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 (see getBiomass()).

Usage

plotBiomass(
  object,
  species = NULL,
  tlim = c(NA, NA),
  y_ticks = 6,
  ylim = c(NA, NA),
  total = FALSE,
  background = TRUE,
  highlight = NULL,
  log = NULL,
  return_data = FALSE,
  log_x = FALSE,
  log_y = TRUE,
  use_cutoff = FALSE,
  ...
)

Arguments

object

An object of class MizerSim

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.

tlim

A numeric vector of length two providing lower and upper limits for the time axis, e.g. c(1980, 2000). Use NA to apply no limit at that end. Default is c(NA, NA).

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.

log

Character string specifying which axes should use log10 scales, in the same form as the base plot() argument. For example, "x", "y", "xy" or "". If supplied, this overrides log_x and log_y. For backward compatibility, TRUE and FALSE are interpreted as setting only log_y.

return_data

A boolean value that determines whether the formatted data used for the plot is returned instead of the plot itself. Default is FALSE.

log_x

If TRUE, use a log10 x-axis. Default is FALSE.

log_y

If TRUE, use a log10 y-axis. Default is TRUE.

use_cutoff

If TRUE, the biomass_cutoff column in the species parameters is used as the minimum weight for each species.

...

Arguments setting the size range over which the biomass is calculated (see getBiomass()):

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, unless return_data = TRUE, in which case a data frame with the four variables 'Year', 'Biomass', 'Species', 'Legend' is returned.

See also

plotting_functions, getBiomass()

Other plotting functions: addPlot(), animate.ArrayTimeBySpeciesBySize(), plot, plot2(), plotCDF(), plotCDF2(), plotDiet(), plotFMort(), plotFeedingLevel(), plotGrowthCurves(), plotMizerParams, plotMizerSim, plotPredMort(), plotRelative(), plotSpectra(), plotSpectra2(), plotSpectraRelative(), plotYield(), plotYieldGear(), plotting_functions

Examples

# \donttest{
plotBiomass(NS_sim)

plotBiomass(NS_sim, species = c("Sandeel", "Herring"), total = TRUE)

plotBiomass(NS_sim, tlim = c(1980, 1990))


# Returning the data frame
fr <- plotBiomass(NS_sim, return_data = TRUE)
str(fr)
#> 'data.frame':	528 obs. of  4 variables:
#>  $ Year   : int  1967 1968 1969 1970 1971 1972 1973 1974 1975 1976 ...
#>  $ Biomass: num  5.08e+10 5.57e+10 5.48e+10 5.32e+10 5.16e+10 ...
#>  $ Species: Factor w/ 12 levels "Sprat","Sandeel",..: 1 1 1 1 1 1 1 1 1 1 ...
#>  $ Legend : Factor w/ 12 levels "Sprat","Sandeel",..: 1 1 1 1 1 1 1 1 1 1 ...
# }