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getERepro.html
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getERepro.html
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growth and metabolism have been accounted for." />
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<h1>Get energy rate available for reproduction</h1>
<small class="dont-index">Source: <a href='https://github.com/sizespectrum/mizer/blob/master/R/rate_functions.R'><code>R/rate_functions.R</code></a></small>
<div class="hidden name"><code>getERepro.Rd</code></div>
</div>
<div class="ref-description">
<p>Calculates the energy rate (grams/year) available for reproduction after
growth and metabolism have been accounted for.</p>
</div>
<pre class="usage"><span class='fu'>getERepro</span>(
<span class='no'>params</span>,
<span class='kw'>n</span> <span class='kw'>=</span> <span class='fu'><a href='initialN-set.html'>initialN</a></span>(<span class='no'>params</span>),
<span class='kw'>n_pp</span> <span class='kw'>=</span> <span class='fu'><a href='initialNResource-set.html'>initialNResource</a></span>(<span class='no'>params</span>),
<span class='kw'>n_other</span> <span class='kw'>=</span> <span class='fu'><a href='initialNOther-set.html'>initialNOther</a></span>(<span class='no'>params</span>),
<span class='kw'>t</span> <span class='kw'>=</span> <span class='fl'>0</span>,
<span class='no'>...</span>
)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>params</th>
<td><p>A <a href='MizerParams-class.html'>MizerParams</a> object</p></td>
</tr>
<tr>
<th>n</th>
<td><p>A matrix of species abundances (species x size).</p></td>
</tr>
<tr>
<th>n_pp</th>
<td><p>A vector of the resource abundance by size</p></td>
</tr>
<tr>
<th>n_other</th>
<td><p>A list of abundances for other dynamical components of the
ecosystem</p></td>
</tr>
<tr>
<th>t</th>
<td><p>The time for which to do the calculation (Not used by standard
mizer rate functions but useful for extensions with time-dependent
parameters.)</p></td>
</tr>
<tr>
<th>...</th>
<td><p>Unused</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>A two dimensional array (prey species x prey size) holding
$$\psi_i(w)E_{r.i}(w)$$
where \(E_{r.i}(w)\) is the rate at which energy becomes available for
growth and reproduction, calculated with <code><a href='getEReproAndGrowth.html'>getEReproAndGrowth()</a></code>,
and \(\psi_i(w)\) is the proportion of this energy that is used for
reproduction. This proportion is taken from the <code>params</code> object and is
set with <code><a href='setReproduction.html'>setReproduction()</a></code>.</p>
<h2 class="hasAnchor" id="your-own-reproduction-rate-function"><a class="anchor" href="#your-own-reproduction-rate-function"></a>Your own reproduction rate function</h2>
<p>By default <code>getERepro()</code> calls <code><a href='mizerERepro.html'>mizerERepro()</a></code>. However you can
replace this with your own alternative reproduction rate function. If
your function is called <code>"myERepro"</code> then you register it in a MizerParams
object <code>params</code> with</p><pre><span class='no'>params</span> <span class='kw'>&</span><span class='no'>lt</span>;- <span class='fu'><a href='setRateFunction.html'>setRateFunction</a></span>(<span class='no'>params</span>, <span class='st'>"ERepro"</span>, <span class='st'>"myERepro"</span>)</pre>
<p>Your function will then be called instead of <code><a href='mizerERepro.html'>mizerERepro()</a></code>, with the
same arguments.</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p>Other rate functions:
<code><a href='getEGrowth.html'>getEGrowth</a>()</code>,
<code><a href='getEReproAndGrowth.html'>getEReproAndGrowth</a>()</code>,
<code><a href='getEncounter.html'>getEncounter</a>()</code>,
<code><a href='getFMortGear.html'>getFMortGear</a>()</code>,
<code><a href='getFMort.html'>getFMort</a>()</code>,
<code><a href='getFeedingLevel.html'>getFeedingLevel</a>()</code>,
<code><a href='getMort.html'>getMort</a>()</code>,
<code><a href='getPredMort.html'>getPredMort</a>()</code>,
<code><a href='getPredRate.html'>getPredRate</a>()</code>,
<code><a href='getRDD.html'>getRDD</a>()</code>,
<code><a href='getRDI.html'>getRDI</a>()</code>,
<code><a href='getResourceMort.html'>getResourceMort</a>()</code></p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='kw'>if</span> (<span class='fl'>FALSE</span>) {
<span class='no'>params</span> <span class='kw'><-</span> <span class='fu'><a href='newMultispeciesParams.html'>newMultispeciesParams</a></span>(<span class='no'>NS_species_params_gears</span>, <span class='no'>inter</span>)
<span class='co'># Project with constant fishing effort for all gears for 20 time steps</span>
<span class='no'>sim</span> <span class='kw'><-</span> <span class='fu'><a href='project.html'>project</a></span>(<span class='no'>params</span>, <span class='kw'>t_max</span> <span class='kw'>=</span> <span class='fl'>20</span>, <span class='kw'>effort</span> <span class='kw'>=</span> <span class='fl'>0.5</span>)
<span class='co'># Get the energy at a particular time step</span>
<span class='fu'>getERepro</span>(<span class='no'>params</span>, <span class='kw'>n</span> <span class='kw'>=</span> <span class='fu'><a href='N.html'>N</a></span>(<span class='no'>sim</span>)[<span class='fl'>15</span>, , ], <span class='kw'>n_pp</span> <span class='kw'>=</span> <span class='fu'><a href='N.html'>NResource</a></span>(<span class='no'>sim</span>)[<span class='fl'>15</span>, ], <span class='kw'>t</span> <span class='kw'>=</span> <span class='fl'>15</span>)
}</div></pre>
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