Sets up parameters for a community-type model

Description

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

Usage

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  set_community_model(max_w = 1e+06, min_w = 0.001,
    z0 = 0.1, alpha = 0.2, h = 10, beta = 100, sigma = 2,
    q = 0.8, n = 2/3, kappa = 1000, lambda = 2 + q - n,
    f0 = 0.7, r_pp = 10, gamma = NA,
    knife_edge_size = 1000, knife_is_min = TRUE,
    recruitment = kappa * min_w^-lambda, rec_mult = 1, ...)

Arguments

z0

The background mortality of the community. The default value is 0.1.

alpha

The assimilation efficiency of the community. The default value is 0.2

f0

The average feeding level of individuals who feed mainly on the resource. This value is to used to calculate the search rate parameter ga,,a (see the package Vignette). The default value is 0.7.

h

The maximum food intake rate. The default value is 10.

beta

The preferred predator prey mass ratio. The default value is 100.

sigma

The width of the prey preference. The default value is 2.0.

q

The search volume exponent. The default value is 0.8.

n

The scaling of the intake. The default value is 2/3.

kappa

The carrying capacity of the background spectrum. The default value is 1000.

lambda

The exponent of the background spectrum. The default value is 2 + q - n.

r_pp

Growth rate of the primary productivity. Default value is 10.

gamma

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

recruitment

The constant recruitment in the smallest size class of the community spectrum. This should be set so that the community spectrum continues the background spectrum. The default value = kappa * min_w^-lambda.

rec_mult

Additional multiplier for the constant recruitment. Default value is 1.

knife_edge_size

The size at the edge of the knife-selectivity function.

knife_is_min

Is the knife-edge selectivity function selecting above (TRUE) or below (FALSE) the edge.

max_w

The maximum size of the community. The w_inf of the species used to represent the community is set to 0.9 * this value. The default value is 1e6.

min_w

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

...

Other arguments to pass to the MizerParams constructor.

Details

The function has many arguments, all of which have default values. The main arguments that the users should be concerned with are z0, recruitment, alpha and f0 as these determine the average growth rate of the community.

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 reduce dt to 0.1 to avoid any instabilities with the solver. You can check this by plotting the biomass or abundance through time after the projection.

Value

An object of type MizerParams

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

MizerParams

Examples

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## Not run: 
params <- set_community_model(f0=0.7, z0=0.2, recruitment=3e7)
sim <- project(params, effort = 0, t_max = 100, dt=0.1)
plotBiomass(sim)
plotSpectra(sim)

## End(Not run)

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