Plot biology related quantities from Stock Synthesis model output, including mean weight, maturity, fecundity, and spawning output.
SSplotBiology(
replist,
plot = TRUE,
print = FALSE,
add = FALSE,
subplots = 1:32,
seas = 1,
morphs = NULL,
forecast = FALSE,
minyr = -Inf,
maxyr = Inf,
colvec = c("red", "blue", "grey20"),
ltyvec = c(1, 2),
shadealpha = 0.1,
imageplot_text = FALSE,
imageplot_text_round = 0,
legendloc = "topleft",
plotdir = "default",
labels = c("Length (cm)", "Age (yr)", "Maturity", "Mean weight (kg) in last year",
"Spawning output", "Length (cm, beginning of the year)", "Natural mortality",
"Female weight (kg)", "Female length (cm)", "Fecundity", "Default fecundity label",
"Year", "Hermaphroditism transition rate", "Fraction females by age at equilibrium"),
pwidth = 6.5,
pheight = 5,
punits = "in",
res = 300,
ptsize = 10,
cex.main = 1,
mainTitle = TRUE,
verbose = TRUE
)A list object created by SS_output().
Plot to active plot device?
Print to PNG files?
add to existing plot
vector controlling which subplots to create Numbering of subplots is as follows:
1 growth curve only
2 growth curve with CV and SD
3 growth curve with maturity and weight
4 distribution of length at age (still in development)
5 length or wtatage matrix
6 maturity
7 fecundity from model parameters
8 fecundity at weight from BIOLOGY section
9 fecundity at length from BIOLOGY section
10 spawning output at length
11 spawning output at age
21 Natural mortality (if age-dependent)
22 Time-varying growth persp
23 Time-varying growth contour
24 plot time-series of any time-varying quantities (created if the MGparm_By_Year_after_adjustments table (report:7) is available in the Report.sso file)
31 hermaphroditism transition probability
32 hermaphroditism cumulative probability
Additional plots not created by default
101 diagram with labels showing female growth curve
102 diagram with labels showing female growth curve & male offsets
103 diagram with labels showing female CV = f(A) (offset type 2)
104 diagram with labels showing female CV = f(A) & male offset (type 2)
105 diagram with labels showing female CV = f(A) (offset type 3)
106 diagram with labels showing female CV = f(A) & male offset (type 3)
which season to plot (values other than 1 only work in seasonal models but but maybe not fully implemented)
Which morphs to plot (if more than 1 per sex)? By default this
will be replist[["mainmorphs"]]
Include forecast years in plots of time-varying biology?
optional input for minimum year to show in plots
optional input for maximum year to show in plots
vector of length 3 with colors for various points/lines
vector of length 2 with lty for females/males in growth plots values can be applied to other plots in the future
Transparency parameter used to make default shadecol values (see ?rgb for more info)
Whether to add numerical text to the image plots when using weight at age. Defaults to FALSE.
The number of significant digits to which the image plot text is rounded. Defaults to 0, meaning whole numbers. If all your values are small and there's no contrast in the text, you might want to make this 1 or 2.
Location of legend (see ?legend for more info)
Directory where PNG files will be written. by default it will be the directory where the model was run.
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
Return updates of function progress to the R GUI?