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<!doctype html>
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<h1 id="dynamic-energy-budget---deb"><strong>D</strong>ynamic <strong>E</strong>nergy <strong>B</strong>udget - DEB</h1>
<p><strong>Table of Contents:</strong></p>
<ul>
<li><a href="#dynamic-energy-budget---deb"><strong>D</strong>ynamic <strong>E</strong>nergy <strong>B</strong>udget - DEB</a></li>
<li><a href="#concept-figure">Concept figure</a></li>
<li><a href="#deb-equations">DEB equations</a>
<ul>
<li><a href="#basics---reserve-dynamics">basics - reserve dynamics</a></li>
<li><a href="#allocation-of-pc">allocation of pC</a></li>
</ul>
</li>
<li><a href="#existing-models">Existing models</a>
<ul>
<li><a href="#matlab-tools-original-deb">MATLAB tools (original DEB)</a></li>
<li><a href="#nichemapr-habitat-modeling">NicheMapR (Habitat modeling)</a></li>
<li><a href="#fabm-fabm-deb-hydrodynamic-coupling">FABM, FABM-DEB (Hydrodynamic coupling)</a></li>
<li><a href="#population-models">Population models</a>
<ul>
<li><a href="#ibm-individual-based-model">IBM (Individual-Based-Model)</a></li>
<li><a href="#ebt">EBT</a></li>
<li><a href="#cpm">CPM</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#useful-web-interfaces">Useful web interfaces</a></li>
<li><a href="#acquire-parameters">Acquire parameters</a>
<ul>
<li><a href="#from-amp-collection">From AmP collection</a>
<ul>
<li><a href="#in-matlab">In MATLAB</a></li>
<li><a href="#in-r">In R</a></li>
</ul>
</li>
<li><a href="#parameter-estimation-with-literatureexperimental-data">Parameter estimation with literature/experimental data</a>
<ul>
<li><a href="#better-to-have-data">Better-to-have data</a></li>
<li><a href="#parameter-estimation-preparation">parameter estimation preparation</a></li>
<li><a href="#parameter-estimation-procedure">Parameter estimation procedure</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#further-deb-modeling">Further DEB modeling</a>
- <a href="#state-variables">State Variables</a>
- <a href="#ode-in-standard-deb-model-std">ODE In standard DEB model (std)</a>
- <a href="#deb-model-can-be-coupled">DEB model can be coupled</a></li>
</ul>
<h1 id="concept-figure">Concept figure</h1>
<p><a href="https://debportal.debtheory.org/docs/">DEB website</a></p>
<blockquote>
<p><img src="./DEB_figures/birdDEB_final.gif" alt="DEB concept -Tongyao"></p>
</blockquote>
<h1 id="deb-equations">DEB equations</h1>
<h2 id="basics---reserve-dynamics">basics - reserve dynamics</h2>
<p>(refer to graph above, from top to bottom, left to right)</p>
<ul>
<li>food ingestion rate <eq><span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mover accent="true"><msub><mi>p</mi><mi>X</mi></msub><mo>˙</mo></mover></mrow><annotation encoding="application/x-tex">\dot{p_X}</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:0.8623000000000001em;vertical-align:-0.19444em;"></span><span class="mord accent"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.66786em;"><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="mord"><span class="mord mathnormal">p</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.32833099999999993em;"><span style="top:-2.5500000000000003em;margin-left:0em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight"><span class="mord mathnormal mtight" style="margin-right:0.07847em;">X</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.15em;"><span></span></span></span></span></span></span></span><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="accent-body" style="left:-0.13889em;"><span class="mord">˙</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.19444em;"><span></span></span></span></span></span></span></span></span></eq> <section><eqn><span class="katex-display"><span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML" display="block"><semantics><mrow><mover accent="true"><msub><mi>p</mi><mi>X</mi></msub><mo>˙</mo></mover><mo>=</mo><mover accent="true"><mrow><mo stretchy="false">{</mo><msub><mi>p</mi><mrow><mi>X</mi><mi>m</mi></mrow></msub><mo stretchy="false">}</mo></mrow><mo>˙</mo></mover><mi>f</mi><mo stretchy="false">(</mo><mi>X</mi><mo stretchy="false">)</mo><msup><mi>L</mi><mn>2</mn></msup></mrow><annotation encoding="application/x-tex">\dot{p_X} = \dot{\{p_{Xm}\}}f(X)L^2</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:0.8623000000000001em;vertical-align:-0.19444em;"></span><span class="mord accent"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.66786em;"><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="mord"><span class="mord mathnormal">p</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.32833099999999993em;"><span style="top:-2.5500000000000003em;margin-left:0em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight"><span class="mord mathnormal mtight" style="margin-right:0.07847em;">X</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.15em;"><span></span></span></span></span></span></span></span><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="accent-body" style="left:-0.13889em;"><span class="mord">˙</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.19444em;"><span></span></span></span></span></span><span class="mspace" style="margin-right:0.2777777777777778em;"></span><span class="mrel">=</span><span class="mspace" style="margin-right:0.2777777777777778em;"></span></span><span class="base"><span class="strut" style="height:1.23686em;vertical-align:-0.25em;"></span><span class="mord accent"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.9868600000000001em;"><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="mord"><span class="mopen">{</span><span class="mord"><span class="mord mathnormal">p</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.32833099999999993em;"><span style="top:-2.5500000000000003em;margin-left:0em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight"><span class="mord mtight"><span class="mord mathnormal mtight" style="margin-right:0.07847em;">X</span><span class="mord mathnormal mtight">m</span></span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.15em;"><span></span></span></span></span></span></span><span class="mclose">}</span></span></span><span style="top:-3.319em;"><span class="pstrut" style="height:3em;"></span><span class="accent-body" style="left:-0.13889em;"><span class="mord">˙</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.25em;"><span></span></span></span></span></span><span class="mord mathnormal" style="margin-right:0.10764em;">f</span><span class="mopen">(</span><span class="mord mathnormal" style="margin-right:0.07847em;">X</span><span class="mclose">)</span><span class="mord"><span class="mord mathnormal">L</span><span class="msupsub"><span class="vlist-t"><span class="vlist-r"><span class="vlist" style="height:0.8641079999999999em;"><span style="top:-3.113em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight"><span class="mord mtight">2</span></span></span></span></span></span></span></span></span></span></span></span></eqn></section></li>
