mizer (version 3.0.0)

matchNumbers: Match numbers to observations

Description

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

Usage

matchNumbers(params, species = NULL, info_level = 3, ...)

Value

A MizerParams object

Arguments

params

A MizerParams object

species

The species to be affected. Optional. By default all observed numbers 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.

info_level

Controls the amount of information messages that are shown. Higher levels lead to more messages.

...

Additional arguments passed to the method.

Details

The function works by multiplying for each species the number density at all sizes by the same factor. This will of course not give a steady state solution, even if the initial number 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 numbers will no longer match exactly. You could then iterate this process. This is described in the blog post at https://blog.mizer.sizespectrum.org/posts/2021-08-20-a-5-step-recipe-for-tuning-the-model-steady-state/.

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

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

Examples

params <- NS_params
species_params(params)$number_observed <-
    c(0.8, 61, 12, 35, 1.6, 20, 10, 7.6, 135, 60, 30, 78)
species_params(params)$number_cutoff <- 10
params <- calibrateNumber(params)
params <- matchNumbers(params)