Set up parameters for a trait-based multispecies model

This functions creates a MizerParams object describing a trait-based model. This is a simplification of the general size-based model used in mizer in which the species-specific parameters are the same for all species, except for the maximum size, which is considered the most important trait characterizing a species. Other parameters are related to the maximum size. For example, the size at maturity is given by w_max * eta, where eta is the same for all species. For the trait-based model the number of species is not important. For applications of the trait-based model see Andersen & Pedersen (2010). See the mizer website for more details and examples of the trait-based model.

Usage

newTraitParams(
  no_sp = 11,
  min_w_max = 10,
  max_w_max = 10^4,
  min_w = 10^(-3),
  max_w = max_w_max,
  eta = 10^(-0.6),
  min_w_mat = min_w_max * eta,
  no_w = round(log10(max_w_max/min_w) * 20 + 1),
  min_w_pp = 1e-10,
  w_pp_cutoff = min_w_mat,
  n = 2/3,
  p = n,
  lambda = 2.05,
  r_pp = 0.1,
  kappa = 0.005,
  alpha = 0.4,
  h = 40,
  beta = 100,
  sigma = 1.3,
  f0 = 0.6,
  fc = 0.25,
  ks = NA,
  gamma = NA,
  ext_mort_prop = 0,
  reproduction_level = 1/4,
  R_factor = deprecated(),
  gear_names = "knife_edge_gear",
  knife_edge_size = 1000,
  egg_size_scaling = FALSE,
  resource_scaling = FALSE,
  perfect_scaling = FALSE,
  min_w_inf = deprecated(),
  max_w_inf = deprecated()
)

Arguments

no_sp: The number of species in the model.
min_w_max: The maximum size of the smallest species in the community. This will be rounded to lie on a grid point.
max_w_max: The maximum size of the largest species in the community. This will be rounded to lie on a grid point.
min_w: The size of the the egg of the smallest species. This also defines the start of the community size spectrum.
max_w: The largest size in the model. By default this is set to the largest maximum size max_w_max. Setting it to something larger only makes sense if you plan to add larger species to the model later.
eta: Ratio between maturity size and maximum size of a species. Ignored if min_w_mat is supplied. Default is 10^(-0.6), approximately 1/4.
min_w_mat: The maturity size of the smallest species. Default value is eta * min_w_max. This will be rounded to lie on a grid point.
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.
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.
w_pp_cutoff: The largest size of the resource spectrum. Default value is min_w_max unless perfect_scaling = TRUE when it is Inf.
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.
r_pp: Growth rate parameter for the resource spectrum.
kappa: Coefficient in abundance power law.
alpha: The assimilation efficiency.
h: Maximum food intake rate.
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).
reproduction_level: A number between 0 an 1 that determines the level of density dependence in reproduction, see setBevertonHolt().
R_factor: Use reproduction_level = 1 / R_factor instead.
gear_names: The names of the fishing gears for each species. A character vector, the same length as the number of species.
knife_edge_size: The minimum size at which the gear or gears select fish. A single value for each gear or a vector with one value for each gear.
egg_size_scaling: If TRUE, the egg size is a constant fraction of the maximum size of each species. This fraction is min_w / min_w_max. If FALSE, all species have the egg size w_min.
resource_scaling: If TRUE, the carrying capacity for larger resource is reduced to compensate for the fact that fish eggs and larvae are present in the same size range.
perfect_scaling: If TRUE then parameters are set so that the community abundance, growth before reproduction and death are perfect power laws. In particular all other scaling corrections are turned on.
min_w_inf: The argument has been renamed to min_w_max to make it clearer that it refers to the maximum size of a species not the von Bertalanffy asymptotic size parameter.
max_w_inf: The argument has been renamed to max_w_max.

Value

An object of type MizerParams

Details

The function has many arguments, all of which have default values. Of particular interest to the user are the number of species in the model and the minimum and maximum sizes.

The characteristic weights of the smallest species are defined by min_w (egg size), min_w_mat (maturity size) and min_w_max (maximum size). The maximum sizes of the no_sp species are logarithmically evenly spaced, ranging from min_w_max to max_w_max. Similarly the maturity sizes of the species are logarithmically evenly spaced, so that the ratio eta between maturity size and maximum size is the same for all species. If egg_size_scaling = TRUE then also the ratio between maximum size and egg size is the same for all species. Otherwise all species have the same egg size.

In addition to setting up the parameters, this function also sets up an initial condition that is close to steady state.

The search rate coefficient gamma is calculated using the expected feeding level, f0.

The option of including fishing is given, but the steady state may loose its natural stability if too much fishing is included. In such a case the user may wish to include stabilising effects (like reproduction_level) to ensure the steady state is stable. Fishing selectivity is modelled as a knife-edge function with one parameter, knife_edge_size, which is the size at which species are selected. Each species can either be fished by the same gear (knife_edge_size has a length of 1) or by a different gear (the length of knife_edge_size has the same length as the number of species and the order of selectivity size is that of the maximum size).

The resulting MizerParams object can be projected forward using project() like any other MizerParams object. When projecting the model it may be necessary to reduce dt below 0.1 to avoid any instabilities with the solver. You can check this by plotting the biomass or abundance through time after the projection.

Examples

params <- newTraitParams()
sim <- project(params, t_max = 5, effort = 0)
plotSpectra(sim)