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Add new species

Source: R/helpers.R
addSpecies.Rd

[Experimental]

Takes a MizerParams object and adds additional species with given parameters to the ecosystem. It sets the initial values for these new species to their steady-state solution in the given initial state of the existing ecosystem. This will be close to the true steady state if the abundances of the new species are sufficiently low. Hence the abundances of the new species are set so that they are at most 1/100th of the resource power law. Their reproductive efficiencies are set so as to keep them at that low level.

Usage

# S3 method for class 'mizerShelf'
addSpecies(params, species_params, ..., steady = FALSE)

Arguments

params

A mizer params object for the original system.

species_params

Data frame with the species parameters of the new species we want to add to the system.

...

Passed to mizer::addSpecies(), for example interaction, gear_params or initial_effort.

steady

Ignored. This method always adds the new species with steady = FALSE because at that point the carrion encounter rate matrix rho still has the old species dimensions, which would make steadySingleSpecies() fail. The steady state for the new species is computed separately afterwards.

Value

An object of type MizerParams

Details

The resulting MizerParams object will use the same size grid where possible, but if one of the new species needs a larger range of w (either because a new species has an egg size smaller than those of existing species or a maximum size larger than those of existing species) then the grid will be expanded and all arrays will be enlarged accordingly.

If any of the rate arrays of the existing species had been set by the user to values other than those calculated as default from the species parameters, then these will be preserved. Only the rates for the new species will be calculated from their species parameters.

After adding the new species, the background species are not retuned and the system is not run to steady state. This could be done with tuneSteadyState(). The new species will have a reproduction level of 1/4, this can then be changed with setBevertonHolt()

See also

removeSpecies()

Examples

params <- newTraitParams()
species_params <- data.frame(
    species = "Mullet",
    w_max = 173,
    w_mat = 15,
    beta = 283,
    sigma = 1.8,
    h = 30,
    a = 0.0085,
    b = 3.11
)
params <- addSpecies(params, species_params)
#> ℹ The species parameter data frame is missing a `w_inf` column. I am using the values from the `w_max` column instead. 
#> ℹ Using f0, h, lambda, kappa and the predation kernel to calculate gamma.
plotSpectra(params)