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

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")

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

See also

Other mizer rate functions: mizerEGrowth(), mizerERepro(), mizerEncounter(), mizerFMort(), mizerFMortGear(), mizerFeedingLevel(), mizerMort(), mizerPredMort(), mizerPredRate(), mizerRDI(), mizerRates(), mizerResourceMort()