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)
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"
)A list object created by SS_output().
Switch set to either 1 for length at true age or 2 for obs. age at true age
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.
Multiplier for bars showing distribution. Species with many ages benefit from expanded bars. NULL value causes function to attempt automatic scaling.
Add to existing plot
A character value specifying the color of the grid lines
The color of the filled polygons.
A numeric value specifying the amount to shift the top of the polygon up.
A numeric value specifying the amount to shift the bottom of the polygon up.
Plot to active plot device?
Print to PNG files?
Vector of labels for plots (titles and axis labels)
Width of plot
Height of plot
Units for PNG file
Resolution of plots printed to files.
The default is res = 300.
Point size for PNG file
Character expansion for plot titles
Logical indicating if a title should be included at the top
directory where PNG files will be written. by default it will be the directory where the model was run.