This function has been deprecated in favour of the function
newCommunityParams() that sets better default values.
set_community_model( max_w = 1e+06, min_w = 0.001, min_w_pp = 1e-10, 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, ... )
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.
The minimum size of the community. Default value is 1e-3.
The smallest size of the resource spectrum.
The background mortality of the community. Default value is 0.1.
The assimilation efficiency of the community. Default value 0.2
The maximum food intake rate. Default value is 10.
The preferred predator prey mass ratio. Default value is 100.
The width of the prey preference. Default value is 2.0.
The search volume exponent. Default value is 0.8.
The scaling of the intake. Default value is 2/3.
The carrying capacity of the resource spectrum. Default value is 1000.
The exponent of the resource spectrum. Default value is 2 + q - n.
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.
Growth rate parameter for the resource spectrum. Default value is 10.
Volumetric search rate. Estimated using
kappa if not supplied.
The size at the edge of the knife-selectivity function. Default value is 1000.
Is the knife-edge selectivity function selecting above (TRUE) or below (FALSE) the edge. Default is TRUE.
The constant recruitment in the smallest size class of the
community spectrum. This should be set so that the community spectrum
continues the resource spectrum. Default value =
Additional multiplier for the constant recruitment. Default value is 1.
Other arguments to pass to the
An object of type
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
The function has many arguments, all of which have default values. The main
arguments that the users should be concerned with are
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
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.
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