Animation of the abundance spectra

Usage

animateSpectra(
  sim,
  species,
  time_range,
  wlim,
  ylim,
  power,
  total,
  resource,
  background,
  ...
)

Arguments

sim

A MizerSim object

species

Name or vector of names of the species to be plotted. By default all species are plotted.

time_range

The time range to animate over. Either a vector of values or a vector of min and max time. Default is the entire time range of the simulation.

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.

total

A boolean value that determines whether the total over all species in the system is plotted as an additional trace called "Total". Default is FALSE.

resource

A boolean value that determines whether resource is included. If TRUE, the resource spectrum is plotted as an additional trace called "Resource". 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.

...

Additional arguments passed to the method.

Value

A plotly object with one animated line trace per plotted group. The y-axis title depends on power.

See also

Other plotting functions: plot, plotBiomass(), plotDiet(), plotFMort(), plotFeedingLevel(), plotGrowthCurves(), plotMizerParams, plotMizerSim, plotPredMort(), plotSpectra(), plotYield(), plotYieldGear(), plotting_functions

Examples

# \donttest{
animateSpectra(NS_sim, power = 2, wlim = c(0.1, NA), time_range = 1997:2007)

# }