R/newSingleSpeciesParams.R
newSingleSpeciesParams.Rd
This functions creates a MizerParams
object with a single
species. This species is embedded in a fixed powerlaw community spectrum
$$N_c(w) = \kappa w^{\lambda}$$
This community provides the food income for the species. Cannibalism is
switched off. The predation mortality arises only from the predators in the
powerlaw community and it is assumed that the predators in the community
have the same feeding parameters as the foreground species. The function has
many arguments, all of which have default values.
newSingleSpeciesParams( species_name = "Target species", w_inf = 100, w_min = 0.001, eta = 10^(0.6), w_mat = w_inf * eta, no_w = log10(w_inf/w_min) * 20 + 1, n = 3/4, p = n, lambda = 2.05, kappa = 0.005, alpha = 0.4, k_vb = 1, beta = 100, sigma = 1.3, f0 = 0.6, fc = 0.25, ks = NA, gamma = NA, ext_mort_prop = 0, reproduction_level = 0, R_factor = deprecated() )
species_name  A string with a name for the species. Will be used in plot legends. 

w_inf  Asymptotic size of species 
w_min  Egg size of species 
eta  Ratio between maturity size 
w_mat  Maturity size of species. Default value is

no_w  The number of size bins in the community spectrum. These bins will be equally spaced on a logarithmic scale. Default value is such that there are 20 bins for each factor of 10 in weight. 
n  Scaling exponent of the maximum intake rate. 
p  Scaling exponent of the standard metabolic rate. By default this is
equal to the exponent 
lambda  Exponent of the abundance power law. 
kappa  Coefficient in abundance power law. 
alpha  The assimilation efficiency. 
k_vb  The von Bertalanffy growth parameter. 
beta  Preferred predator prey mass ratio. 
sigma  Width of prey size preference. 
f0  Expected average feeding level. Used to set 
fc  Critical feeding level. Used to determine 
ks  Standard metabolism coefficient. If not provided, default will be
calculated from critical feeding level argument 
gamma  Volumetric search rate. If not provided, default is determined
by 
ext_mort_prop  The proportion of the total mortality that comes from external mortality, i.e., from sources not explicitly modelled. A number in the interval [0, 1). 
reproduction_level  A number between 0 an 1 that determines the
level of density dependence in reproduction, see 
R_factor 
An object of type MizerParams
In addition to setting up the parameters, this function also sets up an initial condition that is close to steady state, under the assumption of no fishing.
Other functions for setting up models:
newCommunityParams()
,
newMultispeciesParams()
,
newTraitParams()
params < newSingleSpeciesParams() sim < project(params, t_max = 5, effort = 0) plotSpectra(sim)