Plot biomass eaten by predation — plot_b

Total biomass of each species consumed by its predators, summed over sex and age. For an MSE object the projection is summarized across simulations with a mean and a 95% interval.

Usage

plot_b_eaten(
  Rceattle,
  file = NULL,
  model_names = NULL,
  line_col = NULL,
  species = NULL,
  spnames = NULL,
  add_ci = FALSE,
  lwd = 3,
  save = FALSE,
  right_adj = 0,
  width = 7,
  height = 6.5,
  minyr = NULL,
  incl_proj = FALSE,
  mod_cex = 1,
  alpha = 0.4,
  mod_avg = rep(FALSE, length(Rceattle)),
  mse = FALSE,
  OM = TRUE,
  maxyr = NULL,
  lty = 1,
  incl_mean = FALSE,
  top_adj = 0.15
)

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: Ignored. Only the time-series plotters write their series to CSV.
right_adj: Ignored. Base-graphics leftover: the figure widened its right margin to fit the legend. Set margins on the returned ggplot instead.
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 = ...)).
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?
lty: Line type. A vector varies it across the levels of whatever the figure separates by line type.
incl_mean: Add a horizontal line at the hindcast mean of each series.
top_adj: Ignored. Base-graphics leftover; see right_adj.