SSplotAgeMatrix: Plot matrix of either length or observed age at true age

In r4ss: R Code for Stock Synthesis

Plot matrix of either length or observed age at true age

Description

Distribution of length at age or observed age at true age is represented as a histogram. Values are from the AGE_LENGTH_KEY and AGE_AGE_KEY sections of Report.sso ($ALK and $AAK in the list created by SS_output)

Usage

SSplotAgeMatrix(
  replist,
  option = 1,
  slices = NULL,
  scale = NULL,
  add = FALSE,
  col.grid = "grey90",
  col.bars = grey(0, alpha = 0.5),
  shift_hi = 0,
  shift_lo = 0,
  plot = TRUE,
  print = FALSE,
  labels = c("Age", "Length", "True age", "Observed age", "for ageing error type",
    "Distribution of", "at"),
  pwidth = 6.5,
  pheight = 5,
  punits = "in",
  res = 300,
  ptsize = 10,
  cex.main = 1,
  mainTitle = TRUE,
  plotdir = "default"
)

Arguments

replist	A list object created by SS_output().
option	Switch set to either 1 for length at true age or 2 for obs. age at true age
slices	Optional input to choose which matrix (slice of the 3D-array) within $AAK or $ALK to plot. By default all slices will be shown. For ageing imprecision this should correspond to the ageing error matrix number. Distribution of length at age ($ALK) is ordered by season, sub-season, and then morph. A future version could allow subsetting plots by these dimensions.
scale	Multiplier for bars showing distribution. Species with many ages benefit from expanded bars. NULL value causes function to attempt automatic scaling.
add	Add to existing plot
col.grid	A character value specifying the color of the grid lines
col.bars	The color of the filled polygons.
shift_hi	A numeric value specifying the amount to shift the top of the polygon up.
shift_lo	A numeric value specifying the amount to shift the bottom of the polygon up.
plot	Plot to active plot device?
print	Print to PNG files?
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 of plots printed to files. The default is res = 300.
ptsize	Point size for PNG file
cex.main	Character expansion for plot titles
mainTitle	Logical indicating if a title should be included at the top
plotdir	directory where PNG files will be written. by default it will be the directory where the model was run.

Author(s)

Ian G. Taylor

See Also

SSplotNumbers()

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