<li>assimilation flux <eq><span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mover accent="true"><msub><mi>p</mi><mi>A</mi></msub><mo>˙</mo></mover></mrow><annotation encoding="application/x-tex">\dot{p_A}</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:0.8623000000000001em;vertical-align:-0.19444em;"></span><span class="mord accent"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.66786em;"><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="mord"><span class="mord mathnormal">p</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.32833099999999993em;"><span style="top:-2.5500000000000003em;margin-left:0em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight"><span class="mord mathnormal mtight">A</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.15em;"><span></span></span></span></span></span></span></span><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="accent-body" style="left:-0.13889em;"><span class="mord">˙</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.19444em;"><span></span></span></span></span></span></span></span></span></eq> <section><eqn><span class="katex-display"><span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML" display="block"><semantics><mrow><mover accent="true"><msub><mi>p</mi><mi>A</mi></msub><mo>˙</mo></mover><mo>=</mo><mover accent="true"><mrow><mo stretchy="false">{</mo><msub><mi>p</mi><mrow><mi>A</mi><mi>m</mi></mrow></msub><mo stretchy="false">}</mo></mrow><mo>˙</mo></mover><mi>f</mi><mo stretchy="false">(</mo><mi>X</mi><mo stretchy="false">)</mo><msup><mi>L</mi><mn>2</mn></msup></mrow><annotation encoding="application/x-tex">\dot{p_A} = \dot{\{p_{Am}\}} f(X) L^2</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:0.8623000000000001em;vertical-align:-0.19444em;"></span><span class="mord accent"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.66786em;"><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="mord"><span class="mord mathnormal">p</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.32833099999999993em;"><span style="top:-2.5500000000000003em;margin-left:0em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight"><span class="mord mathnormal mtight">A</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.15em;"><span></span></span></span></span></span></span></span><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="accent-body" style="left:-0.13889em;"><span class="mord">˙</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.19444em;"><span></span></span></span></span></span><span class="mspace" style="margin-right:0.2777777777777778em;"></span><span class="mrel">=</span><span class="mspace" style="margin-right:0.2777777777777778em;"></span></span><span class="base"><span class="strut" style="height:1.23686em;vertical-align:-0.25em;"></span><span class="mord accent"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.9868600000000001em;"><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="mord"><span class="mopen">{</span><span class="mord"><span class="mord mathnormal">p</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.32833099999999993em;"><span style="top:-2.5500000000000003em;margin-left:0em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight"><span class="mord mtight"><span class="mord mathnormal mtight">A</span><span class="mord mathnormal mtight">m</span></span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.15em;"><span></span></span></span></span></span></span><span class="mclose">}</span></span></span><span style="top:-3.319em;"><span class="pstrut" style="height:3em;"></span><span class="accent-body" style="left:-0.13889em;"><span class="mord">˙</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.25em;"><span></span></span></span></span></span><span class="mord mathnormal" style="margin-right:0.10764em;">f</span><span class="mopen">(</span><span class="mord mathnormal" style="margin-right:0.07847em;">X</span><span class="mclose">)</span><span class="mord"><span class="mord mathnormal">L</span><span class="msupsub"><span class="vlist-t"><span class="vlist-r"><span class="vlist" style="height:0.8641079999999999em;"><span style="top:-3.113em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight"><span class="mord mtight">2</span></span></span></span></span></span></span></span></span></span></span></span></eqn></section></li>
<li>Reserve <eq><span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mi>E</mi></mrow><annotation encoding="application/x-tex">E</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:0.68333em;vertical-align:0em;"></span><span class="mord mathnormal" style="margin-right:0.05764em;">E</span></span></span></span></eq></li>
</ul>
