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

Description Usage Arguments Author(s) See Also

View source: R/SSplotNumbers.R

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

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SSplotNumbers(replist, subplots = 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"), 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 = 5, punits = "in", res = 300,
  ptsize = 10, cex.main = 1, plotdir = "default",
  mainTitle = FALSE, verbose = TRUE)

Arguments

replist

list created by SSoutput

subplots

vector controlling which subplots to create

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)

add

add to existing plot? (not yet implemented)

labels

vector of labels for plots (titles and axis labels)

pwidth

width of plot

pheight

height of plot

punits

units for PNG file

res

resolution for PNG file

ptsize

point size for PNG file

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 Oct. 30, 2019, 11:25 a.m.