Get diet of predator at size, resolved by prey species

Calculates the rate at which a predator of a particular species and size consumes biomass of each prey species, resource, and other components of the ecosystem. Returns either the rates in grams/year or the proportion of the total consumption rate.

Usage

getDiet(object, proportion = TRUE, ...)

Arguments

object

A MizerParams or MizerSim object.

proportion

If TRUE (default) the function returns the diet as a proportion of the total consumption rate. If FALSE it returns the consumption rate in grams per year.

...

Additional arguments that depend on the class of object.

For a MizerParams object:

n: A matrix of species abundances (species x size). Defaults to the initial abundances stored in object.
n_pp: A vector of the resource abundance by size. Defaults to the initial resource abundance stored in object.
n_other: A named list of the abundances of other dynamical components. Defaults to the initial values stored in object.

For a MizerSim object:

time_range: The time range over which to return the diet. Either a vector of values, a vector of min and max time, or a single value. Defaults to the whole time range of the simulation.
drop: If TRUE then any dimension of length 1 is removed from the returned array.

Value

MizerParams: An array (predator species x predator size x (prey species + resource + other components)). Dimnames are "predator", "w", and "prey".
MizerSim: A four-dimensional array (time x predator species x predator size x prey) with the diet at each selected saved time step. If drop = TRUE then dimensions of length 1 are removed.

Details

The rates $D_{ij}(w)$ at which a predator of species $i$ and size $w$ consumes biomass from prey species $j$ are calculated from the predation kernel $\phi_i(w, w_p)$, the search volume $\gamma_i(w)$, the feeding level $f_i(w)$, the species interaction matrix $\theta_{ij}$ and the prey abundance density $N_j(w_p)$: $$ D_{ij}(w, w_p) = (1-f_i(w)) \gamma_i(w) \theta_{ij} \int N_j(w_p) \phi_i(w, w_p) w_p dw_p. $$ The prey index $j$ runs over all species and the resource.

Extra columns are added for the external encounter rate and for any extra ecosystem components in your model for which you have defined an encounter rate function. These encounter rates are multiplied by $1-f_i(w)$ to give the rate of consumption of biomass from these extra components.

This function performs the same integration as getEncounter() but does not aggregate over prey species, and multiplies by $1-f_i(w)$ to get the consumed biomass rather than the available biomass. Outside the range of sizes for a predator species the returned rate is zero.

Examples

diet <- getDiet(NS_params)
str(diet)
#>  num [1:12, 1:100, 1:14] 8.94e-18 6.86e-19 3.46e-18 1.75e-09 1.12e-17 ...
#>  - attr(*, "dimnames")=List of 3
#>   ..$ predator: chr [1:12] "Sprat" "Sandeel" "N.pout" "Herring" ...
#>   ..$ w       : chr [1:100] "0.001" "0.00119" "0.00142" "0.0017" ...
#>   ..$ prey    : chr [1:14] "Sprat" "Sandeel" "N.pout" "Herring" ...
# \donttest{
# For a MizerSim the diet is returned at each saved time step
sim <- project(NS_params, t_max = 20, effort = 0.5)
# Diet at the saved time steps over years 15 - 20
diet <- getDiet(sim, time_range = c(15, 20))
str(diet)
#>  num [1:6, 1:12, 1:100, 1:14] 8.42e-18 1.37e-17 8.76e-18 7.98e-18 7.49e-18 ...
#>  - attr(*, "dimnames")=List of 4
#>   ..$ time    : chr [1:6] "15" "16" "17" "18" ...
#>   ..$ predator: chr [1:12] "Sprat" "Sandeel" "N.pout" "Herring" ...
#>   ..$ w       : chr [1:100] "0.001" "0.00119" "0.00142" "0.0017" ...
#>   ..$ prey    : chr [1:14] "Sprat" "Sandeel" "N.pout" "Herring" ...
# }