Set up parameters for a community-type model

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
)

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. Estimated using h, f0 and kappa if not supplied.
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 of the initial resource abundance power-law.
lambda: Used to set power-law exponent for resource capacity if the resource_capacity argument is given as a single number.
r_pp: . Use resource_rate argument instead.
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 so that the community spectrum is continuous with the resource spectrum.

Value

An object of type MizerParams

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.

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

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)