R: Get energy rate available for reproduction and growth needed...

mizerEReproAndGrowth {mizer}

R Documentation

Get energy rate available for reproduction and growth needed to project standard mizer model

Description

Calculates the energy rate E_{r.i}(w) (grams/year) available to an individual of species i and size w for reproduction and growth after metabolism and movement have been accounted for. You would not usually call this function directly but instead use getEReproAndGrowth(), which then calls this function unless an alternative function has been registered, see below.

Usage

mizerEReproAndGrowth(
  params,
  n,
  n_pp,
  n_other,
  t,
  encounter,
  feeding_level,
  ...
)

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.)
`encounter`	An array (species x size) with the encounter rate as calculated by `getEncounter()`.
`feeding_level`	An array (species x size) with the feeding level as calculated by `getFeedingLevel()`.
`...`	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")