Set up plankton

Sets the intrinsic plankton growth rate and the intrinsic plankton carrying capacity as well as the name of the function used to simulate the plankton dynamics

setPlankton(
  params,
  rr_pp = NULL,
  cc_pp = NULL,
  r_pp = params@plankton_params[["r_pp"]],
  kappa = params@plankton_params[["kappa"]],
  lambda = params@plankton_params[["lambda"]],
  n = params@plankton_params[["n"]],
  w_pp_cutoff = params@plankton_params[["w_pp_cutoff"]],
  plankton_dynamics = NULL
)

Arguments

params	A MizerParams object
rr_pp	Optional. Vector of plankton intrinsic growth rates
cc_pp	Optional. Vector of plankton intrinsic carrying capacity
r_pp	Coefficient of the intrinsic growth rate
kappa	Coefficient of the intrinsic carrying capacity
lambda	Scaling exponent of the intrinsic carrying capacity
n	Scaling exponent of the intrinsic growth rate
w_pp_cutoff	The upper cut off size of the plankton spectrum. Default is 10 g.
plankton_dynamics	Function that determines plankton dynamics by calculating the plankton spectrum at the next time step from the current state.

Value

A MizerParams object

Setting plankton dynamics

By default, mizer uses a semichemostat model to describe the plankton dynamics in each size class independently. This semichemostat dynamics is implemented by the function plankton_semichemostat. You can change the plankton dynamics by writing your own function, modelled on plankton_semichemostat, and then passing the name of your function in the plankton_dynamics argument.

The rr_pp argument is a vector specifying the intrinsic plankton growth rate for each size class. If it is not supplied, then the intrinsic growth rate \(r_p(w)\) at size \(w\) is set to $$r_p(w) = r_p\, w^{n-1}.$$ The values of \(r_p\) and \(n\) are taken from the r_pp and n arguments.

The cc_pp argument is a vector specifying the intrinsic plankton carrying capacity for each size class. If it is not supplied, then the intrinsic carrying capacity \(c_p(w)\) at size \(w\) is set to $$c_p(w) = \kappa\, w^{-\lambda}$$ for all \(w\) less than w_pp_cutoff and zero for larger sizes. The values of \(\kappa\) and \(\lambda\) are taken from the kappa and lambda arguments.

See also

Other functions for setting parameters: setBMort(), setFishing(), setInitial(), setIntakeMax(), setInteraction(), setMetab(), setParams(), setPredKernel(), setReproduction(), setSearchVolume()