<section><eqn><span class="katex-display"><span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML" display="block"><semantics><mrow><mfrac><mrow><mi>d</mi><mi>E</mi></mrow><mrow><mi>d</mi><mi>t</mi></mrow></mfrac><mo>=</mo><mover accent="true"><msub><mi>p</mi><mi>A</mi></msub><mo>˙</mo></mover><mo>−</mo><mover accent="true"><msub><mi>p</mi><mi>C</mi></msub><mo>˙</mo></mover></mrow><annotation encoding="application/x-tex">\frac{dE}{dt} = \dot{p_A} - \dot{p_C}</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:2.05744em;vertical-align:-0.686em;"></span><span class="mord"><span class="mopen nulldelimiter"></span><span class="mfrac"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:1.37144em;"><span style="top:-2.314em;"><span class="pstrut" style="height:3em;"></span><span class="mord"><span class="mord mathnormal">d</span><span class="mord mathnormal">t</span></span></span><span style="top:-3.23em;"><span class="pstrut" style="height:3em;"></span><span class="frac-line" style="border-bottom-width:0.04em;"></span></span><span style="top:-3.677em;"><span class="pstrut" style="height:3em;"></span><span class="mord"><span class="mord mathnormal">d</span><span class="mord mathnormal" style="margin-right:0.05764em;">E</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.686em;"><span></span></span></span></span></span><span class="mclose nulldelimiter"></span></span><span class="mspace" style="margin-right:0.2777777777777778em;"></span><span class="mrel">=</span><span class="mspace" style="margin-right:0.2777777777777778em;"></span></span><span class="base"><span class="strut" style="height:0.8623000000000001em;vertical-align:-0.19444em;"></span><span class="mord accent"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.66786em;"><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="mord"><span class="mord mathnormal">p</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.32833099999999993em;"><span style="top:-2.5500000000000003em;margin-left:0em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight"><span class="mord mathnormal mtight">A</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.15em;"><span></span></span></span></span></span></span></span><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="accent-body" style="left:-0.13889em;"><span class="mord">˙</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.19444em;"><span></span></span></span></span></span><span class="mspace" style="margin-right:0.2222222222222222em;"></span><span class="mbin">−</span><span class="mspace" style="margin-right:0.2222222222222222em;"></span></span><span class="base"><span class="strut" style="height:0.8623000000000001em;vertical-align:-0.19444em;"></span><span class="mord accent"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.66786em;"><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="mord"><span class="mord mathnormal">p</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.32833099999999993em;"><span style="top:-2.5500000000000003em;margin-left:0em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight"><span class="mord mathnormal mtight" style="margin-right:0.07153em;">C</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.15em;"><span></span></span></span></span></span></span></span><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="accent-body" style="left:-0.13889em;"><span class="mord">˙</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.19444em;"><span></span></span></span></span></span></span></span></span></span></eqn></section></math>
<ul>
<li>Reserve density <eq><span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mi>E</mi><mi mathvariant="normal">/</mi><mi>V</mi></mrow><annotation encoding="application/x-tex">E/V</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:1em;vertical-align:-0.25em;"></span><span class="mord mathnormal" style="margin-right:0.05764em;">E</span><span class="mord">/</span><span class="mord mathnormal" style="margin-right:0.22222em;">V</span></span></span></span></eq></li>
</ul>
<section><eqn><span class="katex-display"><span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML" display="block"><semantics><mrow><mfrac><mrow><mi>d</mi><mo stretchy="false">[</mo><mi>E</mi><mo stretchy="false">]</mo></mrow><mrow><mi>d</mi><mi>t</mi></mrow></mfrac><mo>=</mo><mover accent="true"><mrow><mo stretchy="false">[</mo><msub><mi>p</mi><mi>A</mi></msub><mo stretchy="false">]</mo></mrow><mo>˙</mo></mover><mo>−</mo><mover accent="true"><mrow><mo stretchy="false">[</mo><msub><mi>p</mi><mi>C</mi></msub><mo stretchy="false">]</mo></mrow><mo>˙</mo></mover><mo>−</mo><mo stretchy="false">[</mo><mi>E</mi><mo stretchy="false">]</mo><mover accent="true"><mi>r</mi><mo>˙</mo></mover></mrow><annotation encoding="application/x-tex">\frac{d[E]}{dt} = \dot{[p_A]} - \dot{[p_C]} - [E]\dot{r}</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:2.113em;vertical-align:-0.686em;"></span><span class="mord"><span class="mopen nulldelimiter"></span><span class="mfrac"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:1.427em;"><span style="top:-2.314em;"><span class="pstrut" style="height:3em;"></span><span class="mord"><span class="mord mathnormal">d</span><span class="mord mathnormal">t</span></span></span><span style="top:-3.23em;"><span class="pstrut" style="height:3em;"></span><span class="frac-line" style="border-bottom-width:0.04em;"></span></span><span style="top:-3.677em;"><span class="pstrut" style="height:3em;"></span><span class="mord"><span class="mord mathnormal">d</span><span class="mopen">[</span><span class="mord mathnormal" style="margin-right:0.05764em;">E</span><span class="mclose">]</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.686em;"><span></span></span></span></span></span><span class="mclose nulldelimiter"></span></span><span class="mspace" style="margin-right:0.2777777777777778em;"></span><span class="mrel">=</span><span class="mspace" style="margin-right:0.2777777777777778em;"></span></span><span class="base"><span class="strut" style="height:1.23686em;vertical-align:-0.25em;"></span><span class="mord accent"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.9868600000000001em;"><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="mord"><span class="mopen">[</span><span class="mord"><span class="mord mathnormal">p</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.32833099999999993em;"><span style="top:-2.5500000000000003em;margin-left:0em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight"><span class="mord mathnormal mtight">A</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.15em;"><span></span></span></span></span></span></span><span class="mclose">]</span></span></span><span style="top:-3.319em;"><span class="pstrut" style="height:3em;"></span><span class="accent-body" style="left:-0.13889em;"><span