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Plot biomass consumed of each prey species by predator

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

Function that plots the biomass consumed trends as estimated from Rceattle. Returns and saves a figure with the biomass eaten trajectory.

Usage

plot_b_eaten_prop(
  Rceattle,
  file = NULL,
  model_names = NULL,
  line_col = NULL,
  spnames = NULL,
  species = NULL,
  lwd = 3,
  right_adj = 0,
  top_adj = 0.15,
  minyr = NULL,
  mohns = NULL,
  width = 7,
  height = 6.5,
  incl_proj = FALSE,
  incl_mean = FALSE,
  add_ci = FALSE,
  mod_cex = 1,
  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.

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.

mohns

Ignored. Formerly annotated the figure with Mohn's rho from retrospective(); add it with ggplot2::labs(subtitle = ...) instead.

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.

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.

Details

Colour separates predators; line type separates models. Panels are prey species.