SSplotBiology: Plot biology related quantities.

In r4ss: R Code for Stock Synthesis

Plot biology related quantities.

Description

Plot biology related quantities from Stock Synthesis model output, including mean weight, maturity, fecundity, and spawning output.

Usage

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
)

Arguments

replist	A list object created by SS_output().
plot	Plot to active plot device?
print	Print to PNG files?
add	add to existing plot
subplots	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)
seas	which season to plot (values other than 1 only work in seasonal models but but maybe not fully implemented)
morphs	Which morphs to plot (if more than 1 per sex)? By default this will be replist[["mainmorphs"]]
forecast	Include forecast years in plots of time-varying biology?
minyr	optional input for minimum year to show in plots
maxyr	optional input for maximum year to show in plots
colvec	vector of length 3 with colors for various points/lines
ltyvec	vector of length 2 with lty for females/males in growth plots values can be applied to other plots in the future
shadealpha	Transparency parameter used to make default shadecol values (see ?rgb for more info)
imageplot_text	Whether to add numerical text to the image plots when using weight at age. Defaults to FALSE.
imageplot_text_round	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.
legendloc	Location of legend (see ?legend for more info)
plotdir	Directory where PNG files will be written. by default it will be the directory where the model was run.
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
verbose	Return updates of function progress to the R GUI?

Author(s)

Ian Stewart, Ian Taylor

See Also

SS_plots(), SS_output()

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