class="mord">˙</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.25em;"><span></span></span></span></span></span><span class="mspace" style="margin-right:0.2222222222222222em;"></span><span class="mbin">−</span><span class="mspace" style="margin-right:0.2222222222222222em;"></span></span><span class="base"><span class="strut" style="height:1.23686em;vertical-align:-0.25em;"></span><span class="mord accent"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.9868600000000001em;"><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="mord"><span class="mopen">[</span><span class="mord"><span class="mord mathnormal">p</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.32833099999999993em;"><span style="top:-2.5500000000000003em;margin-left:0em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight"><span class="mord mathnormal mtight" style="margin-right:0.07153em;">C</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.15em;"><span></span></span></span></span></span></span><span class="mclose">]</span></span></span><span style="top:-3.319em;"><span class="pstrut" style="height:3em;"></span><span class="accent-body" style="left:-0.13889em;"><span class="mord">˙</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.25em;"><span></span></span></span></span></span><span class="mspace" style="margin-right:0.2222222222222222em;"></span><span class="mbin">−</span><span class="mspace" style="margin-right:0.2222222222222222em;"></span></span><span class="base"><span class="strut" style="height:1em;vertical-align:-0.25em;"></span><span class="mopen">[</span><span class="mord mathnormal" style="margin-right:0.05764em;">E</span><span class="mclose">]</span><span class="mord accent"><span class="vlist-t"><span class="vlist-r"><span class="vlist" style="height:0.66786em;"><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="mord mathnormal" style="margin-right:0.02778em;">r</span></span><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="accent-body" style="left:-0.08333000000000002em;"><span class="mord">˙</span></span></span></span></span></span></span></span></span></span></span></eqn></section></math>
<ul>
<li>mobilization flux <eq><span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mover accent="true"><msub><mi>p</mi><mi>C</mi></msub><mo>˙</mo></mover></mrow><annotation encoding="application/x-tex">\dot{p_C}</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:0.8623000000000001em;vertical-align:-0.19444em;"></span><span class="mord accent"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.66786em;"><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="mord"><span class="mord mathnormal">p</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.32833099999999993em;"><span style="top:-2.5500000000000003em;margin-left:0em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight"><span class="mord mathnormal mtight" style="margin-right:0.07153em;">C</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.15em;"><span></span></span></span></span></span></span></span><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="accent-body" style="left:-0.13889em;"><span class="mord">˙</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.19444em;"><span></span></span></span></span></span></span></span></span></eq><section><eqn><span class="katex-display"><span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML" display="block"><semantics><mrow><mover accent="true"><msub><mi>p</mi><mi>C</mi></msub><mo>˙</mo></mover><mo>=</mo><mi>E</mi><mo stretchy="false">(</mo><mfrac><mover accent="true"><mi>v</mi><mo>˙</mo></mover><mi>L</mi></mfrac><mo>−</mo><mover accent="true"><mi>r</mi><mo>˙</mo></mover><mo stretchy="false">)</mo></mrow><annotation encoding="application/x-tex">\dot{p_C} = E (\frac{\dot{v}}{L} - \dot{r})</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:0.8623000000000001em;vertical-align:-0.19444em;"></span><span class="mord accent"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.66786em;"><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="mord"><span class="mord mathnormal">p</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.32833099999999993em;"><span style="top:-2.5500000000000003em;margin-left:0em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight"><span class="mord mathnormal mtight" style="margin-right:0.07153em;">C</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.15em;"><span></span></span></span></span></span></span></span><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="accent-body" style="left:-0.13889em;"><span class="mord">˙</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.19444em;"><span></span></span></span></span></span><span class="mspace" style="margin-right:0.2777777777777778em;"></span><span class="mrel">=</span><span class="mspace" style="margin-right:0.2777777777777778em;"></span></span><span class="base"><span class="strut" style="height:2.03086em;vertical-align:-0.686em;"></span><span class="mord mathnormal" style="margin-right:0.05764em;">E</span><span class="mopen">(</span><span class="mord"><span class="mopen nulldelimiter"></span><span class="mfrac"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:1.3448600000000002em;"><span style="top:-2.314em;"><span class="pstrut" style="height:3em;"></span><span class="mord"><span class="mord mathnormal">L</span></span></span><span style="top:-3.23em;"><span class="pstrut" style="height:3em;"></span><span class="frac-line" style="border-bottom-width:0.04em;"></span></span><span style="top:-3.677em;"><span class="pstrut" style="height:3em;"></span><span class="mord"><span class="mord accent"><span class="vlist-t"><span class="vlist-r"><span class="vlist" style="height:0.66786em;"><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="mord mathnormal" style="margin-right:0.03588em;">v</span></span><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="accent-body" style="left:-0.11111000000000001em;"><span class="mord">˙</span></span></span></span></span></span></span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.686em;"><span></span></span></span></span></span><span class="mclose nulldelimiter"></span></span><span class="mspace" style="margin-right:0.2222222222222222em;"></span><span class="mbin">−</span><span class="mspace" style="margin-right:0.2222222222222222em;"></span></span><span class="base"><span class="strut" style="height:1em;vertical-align:-0.25em;"></span><span class="mord accent"><span class="vlist-t"><span class="vlist-r"><span class="vlist" style="height:0.66786em;"><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="mord mathnormal" style="margin-right:0.02778em;">r</span></span><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="accent-body" style="left:-0.08333000000000002em;"><span class="mord">˙</span></span></span></span></span></span></span><span class="mclose">)</span></span></span></span></span></eqn></section></math>
