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Plot exploitable biomass

Source: R/7-plot_ceattle.R
plot_exploitable_biomass.Rd

Plots the mean exploitable biomass (million mt) and 95\

Usage

plot_exploitable_biomass(
  Rceattle,
  file = NULL,
  model_names = NULL,
  line_col = NULL,
  species = NULL,
  spnames = NULL,
  add_ci = FALSE,
  lwd = 3,
  save = FALSE,
  right_adj = 0,
  legend.pos = "topright",
  width = 7,
  height = 6.5,
  minyr = NULL,
  maxyr = NULL,
  incl_proj = FALSE,
  mod_cex = 1,
  lty = rep(1, length(Rceattle)),
  alpha = 0.4,
  mod_avg = rep(FALSE, length(Rceattle)),
  mse = FALSE,
  OM = TRUE,
  reference = NULL,
  ylab = NULL
)

Arguments

Rceattle

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

file

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

model_names

Legend labels for the models.

line_col

Line colours; names, hex, or base-graphics integers. NULL uses the colorblind-safe Okabe-Ito palette. Applied to whichever variable the figure separates by colour, in legend order. Too few colours are recycled, with a warning.

species

Species to include, as indices (c(1, 3)), names, a logical mask, or "all". Default NULL plots every species. Species labels belong in spnames; a character species that matches no species name is read as labels for back-compatibility.

spnames

Species labels, length nspp. Default: the model's own.

add_ci

Add a 95% confidence interval. Only available where the plotted quantity holds standard errors; warns and draws none otherwise.

lwd

Line width on the base-graphics scale: the default 3 renders as a standard-weight ggplot line. A vector varies it across series.

save

Write the plotted series to CSV alongside the figure.

right_adj

Ignored. Base-graphics leftover: the figure widened its right margin to fit the legend. Set margins on the returned ggplot instead.

legend.pos

Ignored. Base-graphics leftover: legend placement. Use p + ggplot2::theme(legend.position = "right").

width, height

Saved figure size in inches.

minyr, maxyr

First / last year to plot.

incl_proj

Include the projection years, with a dashed divider at the last hindcast year.

mod_cex

Ignored. Base-graphics leftover: legend text size. Use p + ggplot2::theme(legend.text = ggplot2::element_text(size = ...)).

lty

Line type. A vector varies it across the levels of whatever the figure separates by line type.

alpha

Transparency of confidence ribbons and shaded areas, between 0 and 1.

mod_avg

TRUE/FALSE

mse

Is an MSE object from load_mse or run_mse

OM

if mse == TRUE, use the OM (TRUE) or EM (FALSE) for plotting?

reference

A model to overlay for comparison, drawn at 1.5x lwd and labelled "Reference". It takes the next colour from the palette, or black if line_col is supplied.

ylab

Y-axis label. NULL (default) derives one from output and the model's minage.

Value

Returns and saves a figure with the exploitable biomass trajectory.