fleets grouped together

• 1 selectivity at length in end year for all fleets shown together

• 2 selectivity at age in end year for all fleets shown together (this includes both age-based selectivity "Asel" and age values derived from length-based, "Asel2". You can choose only one using "agefactors" if needed.)

Plots of time-varying length-based selectivity

• 3 selectivity at length time-varying surface

• 4 selectivity at length time-varying contour

• 5 retention at length time-varying surface

• 6 retention at length time-varying surface

• 7 discard mortality time-varying surface

• 8 discard mortality time-varying contour

Selectivity at length in end year by fleet

• 9 selectivity, retention, and discard mortality at length in ending year

Plots of time-varying age-based selectivity

• 11 selectivity at age time-varying surface

• 12 selectivity at age time-varying contour

Selectivity at age in end year by fleet

• 13 selectivity at age in ending year if time-varying

• 14 selectivity at age in ending year if NOT time-varying

• 15 matrix of selectivity deviations for semi-parametric selectivity

Selectivity for both/either age or length

• 21 selectivity at age and length contour with overlaid growth curve

• 22 selectivity with uncertainty if requested at end of control file

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

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

Default width of plots printed to files in units of punits. The default is pwidth=6.5.

pheight

Height of plots printed to png files in units of punits. Default is designed to allow two plots per page, with pheight_tall used for plots that work best with a taller format and a single plot per page.

punits

Units for pwidth and pheight. Can be "px" (pixels), "in" (inches), "cm" (centimeters), or "mm" (millimeters). The default is punits="in".

res

Resolution of plots printed to files. The default is res = 300.

ptsize

Point size for plotted text in plots printed to files (see help("png") in R for details).

cex.main

character expansion for plot titles

mainTitle

Logical indicating if a title should be included at the top (not yet implemented for all plots)

showmain

Deprecated, use mainTitle instead.

mar

Either NULL to allow the default (which depends on whether the main title is included or not) or a numerical vector of the form c(bottom, left, top, right) which gives the number of lines of margin to be specified on the four sides of the plot, which is passed to par().

plotdir

Directory where PNG files will be written. By default it will be the directory where the model was run.

verbose

A logical value specifying if output should be printed to the screen.

Author(s)

Ian Stewart, Ian Taylor

See Also

SS_plots(), SS_output()