<section><eqn><span class="katex-display"><span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML" display="block"><semantics><mrow><mover accent="true"><mrow><mo stretchy="false">[</mo><msub><mi>p</mi><mi>C</mi></msub><mo stretchy="false">]</mo></mrow><mo>˙</mo></mover><mo>=</mo><mo stretchy="false">[</mo><mi>E</mi><mo stretchy="false">]</mo><mo stretchy="false">(</mo><mfrac><mover accent="true"><mi>v</mi><mo>˙</mo></mover><mi>L</mi></mfrac><mo>−</mo><mover accent="true"><mi>r</mi><mo>˙</mo></mover><mo stretchy="false">)</mo></mrow><annotation encoding="application/x-tex">\dot{[p_C]} = [E](\frac{\dot{v}}{L} - \dot{r})</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:1.23686em;vertical-align:-0.25em;"></span><span class="mord accent"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.9868600000000001em;"><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="mord"><span class="mopen">[</span><span class="mord"><span class="mord mathnormal">p</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.32833099999999993em;"><span style="top:-2.5500000000000003em;margin-left:0em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight"><span class="mord mathnormal mtight" style="margin-right:0.07153em;">C</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.15em;"><span></span></span></span></span></span></span><span class="mclose">]</span></span></span><span style="top:-3.319em;"><span class="pstrut" style="height:3em;"></span><span class="accent-body" style="left:-0.13889em;"><span class="mord">˙</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.25em;"><span></span></span></span></span></span><span class="mspace" style="margin-right:0.2777777777777778em;"></span><span class="mrel">=</span><span class="mspace" style="margin-right:0.2777777777777778em;"></span></span><span class="base"><span class="strut" style="height:2.03086em;vertical-align:-0.686em;"></span><span class="mopen">[</span><span class="mord mathnormal" style="margin-right:0.05764em;">E</span><span class="mclose">]</span><span class="mopen">(</span><span class="mord"><span class="mopen nulldelimiter"></span><span class="mfrac"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:1.3448600000000002em;"><span style="top:-2.314em;"><span class="pstrut" style="height:3em;"></span><span class="mord"><span class="mord mathnormal">L</span></span></span><span style="top:-3.23em;"><span class="pstrut" style="height:3em;"></span><span class="frac-line" style="border-bottom-width:0.04em;"></span></span><span style="top:-3.677em;"><span class="pstrut" style="height:3em;"></span><span class="mord"><span class="mord accent"><span class="vlist-t"><span class="vlist-r"><span class="vlist" style="height:0.66786em;"><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="mord mathnormal" style="margin-right:0.03588em;">v</span></span><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="accent-body" style="left:-0.11111000000000001em;"><span class="mord">˙</span></span></span></span></span></span></span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.686em;"><span></span></span></span></span></span><span class="mclose nulldelimiter"></span></span><span class="mspace" style="margin-right:0.2222222222222222em;"></span><span class="mbin">−</span><span class="mspace" style="margin-right:0.2222222222222222em;"></span></span><span class="base"><span class="strut" style="height:1em;vertical-align:-0.25em;"></span><span class="mord accent"><span class="vlist-t"><span class="vlist-r"><span class="vlist" style="height:0.66786em;"><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="mord mathnormal" style="margin-right:0.02778em;">r</span></span><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="accent-body" style="left:-0.08333000000000002em;"><span class="mord">˙</span></span></span></span></span></span></span><span class="mclose">)</span></span></span></span></span></eqn></section></math>
</li>
</ul>
<h2 id="allocation-of-pc">allocation of pC</h2>
<section><eqn><span class="katex-display"><span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML" display="block"><semantics><mrow><mover accent="true"><msub><mi>p</mi><mi>C</mi></msub><mo>˙</mo></mover><mo>=</mo><mstyle mathcolor="blue"><mover accent="true"><msub><mi>p</mi><mi>S</mi></msub><mo>˙</mo></mover><mo>+</mo><mover accent="true"><msub><mi>p</mi><mi>G</mi></msub><mo>˙</mo></mover></mstyle><mo>+</mo><mstyle mathcolor="red"><mover accent="true"><msub><mi>p</mi><mi>J</mi></msub><mo>˙</mo></mover><mo>+</mo><mover accent="true"><msub><mi>p</mi><mi>R</mi></msub><mo>˙</mo></mover></mstyle></mrow><annotation encoding="application/x-tex">\dot{p_C} = \textcolor{blue}{\dot{p_S} + \dot{p_G} }+ \textcolor{red}{\dot{p_J} + \dot{p_R}}</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:0.8623000000000001em;vertical-align:-0.19444em;"></span><span class="mord accent"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.66786em;"><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="mord"><span class="mord mathnormal">p</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.32833099999999993em;"><span style="top:-2.5500000000000003em;margin-left:0em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight"><span class="mord mathnormal mtight" style="margin-right:0.07153em;">C</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.15em;"><span></span></span></span></span></span></span></span><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="accent-body" style="left:-0.13889em;"><span