plot.srr: Plot the stock-recruitment relationship

In PacificCommunity/ofp-sam-diags4MFCL: R Functions for Presenting MULTIFAN-CL Results and Diagnostics

Plot the stock-recruitment relationship

Description

For each model, the fitted Beverton-Holt stock-recruiment relationship is plotted. Estimated adult biomass and recruitment is also plotted.

Usage

plot.srr(
  rep.list,
  rep.names = NULL,
  show.legend = TRUE,
  palette.func = default.model.colours,
  save.dir,
  save.name,
  annual = FALSE,
  sb.units = 1000,
  rec.units = 1e+06,
  ...
)

Arguments

rep.list	A list of MFCLRep objects or a single MFCLRep object. The reference model should be listed first.
rep.names	A vector of character strings naming the models for plotting purposes. If not supplied, model names will be taken from the names in the rep.list (if available) or generated automatically.
show.legend	Do you want to show the plot legend, TRUE (default) or FALSE.
palette.func	A function to determine the colours of the models. The default palette has the reference model in black. It is possible to determine your own palette function. Two functions currently exist: default.model.colours() and colourblind.model.colours().
save.dir	Path to the directory where the outputs will be saved
save.name	Name stem for the output, useful when saving many model outputs in the same directory
annual	Boolean. Do you want to plot the annual or seasonal SRR. Default is FALSE
sb.units	Divisor for rescaling the biomass units. Default is 1000
rec.units	Divisor for rescaling the recruitment units. Default is 1000000
...	Passes extra arguments to the palette function. Use the argument all.model.colours to ensure consistency of model colours when plotting a subset of models.

PacificCommunity/ofp-sam-diags4MFCL documentation built on Oct. 11, 2023, 1:32 a.m.