mizer (version 1.0.1)

getBiomassFrame: Get data frame of biomass of species through time, ready for ggplot2

Description

After running a projection, the biomass of each species can be plotted against time. The biomass is calculated within user defined size limits (min_w, max_w, min_l, max_l, see getBiomass).

Usage

getBiomassFrame(sim, ...)
# S4 method for MizerSim
getBiomassFrame(sim,
  species = sim@params@species_params$species[!is.na(sim@params@A)],
  start_time = as.numeric(dimnames(sim@n)[[1]][1]),
  end_time = as.numeric(dimnames(sim@n)[[1]][dim(sim@n)[1]]),
  ylim = c(NA, NA), total = FALSE, ...)

Arguments

sim

An object of class '>MizerSim

...

Other arguments to pass to getBiomass method, for example min_w and max_w

species

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

start_time

The first time to be plotted. Default is the beginning of the time series.

end_time

The last time to be plotted. Default is the end of the time series.

ylim

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

total

A boolean value that determines whether the total biomass from all species is plotted as well. Default is FALSE

Value

A data frame that can be used in display_frames

See Also

getBiomass