SSplotBiology: Plot biology related quantities.

Description Usage Arguments Author(s) See Also

View source: R/SSplotBiology.R

Description

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

Usage

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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

List 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

  • 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 for PNG file

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 Oct. 30, 2019, 11:25 a.m.