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Plot the abundance spectra

Source: R/plotSpectra.R
plotSpectra.Rd

Plots the number density multiplied by a power of the weight, with the power specified by the power argument.

Usage

# S3 method for class 'mizerMRSim'
plotSpectra(
  object,
  species = NULL,
  resources = NULL,
  time_range,
  geometric_mean = FALSE,
  wlim = c(NA, NA),
  ylim = c(NA, NA),
  power = 1,
  biomass = TRUE,
  total = FALSE,
  background = TRUE,
  highlight = NULL,
  return_data = FALSE,
  ...
)

# S3 method for class 'mizerMR'
plotSpectra(
  object,
  species = NULL,
  resources = NULL,
  wlim = c(NA, NA),
  ylim = c(NA, NA),
  power = 1,
  total = FALSE,
  background = TRUE,
  highlight = NULL,
  return_data = FALSE,
  ...
)

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.

resources

The resources to be selected. Optional. By default all resources are selected. A vector of resource names, or a numeric vector with the resource indices, or a logical vector indicating for each resource whether it is to be selected (TRUE) or not.

time_range

The time range to average over when called with a MizerSim object.

geometric_mean

Whether to average abundances using a geometric mean when called with a MizerSim object.

wlim

A numeric vector of length two providing lower and upper limits for the w axis. Use NA to refer to the existing minimum or maximum.

ylim

A numeric vector of length two providing lower and upper limits for the y axis. Use NA to refer to the existing minimum or maximum. Any values below 1e-20 are always cut off.

power

The abundance is plotted as the number density times the weight raised to power. The default power = 1 gives the biomass density, whereas power = 2 gives the biomass density with respect to logarithmic size bins.

biomass

Deprecated compatibility argument. If power is missing, power is set to as.numeric(biomass).

total

A boolean value that determines whether the total over all species and resources in the system is plotted as well. Note that even if the plot only shows a selection of species, the total is including all species. Default is FALSE.

background

A boolean value that determines whether background species are included. Ignored if the model does not contain background species. Default is TRUE.

highlight

Name or vector of names of the species to be highlighted.

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

...

Other arguments (currently unused)

Value

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

Details

When called with a MizerSim object, the abundance is averaged over the specified time range (a single value for the time range can be used to plot a single time step). When called with a MizerParams object the initial abundance is plotted.

See also

plotting_functions

Other plotting functions: animateSpectra, plotDiet, plotResourceLevel(), plotResourcePred()