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Plot numbers-at-age related data and fits.

Source: R/SSplotNumbers.R
SSplotNumbers.Rd

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 = NULL,
  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

Optional vector of colors for each area if model has multiple areas. NULL value will be replaced by a default set of areas.

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.

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.

plotdir

Directory where PNG files will be written.

mainTitle

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

verbose

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

See also

SS_output(), SS_plots()

Author

Ian Stewart, Ian Taylor