This functions creates a MizerParams
object describing a
communitytype model.
newCommunityParams( max_w = 1e+06, min_w = 0.001, no_w = 100, min_w_pp = 1e10, 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 )
max_w  The maximum size of the community. The 

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 powerlaw
spectrum. This value is used to calculate the search rate parameter

h  The coefficient of the maximum food intake rate. 
gamma  Volumetric search rate. Estimated using 
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  Coefficient of the intrinsic resource carrying capacity 
lambda  Scaling exponent of the intrinsic resource carrying capacity 
r_pp  Coefficient of the intrinsic resource birth rate 
knife_edge_size  The size at the edge of the knifeedgeselectivity 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. 
An object of type MizerParams
A community model has several features that distinguish it from a multispecies 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
The function has many arguments, all of which have default values.
Fishing selectivity is modelled as a knifeedge 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.
K. H. Andersen,J. E. Beyer and P. Lundberg, 2009, Trophic and individual efficiencies of sizestructured communities, Proceedings of the Royal Society, 276, 109114
Other functions for setting up models:
newMultispeciesParams()
,
newTraitParams()
if (FALSE) { params < newCommunityParams(f0=0.7, z0=0.2, reproduction=3e7) sim < project(params, effort = 0, t_max = 100, dt=0.1) plotBiomass(sim) plotSpectra(sim) }