Plot selectivity

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,
  subplots = 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,
  mar = NULL,
  plotdir = "default",
  verbose = TRUE,
  subplot = lifecycle::deprecated()
)

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

Either the string "all", or a vector of numerical values, like c(1,3), listing fleets or surveys to be included in the plot.

fleetnames

Optional replacement for fleetnames 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 sexes 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.

subplots

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 width for plot elements.

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. Either a string like "topleft" or a vector of two numeric values representing the fraction of the maximum in the x and y dimensions, respectively. See help("legend") for more info on the string options.

pwidth

Default width of plots printed to files in units of punits.

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. The default is cex.main=1.

mainTitle

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

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.

verbose

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

subplot

Deprecated. Use subplots instead.

Author

Ian Stewart, Ian Taylor

Usage

Arguments

See also

Author