setResource: Set resource dynamics

Description

Sets the intrinsic resource birth rate and the intrinsic resource carrying capacity as well as the name of the function used to simulate the resource dynamics. By default, the birth rate and the carrying capacity are changed together in such a way that the resource replenishes at the same rate at which it is consumed. So you should only provide either the resource_rate or the resource_capacity (or resource_level) because the other is determined by the requirement that the resource replenishes at the same rate at which it is consumed.

Usage

setResource(
  params,
  resource_rate = NULL,
  resource_capacity = NULL,
  resource_level = NULL,
  resource_dynamics = NULL,
  balance = NULL,
  lambda = resource_params(params)[["lambda"]],
  n = resource_params(params)[["n"]],
  w_pp_cutoff = resource_params(params)[["w_pp_cutoff"]],
  r_pp = deprecated(),
  kappa = deprecated(),
  ...
)
resource_rate(params)
resource_rate(params) <- value
resource_capacity(params)
resource_capacity(params) <- value
resource_level(params)
resource_level(params) <- value
resource_dynamics(params)
resource_dynamics(params) <- value

Value

setResource: A MizerParams object with updated resource parameters

A vector with the intrinsic resource birth rate for each size class.

A vector with the intrinsic resource capacity for each size class.

A vector with the ratio between the current resource number density and the resource capacity for each size class.

The name of the function that determines the resource dynamics.

Arguments

params: A MizerParams object
resource_rate: Optional. A vector of per-capita resource birth rate for each size class or a single number giving the coefficient in the power-law for this rate, see "Setting resource dynamics" below. Must be strictly positive.
resource_capacity: Optional. Vector of resource intrinsic carrying capacities or coefficient in the power-law for the capacity, see "Setting resource dynamics" below. The resource capacity must be larger than the resource abundance.
resource_level: Optional. The ratio between the current resource number density and the resource capacity. Either a number used at all sizes or a vector specifying a value for each size. Must be strictly between 0 and 1, except at sizes where the resource is zero, where it can be NaN. This determines the resource capacity, so do not specify both this and resource_capacity.
resource_dynamics: Optional. Name of the function that determines the resource dynamics by calculating the resource spectrum at the next time step from the current state.
balance: By default, if possible, the resource parameters are set so that the resource replenishes at the same rate at which it is consumed. In this case you should only specify either the resource rate or the resource capacity (or resource level) because the other is then determined automatically. Set to FALSE if you do not want the balancing.
lambda: Used to set power-law exponent for resource capacity if the resource_capacity argument is given as a single number.
n: Used to set power-law exponent for resource rate if the resource_rate argument is given as a single number.
w_pp_cutoff: The upper cut off size of the resource spectrum power law used when resource_capacity is given as a single number. When changing w_pp_cutoff without providing resource_capacity, the cutoff can only be decreased. In that case, both the carrying capacity and the initial resource abundance will be cut off at the new value. To increase the cutoff, you must also provide the resource_capacity for the extended range.
r_pp: . Use resource_rate argument instead.
kappa: . Use resource_capacity argument instead.
...: Unused
value: The desired new value for the respective parameter.

Setting resource dynamics

The resource_dynamics argument allows you to choose the resource dynamics function. By default, mizer uses a semichemostat model to describe the resource dynamics in each size class independently. This semichemostat dynamics is implemented by the function resource_semichemostat(). You can change that to use a logistic model implemented by resource_logistic() or you can use resource_constant() which keeps the resource constant or you can write your own function.

Both the resource_semichemostat() and the resource_logistic() dynamics are parametrised in terms of a size-dependent birth rate $r_R(w)$ and a size-dependent capacity $c_R$. The help pages of these functions give the details.

The resource_rate argument can be a vector (with the same length as w_full(params)) specifying the intrinsic resource birth rate for each size class. Alternatively it can be a single number that is used as the coefficient in a power law: then the intrinsic birth rate $r_R(w)$ at size $w$ is set to $$r_R(w) = r_R w^{n-1}.$$ The power-law exponent $n$ is taken from the n argument.

The resource_capacity argument can be a vector specifying the intrinsic resource carrying capacity for each size class. Alternatively it can be a single number that is used as the coefficient in a truncated power law: then the intrinsic carrying capacity $c_R(w)$ at size $w$ is set to $$c_R(w) = c_R\, w^{-\lambda}$$ for all $w$ less than w_pp_cutoff and zero for larger sizes. The power-law exponent $\lambda$ is taken from the lambda argument.

The values for lambda, n and w_pp_cutoff are stored in a list in the resource_params slot of the MizerParams object so that they can be re-used automatically in the future. That list can be accessed with resource_params().

Details

You would usually set the resource dynamics only after having finished the calibration of the steady state. Then setting the resource dynamics with this function will preserve that steady state, unless you explicitly choose to set balance = FALSE. Your choice of the resource dynamics only affects the dynamics around the steady state. The higher the resource rate or the lower the resource capacity the less sensitive the model will be to changes in the competition for resource.

If you provide the resource_level then that sets the resource_capacity to the current resource number density divided by the resource level. So in that case you should not specify resource_capacity as well.

If you provide none of the arguments resource_level, resource_rate or resource_capacity then the resource rate is kept at its previous value.

Examples

Run this code

params <- NS_params
resource_dynamics(params)
resource_dynamics(params) <- "resource_constant"

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