plotSpectra: Plot the abundance spectra

Description

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

Usage

plotSpectra(
  object,
  species = NULL,
  time_range,
  geometric_mean = FALSE,
  wlim = c(NA, NA),
  ylim = c(NA, NA),
  power = 1,
  biomass = TRUE,
  total = FALSE,
  resource = TRUE,
  background = TRUE,
  highlight = NULL,
  return_data = FALSE,
  ...
)
plotlySpectra(
  object,
  species = NULL,
  time_range,
  geometric_mean = FALSE,
  wlim = c(NA, NA),
  ylim = c(NA, NA),
  power = 1,
  biomass = TRUE,
  total = FALSE,
  resource = TRUE,
  background = TRUE,
  highlight = NULL,
  ...
)

Value

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

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.
time_range: The time range (either a vector of values, a vector of min and max time, or a single value) to average the abundances over. Default is the final time step. Ignored when called with a MizerParams object.
geometric_mean: If TRUE then the average of the abundances over the time range is a geometric mean instead of the default arithmetic mean.
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: Only used if power argument is missing. Then biomass = TRUE is equivalent to power=1 and biomass = FALSE is equivalent to power=0
total: A boolean value that determines whether the total over all species 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.
resource: A boolean value that determines whether resource is included. Default is TRUE.
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)

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.

Examples

Run this code

# \donttest{
params <-  NS_params
sim <- project(params, effort=1, t_max=20, t_save = 2, progress_bar = FALSE)
plotSpectra(sim)
plotSpectra(sim, wlim = c(1e-6, NA))
plotSpectra(sim, time_range = 10:20)
plotSpectra(sim, time_range = 10:20, power = 0)
plotSpectra(sim, species = c("Cod", "Herring"), power = 1)

# Returning the data frame
fr <- plotSpectra(sim, return_data = TRUE)
str(fr)
# }