matchYields: Match yields to observations

In mizer: Dynamic Multi-Species Size Spectrum Modelling

Match yields to observations

Description

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.

Usage

matchYields(params, species = NULL)

Arguments

params	A MizerParams object
species	The species to be affected. Optional. By default all observed yields 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.

Details

If you want to match the yields to observations, you should use the matchYield() function from the mizerExperimental package instead, which adjusts the catchability to match the yield rather than by adjusting the biomass.

The function adjusts the abundances of the species in the model so that their yearly yields under the given fishing mortalities match with observations.

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 yields 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 yield_observed column to your model which gives the observed yields in grams per year. For species for which you have no observed biomass, you should set the value in the yield_observed column to 0 or NA.

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)
params <- calibrateYield(params)
params <- matchYields(params)
plotYieldObservedVsModel(params)

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