calibrateBiomass {mizer}

Calibrate the model scale to match total observed biomass

Description

Given a MizerParams object params for which biomass observations are available for at least some species via the biomass_observed column in the species_params data frame, this function returns an updated MizerParams object which is rescaled with scaleModel() so that the total biomass in the model agrees with the total observed biomass.

Usage

calibrateBiomass(params)

Arguments

params

A MizerParams object

Details

Biomass observations usually only include individuals above a certain size. This size should be specified in a biomass_cutoff column of the species parameter data frame. If this is missing, it is assumed that all sizes are included in the observed biomass, i.e., it includes larval biomass.

After using this function the total biomass in the model will match the total biomass, summed over all species. However the biomasses of the individual species will not match observations yet, with some species having biomasses that are too high and others too low. So after this function you may want to use matchBiomasses(). This is described in the blog post at https://bit.ly/2YqXESV.

If you have observations of the yearly yield instead of biomasses, you can use calibrateYield() instead of this function.

Value

A MizerParams object

Examples

params <- NS_params
species_params(params)$biomass_observed <- 
    c(0.8, 61, 12, 35, 1.6, 20, 10, 7.6, 135, 60, 30, 78)
species_params(params)$biomass_cutoff <- 10
params2 <- calibrateBiomass(params)
plotBiomassObservedVsModel(params2)