Fishery catch fits

Plots fitted fishery catch: observed points with lognormal 95% intervals and the model-predicted catch, faceted by fishery fleet. For MSE objects the projection period is summarized with 50% / 95% ribbons across simulations.

Usage

plot_catch(
  Rceattle,
  file = NULL,
  model_names = NULL,
  species = NULL,
  incl_proj = FALSE,
  width = 7,
  height = 6.5,
  error = TRUE,
  maxyr = NULL,
  mse = FALSE,
  fleets = NULL,
  line_col = NULL,
  right_adj = 0,
  top_adj = 1.2,
  single.plots = FALSE,
  alpha = 0.4,
  lwd = 2,
  ymax = NULL
)

Arguments

Rceattle

A single fit_mod() object or a list of them (overlaid).

file

Optional file stem; if given the figure is written to <file>_survey_indices.png.

model_names

Legend labels for the models.

species

Species (indices) to include. Default all.

incl_proj

Include projection years.

width, height

Saved figure size (inches).

error

Draw observed points and error bars.

maxyr

Last year to plot.

mse

Is Rceattle an MSE object (operating models)?

fleets

Fishery fleets to include (indices into the sorted fleet codes). Default all.

line_col, right_adj, top_adj, single.plots

Deprecated base-graphics arguments, retained for back-compatibility and ignored.

alpha, lwd, ymax

Deprecated base-graphics arguments, ignored.

Value

A ggplot object.

Details

The predicted line is the MEDIAN, as in plot_index(): catch_hat * exp(-bias_adjust_obs * sd^2 / 2). The catch likelihood is lognormal for every fishery, so this applies throughout.