Plot predation mortality by age and predator — plot_m2_at_age

Share of the predation mortality (M2) on each prey age that is attributable to each predator species. The shares sum to 1 across predators for every prey age and year; a year with no predation on that age leaves them undefined and draws nothing.

Usage

plot_m2_at_age_prop(
  Rceattle,
  file = NULL,
  age = 1,
  model_names = NULL,
  line_col = NULL,
  spnames = NULL,
  species = NULL,
  lwd = 3,
  right_adj = 0,
  top_adj = 0.15,
  minyr = NULL,
  width = 7,
  height = 6.5,
  incl_proj = FALSE,
  incl_mean = FALSE,
  add_ci = FALSE,
  maxyr = NULL,
  lty = 1
)

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.
age: Prey age to plot the M2 proportions at, on the prey species' own age scale rather than as an age-bin index. A prey species that has no such age is dropped, with a warning.
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.
spnames: Species labels, length nspp. Default: the model's own.
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.
lwd: Line width on the base-graphics scale: the default 3 renders as a standard-weight ggplot line. A vector varies it across series.
right_adj: Ignored. Base-graphics leftover: the figure widened its right margin to fit the legend. Set margins on the returned ggplot instead.
top_adj: Ignored. Base-graphics leftover; see right_adj.
minyr, maxyr: First / last year to plot.
width, height: Saved figure size in inches.
incl_proj: Include the projection years, with a dashed divider at the last hindcast year.
incl_mean: Add a horizontal line at the hindcast mean of each series.
add_ci: Add a 95% confidence interval. Only available where the plotted quantity holds standard errors; warns and draws none otherwise.
lty: Line type. A vector varies it across the levels of whatever the figure separates by line type.

Details

Colour separates predators; line type separates models. Panels are prey species (and sex, where the prey is sexed).