Get encounter rate

Returns the rate at which a predator of species $i$ and weight $w$ encounters food (grams/year).

Usage

getEncounter(object, ...)

Arguments

object

A MizerParams or MizerSim object.

...

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.
t: The time for which to do the calculation. Defaults to 0.

For a MizerSim object:

time_range: The time range over which to return the rates. 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 ArraySpeciesBySize object (predator species x predator size) with the encounter rates.
MizerSim: An ArrayTimeBySpeciesBySize object (time step x predator species x predator size) with the encounter rates at every time step. If drop = TRUE then dimensions of length 1 will be removed.

Predation encounter

The encounter rate $E_i(w)$ at which a predator of species $i$ and weight $w$ encounters food has contributions from the encounter of fish prey and of resource. This is determined by summing over all prey species and the resource spectrum and then integrating over all prey sizes $w_p$, weighted by predation kernel $\phi(w,w_p)$: $$ E_i(w) = \gamma_i(w) \int \left( \theta_{ip} N_R(w_p) + \sum_{j} \theta_{ij} N_j(w_p) \right) \phi_i(w,w_p) w_p \, dw_p. $$ Here $N_j(w)$ is the abundance density of species $j$ and $N_R(w)$ is the abundance density of resource. The overall prefactor $\gamma_i(w)$ determines the predation power of the predator. It could be interpreted as a search volume and is set with the setSearchVolume() function. The predation kernel $\phi(w,w_p)$ is set with the setPredKernel() function. The species interaction matrix $\theta_{ij}$ is set with setInteraction() and the resource interaction vector $\theta_{ip}$ is taken from the interaction_resource column in params@species_params.

Details

The encounter rate is multiplied by $1-f_0$ to obtain the consumption rate, where $f_0$ is the feeding level calculated with getFeedingLevel(). This is used by the project() function for performing simulations.

The function returns values also for sizes outside the size-range of the species. These values should not be used, as they are meaningless.

If your model contains additional components that you added with setComponent() and for which you specified an encounter_fun function then the encounters of these components will be included in the returned value.

Extension hook

projectEncounter() is the S3 generic used by extension-aware projections. Extension packages can add methods for their marker classes and call NextMethod() to compose encounter-rate changes. The MizerParams method contains the standard mizer calculation and is also exported as mizerEncounter() for compatibility.

Your own encounter function

By default getEncounter() calls mizerEncounter() on models without extensions. However you can replace this with your own alternative encounter function. If your function is called "myEncounter" then you register it in a MizerParams object params with

params <- setRateFunction(params, "Encounter", "myEncounter")

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

Examples

encounter <- getEncounter(NS_params)
str(encounter)
#>  'ArraySpeciesBySize' num [1:12, 1:100] 0.299 0.453 0.502 0.575 0.492 ...
#>  - attr(*, "dimnames")=List of 2
#>   ..$ sp: chr [1:12] "Sprat" "Sandeel" "N.pout" "Herring" ...
#>   ..$ w : chr [1:100] "0.001" "0.00119" "0.00142" "0.0017" ...
#>  - attr(*, "value_name")= chr "Encounter rate"
#>  - attr(*, "units")= chr "g/year"
#>  - attr(*, "params")=Formal class 'MizerParams' [package "mizer"] with 46 slots