Set up parameters for a community-type model

Edit this page.   Source: R/wrapper_functions.R

This functions creates a MizerParams object so that community-type models can be easily set up and run.

newCommunityParams(
  max_w = 1e+06,
  min_w = 0.001,
  z0 = 0.1,
  starv_coef = 10,
  alpha = 0.2,
  h = 10,
  beta = 100,
  sigma = 2,
  n = 2/3,
  kappa = 1000,
  lambda = 2.05,
  f0 = 0.7,
  r_pp = 10,
  gamma = NA,
  knife_edge_size = 1000,
  recruitment,
  ...
)

Arguments

max_w

The maximum size of the community. The w_inf of the species used to represent the community is set to this value. The default value is 1e6.
min_w

The minimum size of the community. Default value is 1e-3.
z0

The background mortality of the community. Default value is 0.1.
starv_coef

Proportionality constant for starvation mortality. When starv_coef is equal to 10 the instantaneous starvation mortality (1/year) is 1 when energy deficit is 10 is no starvation mortality
alpha

The assimilation efficiency of the community. Default value 0.2
h

The maximum food intake rate. Default value is 10.
beta

The preferred predator prey mass ratio. Default value is 100.
sigma

The width of the prey preference. Default value is 2.0.
n

The scaling exponent of the maximum intake rate. Default value is 2/3.
kappa

The carrying capacity of the plankton spectrum. Default value is 1000.
lambda

The exponent of the plankton spectrum. Default value is 2.05.
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 (see the package vignette). Default value is 0.7.
r_pp

Growth rate parameter for the plankton spectrum. Default value is 10.
gamma

Volumetric search rate. Estimated using h, f0 and kappa if not supplied.
knife_edge_size

The size at the edge of the knife-selectivity function. Default value is 1000.
recruitment

The constant recruitment in the smallest size class of the community spectrum. By default this is set so that the community spectrum continues the plankton spectrum.
...

Other arguments to pass to the MizerParams constructor.

Value

An object of type MizerParams

Details

A community model has several features that distinguish it from the food-web type models. Only one 'species' is resolved, i.e. one 'species' is used to represent the whole community. The plankton spectrum only extends to the start of the community spectrum. Recruitment to the smallest size in the community spectrum is constant and set by the user. As recruitment is constant, the proportion of energy invested in reproduction (the slot psi of the returned MizerParams object) is set to 0. Standard metabolism has been turned off (the parameter ks is set to 0). Consequently, the growth rate is now determined solely by the assimilated food (see the package vignette for more details).

The function has many arguments, all of which have default values.

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

See also

Other functions for setting up models: newMultispeciesParams(), newSheldonParams(), newTraitParams()

Examples

if (FALSE) {
params <- newCommunityParams(f0=0.7, z0=0.2, recruitment=3e7)
sim <- project(params, effort = 0, t_max = 100, dt=0.1)
plotBiomass(sim)
plotSpectra(sim)
}