Set up parameters for a community-type modelSource:
This functions creates a
MizerParams object describing a
The function has many arguments, all of which have default values.
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 )
The maximum size of the community. The
w_maxof the species used to represent the community is set to this value.
The minimum size of the community.
The number of size bins in the consumer spectrum.
The smallest size of the resource spectrum. By default this is set to the smallest value at which any of the consumers can feed.
The background mortality of the community.
The assimilation efficiency of the community.
The average feeding level of individuals who feed on a power-law spectrum. This value is used to calculate the search rate parameter
The coefficient of the maximum food intake rate.
Volumetric search rate. Estimated using
kappaif not supplied.
The preferred predator prey mass ratio.
The width of the prey preference.
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.
The coefficient of the initial resource abundance power-law.
Used to set power-law exponent for resource capacity if the
resource_capacityargument is given as a single number.
The size at the edge of the knife-edge-selectivity function.
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.
An object of type
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
ksis 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
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
Other functions for setting up models:
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)