newCommunityParams: Set up parameters for a community-type model

Description

This functions creates a MizerParams object describing a community-type model. The function has many arguments, all of which have default values.

Usage

newCommunityParams(
  max_w = 1e+06,
  min_w = 0.001,
  no_w = 100,
  min_w_pp = 1e-10,
  z0 = 0.1,
  alpha = 0.2,
  f0 = 0.7,
  h = 10,
  gamma = NA,
  beta = 100,
  sigma = 2,
  n = 2/3,
  kappa = 1000,
  lambda = 2.05,
  r_pp = 10,
  knife_edge_size = 1000,
  reproduction,
  second_order_w = FALSE,
  info_level = 2
)

Value

An object of type MizerParams

Arguments

max_w: The maximum size of the community. The w_max of the species used to represent the community is set to this value.
min_w: The minimum size of the community.
no_w: The number of size bins in the consumer spectrum.
min_w_pp: The smallest size of the resource spectrum. By default this is set to the smallest value at which any of the consumers can feed.
z0: The background mortality of the community.
alpha: The assimilation efficiency of the community.
f0: The average feeding level of individuals who feed on a power-law spectrum. This value is used to calculate the search rate parameter gamma.
h: The coefficient of the maximum food intake rate.
gamma: Volumetric search rate. Passed through to newMultispeciesParams(), which estimates it from h, f0, and kappa if it is left as NA.
beta: The preferred predator prey mass ratio.
sigma: The width of the prey preference.
n: The allometric growth exponent. Used as allometric exponent for the maximum intake rate of the community as well as the intrinsic growth rate of the resource.
kappa: The coefficient \(\kappa\) of the resource carrying capacity power law \(c_R(w) = \kappa\, w^{-\lambda}\), which also sets the initial resource abundance. See resource_params().
lambda: Used to set power-law exponent for resource capacity if the resource_capacity argument is given as a single number.
r_pp: Growth rate parameter for the resource spectrum.
knife_edge_size: The size at the edge of the knife-edge-selectivity function.
reproduction: The constant reproduction in the smallest size class of the community spectrum. By default this is set to the rate required to maintain the constructed initial egg abundance.
second_order_w: Selects the second-order numerical scheme for the new model. Accepts the same values as the second_order_w() setter: a single logical (TRUE switches on both second-order flux and bin-averaging), a single flux scheme name ("upwind", "van_leer" or "centred"), or a named vector with entries flux and/or bin_average. The bin_average choice is applied before the resource and abundance power laws are constructed, so they are built bin-averaged from the start (unlike setting second_order_w() on an existing object). The flux scheme governs time projection only, so the robust first-order upwind scheme is used for the construction-time steady-state solve and the chosen scheme is then activated for the returned model. Defaults to FALSE (the first-order behaviour of previous mizer).
info_level: Controls the amount of information messages that are shown when the function sets default values for parameters. Higher levels lead to more messages.

Details

A community model has several features that distinguish it from a multi-species model:

Species identities of individuals are ignored. All are aggregated into a single community.
The resource spectrum only extends to the start of the community spectrum.
Reproductive rate is constant, independent of the energy invested in reproduction, which is set to 0.
Standard metabolism is turned off (the parameter ks is set to 0). Consequently, the growth rate is now determined solely by the assimilated food

Fishing selectivity is modelled as a knife-edge function with one parameter, knife_edge_size, which determines the size at which species are selected.

Because this constructor does not yet set up stochastic growth by diffusion, the size grid is not extended beyond the community's maximum size max_w (so that w_max = w_repro_max), rather than leaving the headroom that newMultispeciesParams() uses to accommodate stochastic growth. This will be revisited once these constructors gain a diffusion parameter, see https://github.com/sizespectrum/mizer/issues/339.

The resulting MizerParams object can be projected forward using project() like any other MizerParams object. When projecting the community model it may be necessary to keep a small time step size dt of around 0.1 to avoid any instabilities with the solver. You can check for these numerical instabilities by plotting the biomass or abundance through time after the projection.

References

K. H. Andersen,J. E. Beyer and P. Lundberg, 2009, Trophic and individual efficiencies of size-structured communities, Proceedings of the Royal Society, 276, 109-114

Examples

Run this code

params <- newCommunityParams()
sim <- project(params, t_max = 10)
plotBiomass(sim)
plotSpectra(sim, power = 2)

# More satiation. More mortality
params <- newCommunityParams(f0 = 0.8, z0 = 0.4)
sim <- project(params, t_max = 10)
plotBiomass(sim)
plotSpectra(sim, power = 2)

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