class="mord">˙</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.19444em;"><span></span></span></span></span></span><span class="mspace" style="margin-right:0.2777777777777778em;"></span><span class="mrel">=</span><span class="mspace" style="margin-right:0.2777777777777778em;"></span></span><span class="base"><span class="strut" style="height:0.8623000000000001em;vertical-align:-0.19444em;"></span><span class="mord accent" style="color:blue;"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.66786em;"><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="mord" style="color:blue;"><span class="mord mathnormal" style="color:blue;">p</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.32833099999999993em;"><span style="top:-2.5500000000000003em;margin-left:0em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight" style="color:blue;"><span class="mord mathnormal mtight" style="margin-right:0.05764em;color:blue;">S</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.15em;"><span></span></span></span></span></span></span></span><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="accent-body" style="left:-0.13889em;"><span class="mord" style="color:blue;">˙</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.19444em;"><span></span></span></span></span></span><span class="mspace" style="margin-right:0.2222222222222222em;"></span><span class="mbin" style="color:blue;">+</span><span class="mspace" style="margin-right:0.2222222222222222em;"></span></span><span class="base"><span class="strut" style="height:0.8623000000000001em;vertical-align:-0.19444em;"></span><span class="mord accent" style="color:blue;"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.66786em;"><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="mord" style="color:blue;"><span class="mord mathnormal" style="color:blue;">p</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.32833099999999993em;"><span style="top:-2.5500000000000003em;margin-left:0em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight" style="color:blue;"><span class="mord mathnormal mtight" style="color:blue;">G</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.15em;"><span></span></span></span></span></span></span></span><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="accent-body" style="left:-0.13889em;"><span class="mord" style="color:blue;">˙</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.19444em;"><span></span></span></span></span></span><span class="mspace" style="margin-right:0.2222222222222222em;"></span><span class="mbin">+</span><span class="mspace" style="margin-right:0.2222222222222222em;"></span></span><span class="base"><span class="strut" style="height:0.8623000000000001em;vertical-align:-0.19444em;"></span><span class="mord accent" style="color:red;"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.66786em;"><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="mord" style="color:red;"><span class="mord mathnormal" style="color:red;">p</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.32833099999999993em;"><span style="top:-2.5500000000000003em;margin-left:0em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight" style="color:red;"><span class="mord mathnormal mtight" style="margin-right:0.09618em;color:red;">J</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.15em;"><span></span></span></span></span></span></span></span><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="accent-body" style="left:-0.13889em;"><span class="mord" style="color:red;">˙</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.19444em;"><span></span></span></span></span></span><span class="mspace" style="margin-right:0.2222222222222222em;"></span><span class="mbin" style="color:red;">+</span><span class="mspace" style="margin-right:0.2222222222222222em;"></span></span><span class="base"><span class="strut" style="height:0.8623000000000001em;vertical-align:-0.19444em;"></span><span class="mord accent" style="color:red;"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.66786em;"><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="mord" style="color:red;"><span class="mord mathnormal" style="color:red;">p</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.32833099999999993em;"><span style="top:-2.5500000000000003em;margin-left:0em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight" style="color:red;"><span class="mord mathnormal mtight" style="margin-right:0.00773em;color:red;">R</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.15em;"><span></span></span></span></span></span></span></span><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="accent-body" style="left:-0.13889em;"><span class="mord" style="color:red;">˙</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.19444em;"><span></span></span></span></span></span></span></span></span></span></eqn></section></math>
<p>fraction <eq><span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mstyle mathcolor="blue"><mi>κ</mi></mstyle></mrow><annotation encoding="application/x-tex">\color{blue}\kappa</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:0.43056em;vertical-align:0em;"></span><span class="mord mathnormal" style="color:blue;">κ</span></span></span></span></eq> --> <eq><span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mstyle mathcolor="blue"><mover accent="true"><msub><mi>p</mi><mi>S</mi></msub><mo>˙</mo></mover></mstyle></mrow><annotation encoding="application/x-tex">\color{blue}\dot{p_S}</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:0.8623000000000001em;vertical-align:-0.19444em;"></span><span class="mord accent" style="color:blue;"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.66786em;"><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="mord" style="color:blue;"><span class="mord mathnormal" style="color:blue;">p</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.32833099999999993em;"><span style="top:-2.5500000000000003em;margin-left:0em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight" style="color:blue;"><span class="mord mathnormal