getFeedingLevel: getFeedingLevel method for the size based model

In pwoodworth-jefcoats/Size-Based-Modeling: Mizer With The Effects Of Temperature Included

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_therMizer method for performing simulations.

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

getFeedingLevel method for a therMizerSim object.

Usage

getFeedingLevel(object, n, n_pp, ocean_temp, phi_prey, ...)


  ## S4 method for signature 'therMizerParams,matrix,numeric,numeric,matrix'
getFeedingLevel(object,
  n, n_pp, ocean_temp, phi_prey, ...)


  ## S4 method for signature 'therMizerSim,missing,missing,missing,missing'
getFeedingLevel(object,
  ocean_temp, time_range = dimnames(object@ocean_temp)$time, drop = FALSE,
  ...)

Arguments

object	A therMizerParams or therMizerSim object
n	A matrix of species abundance (species x size). Only used if object argument is of type therMizerParams.
n_pp	A vector of the background abundance by size. Only used if object argument is of type therMizerParams.
ocean_temp	A numeric vectory of the ocean temperature by realm or a single numeric temperature value which is used for all realms.
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 therMizerParams.
...	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 therMizerSim.
drop	should extra dimensions of length 1 in the output be dropped, simplifying the output. Defaults to TRUE.

Note

If a therMizerParams object is passed in, the method returns a two dimensional array (predator species x predator size) based on the abundances also passed in.

If a therMizerSim object is passed in, the method returns a three dimensional array (time step x predator species x predator size) with the feeding level calculated at every time step in the simulation.

See Also

getPhiPrey

Examples

## Not run: 
data(NS_species_params_gears)
data(inter)
params <- therMizerParams(NS_species_params_gears, inter)
# With constant fishing effort for all gears for 20 time steps
sim <- project_therMizer(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))

## End(Not run)

pwoodworth-jefcoats/Size-Based-Modeling documentation built on Sept. 15, 2023, 8:13 a.m.