Match biomasses to observations

The function adjusts the abundances of the species in the model so that their biomasses match with observations.

Usage

matchBiomasses(params, species = NULL)

Arguments

params

A MizerParams object

species

The species to be affected. Optional. By default all observed biomasses will be matched. 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 affected (TRUE) or not.

Value

A MizerParams object

Details

The function works by multiplying for each species the abundance density at all sizes by the same factor. This will of course not give a steady state solution, even if the initial abundance densities were at steady state. So after using this function you may want to use steady() to run the model to steady state, after which of course the biomasses will no longer match exactly. You could then iterate this process. This is described in the blog post at https://bit.ly/2YqXESV.

Before you can use this function you will need to have added a biomass_observed column to your model which gives the observed biomass in grams. For species for which you have no observed biomass, you should set the value in the biomass_observed column to 0 or NA.

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.

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
params <- calibrateBiomass(params)
params <- matchBiomasses(params)
plotBiomassObservedVsModel(params)