R/project_methods.R
getEReproAndGrowth.RdCalculates the energy rate \(E_{r.i}(w)\) (grams/year) available for reproduction and growth after metabolism and movement have been accounted for.
getEReproAndGrowth( params, n = params@initial_n, n_pp = params@initial_n_pp, n_other = params@initial_n_other, encounter = getEncounter(params, n = n, n_pp = n_pp, n_other = n_other), feeding_level = getFeedingLevel(params, n = n, n_pp = n_pp, n_other = n_other, encounter = encounter) )
| params | A MizerParams object |
|---|---|
| n | A matrix of species abundances (species x size). |
| n_pp | A vector of the plankton abundance by size |
| n_other | A list of abundances for other dynamical components of the ecosystem |
| encounter | The encounter rate matrix (optional) of dimension no.
species x no. size bins. If not passed in, it is calculated internally
using the |
| feeding_level | The current feeding level (optional). A matrix of size
no. species x no. size bins. If not supplied, is calculated internally
using the |
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
setIntakeMax.
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 setMetab.
The return value can be negative, which means that the energy intake does not cover the cost of metabolism and movement.
The parts of this energy rate that is invested into growth is
calculated with getERepro and the part that is invested into
reproduction is calculated with getEGrowth.
Other rate functions:
getEGrowth(),
getERepro(),
getEncounter(),
getFMortGear(),
getFMort(),
getFeedingLevel(),
getMort(),
getPlanktonMort(),
getPredMort(),
getPredRate(),
getRDD(),
getRDI(),
getRates(),
getStarvMort()
if (FALSE) { data(NS_species_params_gears) data(inter) params <- newMultispeciesParams(NS_species_params_gears, inter) # 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 getEReproAndGrowth(params,sim@n[21,,],sim@n_pp[21,]) }