getEReproAndGrowth: Get energy rate available for reproduction and growth

In mizer: Dynamic Multi-Species Size Spectrum Modelling

Get energy rate available for reproduction and growth

Description

Calculates the energy rate E_{r.i}(w) (grams/year) available for reproduction and growth after metabolism and movement have been accounted for.

Usage

getEReproAndGrowth(
  params,
  n = initialN(params),
  n_pp = initialNResource(params),
  n_other = initialNOther(params),
  t = 0,
  ...
)

Arguments

params	A MizerParams object
n	A matrix of species abundances (species x size).
n_pp	A vector of the resource abundance by size
n_other	A list of abundances for other dynamical components of the ecosystem
t	The time for which to do the calculation (Not used by standard mizer rate functions but useful for extensions with time-dependent parameters.)
...	Unused

Value

A two dimensional array (species x size) holding

E_{r.i}(w) = \max(0, \alpha_i\, (1 - {\tt feeding\_level}_i(w))\, {\tt encounter}_i(w) - {\tt metab}_i(w)).

Due to the form of the feeding level, calculated by getFeedingLevel(), this can also be expressed as

E_{r.i}(w) = \max(0, \alpha_i\, {\tt feeding\_level}_i(w)\, h_i(w) - {\tt metab}_i(w))

where h_i is the maximum intake rate, set with setMaxIntakeRate(). The assimilation rate \alpha_i is taken from the species parameter data frame in params. The metabolic rate metab is taken from params and set with setMetabolicRate().

The return value can be negative, which means that the energy intake does not cover the cost of metabolism and movement.

Your own energy rate function

By default getEReproAndGrowth() calls mizerEReproAndGrowth(). However you can replace this with your own alternative energy rate function. If your function is called "myEReproAndGrowth" then you register it in a MizerParams object params with

params <- setRateFunction(params, "EReproAndGrowth", "myEReproAndGrowth")

Your function will then be called instead of mizerEReproAndGrowth(), with the same arguments.

See Also

The part of this energy rate that is invested into growth is calculated with getEGrowth() and the part that is invested into reproduction is calculated with getERepro().

Other rate functions: getEGrowth(), getERepro(), getEncounter(), getFMort(), getFMortGear(), getFeedingLevel(), getMort(), getPredMort(), getPredRate(), getRDD(), getRDI(), getRates(), getResourceMort()

Examples

params <- NS_params
# Project with constant fishing effort for all gears for 20 time steps
sim <- project(params, t_max = 20, effort = 0.5)
# Get the energy at a particular time step
e <- getEReproAndGrowth(params, n = N(sim)[15, , ], 
                        n_pp = NResource(sim)[15, ], t = 15)
# Rate at this time for Sprat of size 2g
e["Sprat", "2"]

mizer documentation built on Oct. 17, 2024, 9:07 a.m.