Plot biology related quantities.

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"),
  areacols = NULL,
  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",
    replist[["SpawnOutputLabel"]], "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 in ending year"),
  pwidth = 6.5,
  pheight = 5,
  pheight_tall = 6.5,
  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 sex ratio in ending year (only plotted when model has hermaphroditism)

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

areacols

Optional vector of colors for each area if model has multiple areas. NULL value will be replaced by a default set of areas.

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. Either a string like "topleft" or a vector of two numeric values representing the fraction of the maximum in the x and y dimensions, respectively. See help("legend") for more info on the string options.

plotdir

Directory where PNG files will be written.

labels

Vector of labels for plots (titles and axis labels).

pwidth

Default width of plots printed to files in units of punits.

pheight

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.

pheight_tall

Height of tall plots printed to png files in units of punits, where the tall plots are a subset of the plots which typically work best in a taller format.

punits

Units for pwidth and pheight. Can be "px" (pixels), "in" (inches), "cm" (centimeters), or "mm" (millimeters). The default is punits="in".

res

Resolution of plots printed to files. The default is res = 300.

ptsize

Point size for plotted text in plots printed to files (see help("png") in R for details).

cex.main

Character expansion for plot titles. The default is cex.main=1.

mainTitle

Logical indicating if a title should be included at the top (not yet implemented for all plots).

verbose

A logical value specifying if output should be printed to the screen.

Author

Ian Stewart, Ian Taylor

Usage

Arguments

See also

Author