getEncounter

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

A set of classes and methods to set up and run multi-species, trait
based and community size spectrum ecological models, focused on the marine
environment.

Gustav Delius

mizer

Dynamic Multi-Species Size Spectrum Modelling

Finlay Scott

Julia Blanchard

Ken Andersen

Richard Southwell

getEncounter function

<dl><dt>params</dt>
<dd>A MizerParams object</dd>
<dt>n</dt>
<dd>A matrix of species abundances (species x size).</dd>
<dt>n_pp</dt>
<dd>A vector of the resource abundance by size</dd>
<dt>n_other</dt>
<dd>A list of abundances for other dynamical components of the
ecosystem</dd>
<dt>t</dt>
<dd>The time for which to do the calculation (Not used by standard
mizer rate functions but useful for extensions with time-dependent
parameters.)</dd>
<dt>...</dt>
<dd>Unused</dd></dl>

Arguments

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
<code>setSearchVolume()</code> function. The predation kernel
$\phi(w,w_p)$ is set with the <code>setPredKernel()</code> function. The
species interaction matrix $\theta_{ij}$ is set with <code>setInteraction()</code>
and the resource interaction vector $\theta_{ip}$ is taken from the
<code>interaction_resource</code> column in <code>params@species_params</code>.

Predation encounter

By default <code>getEncounter()</code> calls <code>mizerEncounter()</code>. However you can
replace this with your own alternative encounter function. If
your function is called <code>"myEncounter"</code> then you register it in a MizerParams
object <code>params</code> with
<div class="sourceCode"></div><pre><code>params &lt;- setRateFunction(params, "Encounter", "myEncounter")
</code></pre>
Your function will then be called instead of <code>mizerEncounter()</code>, with the
same arguments.

Your own encounter function

Get encounter rate — getEncounter

<dl>

<dt>params</dt>
<dd>A MizerParams object</dd>


<dt>n</dt>
<dd>A matrix of species abundances (species x size).</dd>


<dt>n_pp</dt>
<dd>A vector of the resource abundance by size</dd>


<dt>n_other</dt>
<dd>A list of abundances for other dynamical components of the
ecosystem</dd>


<dt>t</dt>
<dd>The time for which to do the calculation (Not used by standard
mizer rate functions but useful for extensions with time-dependent
parameters.)</dd>


<dt>...</dt>
<dd>Unused</dd>

</dl>

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
<code>setSearchVolume()</code> function. The predation kernel
$\phi(w,w_p)$ is set with the <code>setPredKernel()</code> function. The
species interaction matrix $\theta_{ij}$ is set with <code>setInteraction()</code>
and the resource interaction vector $\theta_{ip}$ is taken from the
<code>interaction_resource</code> column in <code>params@species_params</code>.

By default <code>getEncounter()</code> calls <code>mizerEncounter()</code>. However you can
replace this with your own alternative encounter function. If
your function is called <code>"myEncounter"</code> then you register it in a MizerParams
object <code>params</code> with
<div class="sourceCode"><pre><code>params &lt;- setRateFunction(params, "Encounter", "myEncounter")
</code></pre></div>
Your function will then be called instead of <code>mizerEncounter()</code>, with the
same arguments.

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getEncounter: Get encounter rate

Description

Usage

Value

Arguments

Predation encounter

Your own encounter function

Details

See Also

Examples