SSplotSelex: Plot selectivity

In r4ss: R Code for Stock Synthesis

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()

r4ss documentation built on May 28, 2022, 1:11 a.m.