Plot the biomass of species through time

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).

plotBiomass(
  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]]),
  y_ticks = 6,
  ylim = c(NA, NA),
  total = FALSE,
  background = TRUE,
  highlight = NULL,
  ...
)

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.
y_ticks	The approximate number of ticks desired on the y axis
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.
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.
...	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 ggplot2 object

See also

plotting_functions, getBiomass

Other plotting functions: animateSpectra(), displayFrames(), plot,MizerSim,missing-method, plotDiet(), plotFMort(), plotFeedingLevel(), plotGrowthCurves(), plotPredMort(), plotSpectra(), plotYieldGear(), plotYield(), plotlyBiomass(), plotlyFMort(), plotlyFeedingLevel(), plotlyGrowthCurves(), plotlyPredMort(), plotlySpectra(), plotlyYieldGear(), plotlyYield(), plotting_functions

Examples

# Set up example MizerParams and MizerSim objects
data(NS_species_params_gears)
data(inter)
params <- suppressMessages(newMultispeciesParams(NS_species_params_gears, inter))
sim <- project(params, effort = 1, t_max = 20, t_save = 0.2, progress_bar = FALSE)

plotBiomass(sim)
plotBiomass(sim, species = c("Cod", "Haddock"), total = TRUE)
plotBiomass(sim, min_w = 10, max_w = 1000)
plotBiomass(sim, start_time = 10, end_time = 15)
plotBiomass(sim, y_ticks = 3)