plotDiet: Plot diet, resolved by prey species, as function of predator at size.

Description

Plots the proportions with which each prey species contributes to the total biomass consumed by the specified predator species, as a function of the predator's size. These proportions are obtained with getDiet().

Usage

plotDiet(
  object,
  species = NULL,
  wlim = c(NA, NA),
  llim = c(NA, NA),
  size_axis = c("w", "l"),
  return_data = FALSE,
  log_x = TRUE,
  log_y = FALSE,
  log = NULL,
  ...
)

Value

A ggplot2 object, unless return_data = TRUE, in which case a data frame with the four variables 'Predator', 'w' (or 'l' if size_axis = "l"), 'Proportion', 'Prey' is returned.

plotlyDiet() returns a plotly object.

Arguments

object: An object of class MizerSim or MizerParams.
species: The species to be selected. Optional. By default all target species are selected. A vector of species names, or a numeric vector with the species indices, or a logical vector indicating for each species whether it is to be selected (TRUE) or not.
wlim: A numeric vector of length two providing lower and upper limits for the weight (x) axis. Use NA to auto-scale to the data range.
llim: A numeric vector of length two providing lower and upper limits for the length (x) axis when size_axis = "l". Use NA to auto-scale to the data range.
size_axis: Whether to plot size as weight ("w", default) or length ("l"), using the allometric weight-length relationship.
return_data: A boolean value that determines whether the formatted data used for the plot is returned instead of the plot itself. Default is FALSE.
log_x: If TRUE (default), use a log10 x-axis.
log_y: If TRUE, use a log10 y-axis. Default is FALSE.
log: Character string specifying which axes should use log10 scales, in the same form as the base plot() argument. For example, "x", "y", "xy" or "". If supplied, this overrides log_x and log_y.
...: Unused.

Details

Prey species that contribute less than 1 permille to the diet are suppressed in the plot. The plot only extends to predator sizes where the predator has a meaningful abundance (defined as having a biomass density greater than 0.1% of its maximum biomass density).

If more than one predator species is selected, then the plot contains one facet for each species.

Examples

Run this code

# \donttest{
plotDiet(NS_params, species = "Cod")
plotDiet(NS_params, species = 5:9)

# Returning the data frame
fr <- plotDiet(NS_params, species = "Cod", return_data = TRUE)
str(fr)
# }