addSpecies: Add new species

Description

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 the maximal biomass density of each new species lies at 1/100 of the community power law. The reproductive efficiencies of the new species are set so as to keep them at that low level.

Usage

addSpecies(
  params,
  species_params,
  gear_params = data.frame(),
  initial_effort,
  interaction
)

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.

gear_params

Optional data frame with the gear parameters for the new species.

initial_effort

A named vector with the effort for new fishing gear introduced in gear_params. Only needed if new gear are introduced, not if the new species are fished only by existing gear.

interaction

Interaction matrix. A square matrix giving either the interaction coefficients between all species or only those between the new species. In the latter case all interaction between an old and a new species are set to 1. If this argument is missing, all interactions involving a new species are set to 1.

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 had been set by the user to values other than those calculated as default from the species parameters, then these will be preserved.

After adding the new species, the background species are not retuned and the system is not run to steady state.

Examples

Run this code

# NOT RUN {
params <- newTraitParams()
a_m <- 0.0085
b_m <- 3.11
L_inf_m <- 24.3
L_mat <- 11.1
species_params <- data.frame(
    species = "mullet",
    w_min = 0.001,
    w_inf = a_m*L_inf_m^b_m,
    w_mat = a_m*L_mat^b_m,
    beta = 283,
    sigma = 1.8,
    z0 = 0,
    alpha = 0.6,
    sel_func = "knife_edge",
    knife_edge_size = 100,
    gear = "knife_edge_gear",
    k = 0,
    k_vb = 0.6,
    a = a_m,
    b = b_m
)
params <- addSpecies(params, species_params)
plotSpectra(params)
sim <- project(params, t_max=50, progress_bar = FALSE)
plotBiomass(sim)
# }