SSplotNumbers: Plot numbers-at-age related data and fits.

In r4ss: R Code for Stock Synthesis

Plot numbers-at-age related data and fits.

Description

Plot numbers-at-age related data and fits from Stock Synthesis output. Plots include bubble plots, mean age, equilibrium age composition, sex-ratio, and ageing imprecision patterns.

Usage

SSplotNumbers(
  replist,
  subplots = c(1:10),
  plot = TRUE,
  print = FALSE,
  numbers.unit = 1000,
  areas = "all",
  areanames = "default",
  areacols = "default",
  pntscalar = 2.6,
  bub.bg = gray(0.5, alpha = 0.5),
  bublegend = TRUE,
  period = c("B", "M"),
  meanlines = TRUE,
  add = FALSE,
  labels = c("Year", "Age", "True age (yr)", "SD of observed age (yr)",
    "Mean observed age (yr)", "Mean age (yr)", "mean age in the population",
    "Ageing imprecision", "Numbers at age at equilibrium",
    "Equilibrium age distribution", "Fraction female in numbers at age", "Length",
    "Mean length (cm)", "mean length (cm) in the population", "expected numbers at age",
    "Beginning of year", "Middle of year", "expected numbers at length",
    "Fraction female in numbers at length"),
  pwidth = 6.5,
  pheight = 6.5,
  punits = "in",
  res = 300,
  ptsize = 10,
  cex.main = 1,
  plotdir = "default",
  mainTitle = FALSE,
  verbose = TRUE
)

Arguments

replist	A list object created by SS_output().
subplots	vector controlling which subplots to create Numbering of subplots is as follows, 1: Expected numbers at age 2: Mean age in the population 3: Fraction female in numbers at age 4: Equilibrium age distribution 5: Ageing imprecision: SD of observed age (plot using image() formerly included in this group but now replaced by better distribution plots) 6: Expected numbers at length 7: Mean length in the population 8: Fraction female in numbers at length 9: no plot yet 10: Distribution of observed age at true age by ageing error type
plot	plot to active plot device?
print	print to PNG files?
numbers.unit	Units for numbers. Default (based on typical Stock Synthesis setup) is thousands (numbers.unit=1000).
areas	optional subset of areas to plot for spatial models
areanames	names for areas. Default is to use Area1, Area2,...
areacols	vector of colors by area
pntscalar	maximum bubble size for bubble plots; each plot scaled independently based on this maximum size and the values plotted. Often some plots look better with one value and others with a larger or smaller value. Default=2.6
bub.bg	background color for bubbles (no control over black border at this time)
bublegend	Add legend with example bubble sizes?
period	indicator of whether to make plots using numbers at age just from the beginning ("B") or middle of the year ("M") (new option starting with SSv3.11)
meanlines	add lines for mean age or length on top of bubble plots
add	add to existing plot? (not yet implemented)
labels	vector of labels for plots (titles and axis labels)
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
plotdir	directory where PNG files will be written. by default it will be the directory where the model was run.
mainTitle	Logical indicating if a title should be included at the top
verbose	report progress to R GUI?

Author(s)

Ian Stewart, Ian Taylor

See Also

SS_output(), SS_plots()

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