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.
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
)A list object created by SS_output().
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 to active plot device?
print to PNG files?
Units for numbers. Default (based on typical Stock Synthesis setup) is thousands (numbers.unit=1000).
optional subset of areas to plot for spatial models
names for areas. Default is to use Area1, Area2,...
vector of colors by area
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
background color for bubbles (no control over black border at this time)
Add legend with example bubble sizes?
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 lines for mean age or length on top of bubble plots
add to existing plot? (not yet implemented)
vector of labels for plots (titles and axis labels)
Default width of plots printed to files in units of
punits. The default is pwidth=6.5.
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.
Units for pwidth and pheight. Can be "px"
(pixels), "in" (inches), "cm" (centimeters), or "mm" (millimeters).
The default is punits="in".
Resolution of plots printed to files.
The default is res = 300.
Point size for plotted text in plots printed to files (see
help("png") in R for details).
character expansion for plot titles
directory where PNG files will be written. by default it will be the directory where the model was run.
Logical indicating if a title should be included at the top
report progress to R GUI?