plot.rec.devs: Plot estimated recruitment deviates

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

Plot estimated recruitment deviates

Description

Plot estimated recruitment deviates for a single model, by quarter and region. A loess smoothed fit is shown.

Usage

plot.rec.devs(
  par.list,
  par.names = NULL,
  show.legend = TRUE,
  show.points = FALSE,
  palette.func = default.model.colours,
  save.dir,
  save.name,
  ...
)

Arguments

par.list	A list of MFCLRep objects or a single MFCLRep object. The reference model should be listed first.
par.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.
show.points	Do you want to show points as well as the smoother for the difference plots? Default is 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
...	Passes extra arguments to the palette function. Use the argument all.model.names 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.