mizer (version 2.2.0)

newSingleSpeciesParams: Set up parameters for a single species in a power-law background

Description

This functions creates a MizerParams object with a single species. This species is embedded in a fixed power-law 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 power-law 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.

Usage

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,
  R_factor = 4,
  version
)

Arguments

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 and asymptotic size w_inf. Default is 10^(-0.6), approximately 1/4. Ignored if w_mat is supplied explicitly.

w_mat

Maturity size of species. Default value is eta * w_inf.

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 n.

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 gamma, the coefficient in the search rate. Ignored if gamma is given explicitly.

fc

Critical feeding level. Used to determine ks if it is not given explicitly.

ks

Standard metabolism coefficient. If not provided, default will be calculated from critical feeding level argument fc.

gamma

Volumetric search rate. If not provided, default is determined by get_gamma_default() using the value of f0.

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).

R_factor

The factor such that R_max = R_factor * R, where R_max is the maximum reproduction rate allowed and R is the steady-state reproduction rate. Thus the larger R_factor the less the impact of the density-dependence.

version

A string specifying the version of mizer. If you want to make sure that your code will still set up the model with the exact same default values even if it is run with a future versions of mizer that would choose defaults differently, then set this argument to "v2.2.0".

Value

An object of type MizerParams

Details

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.

Although the steady state is often stable without imposing a stock recruitment relationship, the function can set a Beverton-Holt type stock recruitment relationship that imposes a maximal reproduction rate that is a multiple of the recruitment rate at steady state. That multiple is set by the argument R_factor.

See Also

Other functions for setting up models: newCommunityParams(), newMultispeciesParams(), newTraitParams()

Examples

# NOT RUN {
params <- newSingleSpeciesParams()
sim <- project(params, t_max = 5, effort = 0)
plotSpectra(sim)
# }