mizer (version 0.4)

getFeedingLevel: getFeedingLevel method for the size based model

Description

Calculates the amount of food \(f_i(w)\) consumed by a predator by predator size based on food availability, search volume and maximum intake. This method is used by the project method for performing simulations.

getFeedingLevel method for a MizerParams object with already calculated phi_prey matrix.

getFeedingLevel method for a MizerParams object without the phi_prey matrix argument.

getFeedingLevel method for a MizerSim object.

Usage

getFeedingLevel(object, n, n_pp, phi_prey, ...)
# S4 method for MizerParams,matrix,numeric,matrix
getFeedingLevel(object, n, n_pp,
  phi_prey, ...)
# S4 method for MizerParams,matrix,numeric,missing
getFeedingLevel(object, n, n_pp,
  phi_prey, ...)
# S4 method for MizerSim,missing,missing,missing
getFeedingLevel(object,
  time_range = dimnames(object@n)$time, drop = FALSE, ...)

Arguments

object

A MizerParams or MizerSim object

n

A matrix of species abundance (species x size). Only used if object argument is of type MizerParams.

n_pp

A vector of the background abundance by size. Only used if object argument is of type MizerParams.

phi_prey

The PhiPrey matrix (optional) of dimension no. species x no. size bins. If not passed in, it is calculated internally using the getPhiPrey method. Only used if object argument is of type MizerParams.

...

Other arguments (currently unused).

time_range

Subset the returned fishing mortalities by time. The time range is either a vector of values, a vector of min and max time, or a single value. Default is the whole time range. Only used if the object argument is of type MizerSim.

drop

should extra dimensions of length 1 in the output be dropped, simplifying the output. Defaults to TRUE.

See Also

getPhiPrey

Examples

# NOT RUN {
data(NS_species_params_gears)
data(inter)
params <- MizerParams(NS_species_params_gears, inter)
# With constant fishing effort for all gears for 20 time steps
sim <- project(params, t_max = 20, effort = 0.5)
# Get the feeding level at one time step
n <- sim@n[21,,]
n_pp <- sim@n_pp[21,]
fl <- getFeedingLevel(params,n,n_pp)
# Get the feeding level at all saved time steps
fl <- getFeedingLevel(sim)
# Get the feeding level for time 15 - 20
fl <- getFeedingLevel(sim, time_range = c(15,20))
# }