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

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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). This function returns a dataframe that can be displayed with displayFrames.

getBiomassFrame(
  sim,
  species = dimnames(sim@n)$sp[!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
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 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.
total

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

Arguments passed on to get_size_range_array

min_w

Smallest weight in size range. Defaults to smallest weight in the model.

max_w

Largest weight in size range. Defaults to largest weight in the model.

min_l

Smallest length in size range. If supplied, this takes precedence over min_w.

max_l

Largest length in size range. If supplied, this takes precedence over max_w.

Value

A data frame that can be used in displayFrames

See also

getBiomass, displayFrames

Other frame functions: displayFrames(), getSSBFrame()

Examples

# Set up example MizerParams and MizerSim objects
data(NS_species_params_gears)
data(inter)
params <- suppressMessages(newMultispeciesParams(NS_species_params_gears, inter))
sim0 <- project(params, effort=0, t_max=20, progress_bar = FALSE)
sim1 <- project(params, effort=1, t_max=20, progress_bar = FALSE)

# Display biomass from each simulation next to each other
displayFrames(getBiomassFrame(sim0), getBiomassFrame(sim1), params)