plot.effort.devs: Plot effort deviations over time by fishery

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

Plot effort deviations over time by fishery

Description

The effort deviations are in the 'par' object. The 'frq' object is needed to get the time series of fishing realisations. Only effort deviations that have a corresponding effort in the 'frq' object are plotted. A loess smoothed fit is shown.

Usage

plot.effort.devs(
  frqreal.list,
  par.list,
  model.names = NULL,
  fisheries,
  fishery.names = as.character(fisheries),
  show.legend = TRUE,
  show.points = FALSE,
  palette.func = default.model.colours,
  save.dir,
  save.name,
  ...
)

Arguments

frqreal.list	A list of, or single instance of, data.frames, each one from calling realisations() on an MFCLFrq.
par.list	A list of MFCLPar objects or a single MFCLFrq that contain the effort deviations.
model.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 frqreal.list (if available) or generated automatically.
fisheries	The numbers of the fisheries to plot.
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.
fishery_names	The names of the fisheries to plot. If not supplied, the fishery numbers from the fisheries argument is used.

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