mizer (version 3.0.0)

getBiomass: Calculate the total biomass of each species within a size range at each time step.

Description

Calculates the total biomass through time within user defined size limits. The default option is to use the size range starting at the size specified by the biomass_cutoff species parameter, if it is set, or else the full size range of each species. You can specify minimum and maximum weight or length range for the species. Lengths take precedence over weights (i.e. if both min_l and min_w are supplied, only min_l will be used).

Usage

getBiomass(object, use_cutoff = FALSE, ...)

Value

If called with a MizerParams object, a named vector with the biomass in grams for each species in the model. If called with a MizerSim object, an ArrayTimeBySpecies object (time x species) containing the biomass in grams at each time step for all species.

Arguments

object

An object of class MizerParams or MizerSim.

use_cutoff

If TRUE, the biomass_cutoff column in the species parameters is used as the minimum weight for each species (ignoring any size range arguments in ...). If FALSE (default), the specified size range arguments are used, if provided, or the full size range of the species is used.

...

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.

Details

When no size range arguments are provided, the function checks if the biomass_cutoff column exists in the species parameters. If it does, those values are used as the minimum weight for each species. For species with NA values in biomass_cutoff, the default minimum weight (smallest weight in the model) is used.

See Also

Other summary functions: getDiet(), getGrowthCurves(), getN(), getSSB(), getTrophicLevel(), getTrophicLevelBySpecies(), getYield(), getYieldGear()

Examples

biomass <- getBiomass(NS_sim)
biomass["1972", "Herring"]
biomass <- getBiomass(NS_sim, min_w = 10, max_w = 1000)
biomass["1972", "Herring"]

# If species_params contains a `biomass_cutoff`` column, it can be used
# as the minimum weight when use_cutoff = TRUE
species_params(NS_sim@params)$biomass_cutoff <- 10
biomass <- getBiomass(NS_sim, use_cutoff = TRUE)  # Uses biomass_cutoff as min_w
biomass["1972", "Herring"]