Plot the sources of external, predation and fishing mortality per species and size

This is a generic function with methods for objects of class MizerSim and MizerParams. The method for a MizerSim object plots the mortality in the initial state of the simulation. An interactive version is available as plotlyDeath().

Usage

plotDeath(
  object,
  species = NULL,
  proportion = TRUE,
  return_data = FALSE,
  xtrans = c("log10", "identity"),
  ...
)

plotlyDeath(object, species = NULL, proportion = TRUE, ...)

Arguments

object

An object of class MizerSim or MizerParams.

species

The name of the predator species for which to plot the mortality.

proportion

A boolean value that determines whether values should be displayed as proportions from 0 to 1 or with their actual values. Default is TRUE.

return_data

A boolean value that determines whether the formatted data used for the plot is returned instead of the plot itself. Default value is FALSE

xtrans

The transformation to apply to the x-axis. Either "log10" (default) or "identity".

...

Other arguments (currently unused)

Value

A ggplot2 object, unless return_data = TRUE, in which case a data frame with the four variables 'w', 'value', 'Cause', 'Species' is returned.

See also

plotting_functions

Other plotting functions: plotEnergyBudget(), plotResourceLevel(), plotResourcePred(), plotYieldVsF(), plotYieldVsSize()

Examples

# \donttest{
plotDeath(NS_params, species = "Cod")


# Returning the data frame
fr <- plotDeath(NS_params, species = "Cod", return_data = TRUE)
str(fr)
#> 'data.frame':	1400 obs. of  4 variables:
#>  $ w    : num  0.001 0.00119 0.00142 0.0017 0.00203 ...
#>  $ value: num  0.00345 0.00345 0.00344 0.00341 0.00338 ...
#>  $ Cause: chr  "External" "External" "External" "External" ...
#>  $ Prey : chr  "Cod" "Cod" "Cod" "Cod" ...
# }