mtight" style="margin-right:0.05764em;color:blue;">S</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.15em;"><span></span></span></span></span></span></span></span><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="accent-body" style="left:-0.13889em;"><span class="mord" style="color:blue;">˙</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.19444em;"><span></span></span></span></span></span></span></span></span></eq> and <eq><span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mstyle mathcolor="blue"><mover accent="true"><msub><mi>p</mi><mi>G</mi></msub><mo>˙</mo></mover></mstyle></mrow><annotation encoding="application/x-tex">\color{blue}\dot{p_G}</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:0.8623000000000001em;vertical-align:-0.19444em;"></span><span class="mord accent" style="color:blue;"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.66786em;"><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="mord" style="color:blue;"><span class="mord mathnormal" style="color:blue;">p</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.32833099999999993em;"><span style="top:-2.5500000000000003em;margin-left:0em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight" style="color:blue;"><span class="mord mathnormal mtight" style="color:blue;">G</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.15em;"><span></span></span></span></span></span></span></span><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="accent-body" style="left:-0.13889em;"><span class="mord" style="color:blue;">˙</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.19444em;"><span></span></span></span></span></span></span></span></span></eq>,</p>
<p>fraction <eq><span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mstyle mathcolor="red"><mn>1</mn><mo>−</mo><mi>κ</mi></mstyle></mrow><annotation encoding="application/x-tex">\color{red}1-\kappa</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:0.72777em;vertical-align:-0.08333em;"></span><span class="mord" style="color:red;">1</span><span class="mspace" style="margin-right:0.2222222222222222em;"></span><span class="mbin" style="color:red;">−</span><span class="mspace" style="margin-right:0.2222222222222222em;"></span></span><span class="base"><span class="strut" style="height:0.43056em;vertical-align:0em;"></span><span class="mord mathnormal" style="color:red;">κ</span></span></span></span></eq> --> <eq><span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mstyle mathcolor="red"><mover accent="true"><msub><mi>p</mi><mi>J</mi></msub><mo>˙</mo></mover></mstyle></mrow><annotation encoding="application/x-tex">\color{red}\dot{p_J}</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:0.8623000000000001em;vertical-align:-0.19444em;"></span><span class="mord accent" style="color:red;"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.66786em;"><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="mord" style="color:red;"><span class="mord mathnormal" style="color:red;">p</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.32833099999999993em;"><span style="top:-2.5500000000000003em;margin-left:0em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight" style="color:red;"><span class="mord mathnormal mtight" style="margin-right:0.09618em;color:red;">J</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.15em;"><span></span></span></span></span></span></span></span><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="accent-body" style="left:-0.13889em;"><span class="mord" style="color:red;">˙</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.19444em;"><span></span></span></span></span></span></span></span></span></eq> and <eq><span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mstyle mathcolor="red"><mover accent="true"><msub><mi>p</mi><mi>R</mi></msub><mo>˙</mo></mover></mstyle></mrow><annotation encoding="application/x-tex">\color{red}\dot{p_R}</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:0.8623000000000001em;vertical-align:-0.19444em;"></span><span class="mord accent" style="color:red;"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.66786em;"><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="mord" style="color:red;"><span class="mord mathnormal" style="color:red;">p</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.32833099999999993em;"><span style="top:-2.5500000000000003em;margin-left:0em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight" style="color:red;"><span class="mord mathnormal mtight" style="margin-right:0.00773em;color:red;">R</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.15em;"><span></span></span></span></span></span></span></span><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="accent-body" style="left:-0.13889em;"><span class="mord" style="color:red;">˙</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.19444em;"><span></span></span></span></span></span></span></span></span></eq></p>
<ul>
<li>
<p>somatic maintenance <eq><span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mstyle mathcolor="blue"><mover accent="true"><msub><mi>p</mi><mi>S</mi></msub><mo>˙</mo></mover></mstyle></mrow><annotation encoding="application/x-tex">\color{blue}\dot{p_S}</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:0.8623000000000001em;vertical-align:-0.19444em;"></span><span class="mord accent" style="color:blue;"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.66786em;"><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="mord" style="color:blue;"><span class="mord mathnormal" style="color:blue;">p</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.32833099999999993em;"><span style="top:-2.5500000000000003em;margin-left:0em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight" style="color:blue;"><span class="mord mathnormal mtight" style="margin-right:0.05764em;color:blue;">S</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.15em;"><span></span></span></span></span></span></span></span><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="accent-body" style="left:-0.13889em;"><span class="mord" style="color:blue;">˙</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.19444em;"><span></span></span></span></span></span></span></span></span></eq></p>
