calibrateYield: Calibrate the model scale to match total observed yield

In mizer: Dynamic Multi-Species Size Spectrum Modelling

Calibrate the model scale to match total observed yield

Description

Usage

calibrateYield(params)

Arguments

params

A MizerParams object

Details

This function has been deprecated and will be removed in the future unless you have a use case for it. If you do have a use case for it, please let the developers know by creating an issue at https://github.com/sizespectrum/mizer/issues.

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

After using this function the total yield in the model will match the total observed yield, summed over all species. However the yields of the individual species will not match observations yet, with some species having yields that are too high and others too low. So after this function you may want to use matchYields().

If you have observations of species biomasses instead of yields, you can use calibrateBiomass() instead of this function.

Value

A MizerParams object

Examples

params <- NS_params
species_params(params)$yield_observed <-
    c(0.8, 61, 12, 35, 1.6, 20, 10, 7.6, 135, 60, 30, 78)
gear_params(params)$catchability <-
    c(1.3, 0.065, 0.31, 0.18, 0.98, 0.24, 0.37, 0.46, 0.18, 0.30, 0.27, 0.39)
params2 <- calibrateYield(params)
plotYieldObservedVsModel(params2)

mizer documentation built on Oct. 17, 2024, 9:07 a.m.