<section><eqn><span class="katex-display"><span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML" display="block"><semantics><mrow><mover accent="true"><msub><mi>p</mi><mi>S</mi></msub><mo>˙</mo></mover><mo>=</mo><mover accent="true"><mrow><mo stretchy="false">[</mo><msub><mi>p</mi><mi>M</mi></msub><mo stretchy="false">]</mo></mrow><mo>˙</mo></mover><msup><mi>L</mi><mn>2</mn></msup><mo>+</mo><mover accent="true"><mrow><mo stretchy="false">{</mo><msub><mi>p</mi><mi>T</mi></msub><mo stretchy="false">}</mo></mrow><mo>˙</mo></mover><msup><mi>L</mi><mn>3</mn></msup></mrow><annotation encoding="application/x-tex">\dot{p_S} = \dot{[p_M]} L^2 + \dot{\{p_T\}} L^3</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:0.8623000000000001em;vertical-align:-0.19444em;"></span><span class="mord accent"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.66786em;"><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="mord"><span class="mord mathnormal">p</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.32833099999999993em;"><span style="top:-2.5500000000000003em;margin-left:0em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight"><span class="mord mathnormal mtight" style="margin-right:0.05764em;">S</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.15em;"><span></span></span></span></span></span></span></span><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="accent-body" style="left:-0.13889em;"><span class="mord">˙</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.19444em;"><span></span></span></span></span></span><span class="mspace" style="margin-right:0.2777777777777778em;"></span><span class="mrel">=</span><span class="mspace" style="margin-right:0.2777777777777778em;"></span></span><span class="base"><span class="strut" style="height:1.23686em;vertical-align:-0.25em;"></span><span class="mord accent"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.9868600000000001em;"><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="mord"><span class="mopen">[</span><span class="mord"><span class="mord mathnormal">p</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.32833099999999993em;"><span style="top:-2.5500000000000003em;margin-left:0em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight"><span class="mord mathnormal mtight" style="margin-right:0.10903em;">M</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.15em;"><span></span></span></span></span></span></span><span class="mclose">]</span></span></span><span style="top:-3.319em;"><span class="pstrut" style="height:3em;"></span><span class="accent-body" style="left:-0.13889em;"><span class="mord">˙</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.25em;"><span></span></span></span></span></span><span class="mord"><span class="mord mathnormal">L</span><span class="msupsub"><span class="vlist-t"><span class="vlist-r"><span class="vlist" style="height:0.8641079999999999em;"><span style="top:-3.113em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight"><span class="mord mtight">2</span></span></span></span></span></span></span></span><span class="mspace" style="margin-right:0.2222222222222222em;"></span><span class="mbin">+</span><span class="mspace" style="margin-right:0.2222222222222222em;"></span></span><span class="base"><span class="strut" style="height:1.23686em;vertical-align:-0.25em;"></span><span class="mord accent"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.9868600000000001em;"><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="mord"><span class="mopen">{</span><span class="mord"><span class="mord mathnormal">p</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.32833099999999993em;"><span style="top:-2.5500000000000003em;margin-left:0em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight"><span class="mord mathnormal mtight" style="margin-right:0.13889em;">T</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.15em;"><span></span></span></span></span></span></span><span class="mclose">}</span></span></span><span style="top:-3.319em;"><span class="pstrut" style="height:3em;"></span><span class="accent-body" style="left:-0.13889em;"><span class="mord">˙</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.25em;"><span></span></span></span></span></span><span class="mord"><span class="mord mathnormal">L</span><span class="msupsub"><span class="vlist-t"><span class="vlist-r"><span class="vlist" style="height:0.8641079999999999em;"><span style="top:-3.113em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight"><span class="mord mtight">3</span></span></span></span></span></span></span></span></span></span></span></span></eqn></section></math>
</li>
<li>
<p>energy allocated to growth <eq><span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mstyle mathcolor="blue"><mover accent="true"><msub><mi>p</mi><mi>G</mi></msub><mo>˙</mo></mover></mstyle></mrow><annotation encoding="application/x-tex">\color{blue}\dot{p_G}</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:0.8623000000000001em;vertical-align:-0.19444em;"></span><span class="mord accent" style="color:blue;"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.66786em;"><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="mord" style="color:blue;"><span class="mord mathnormal" style="color:blue;">p</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.32833099999999993em;"><span style="top:-2.5500000000000003em;margin-left:0em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight" style="color:blue;"><span class="mord mathnormal mtight" style="color:blue;">G</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.15em;"><span></span></span></span></span></span></span></span><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="accent-body" style="left:-0.13889em;"><span class="mord" style="color:blue;">˙</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.19444em;"><span></span></span></span></span></span></span></span></span></eq></p>
<section><eqn><span class="katex-display"><span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML" display="block"><semantics><mrow><mover accent="true"><msub><mi>p</mi><mi>G</mi></msub><mo>˙</mo></mover><mo>=</mo><mi>κ</mi><mover accent="true"><msub><mi>p</mi><mi>C</mi></msub><mo>˙</mo></mover><mo>−</mo><mover accent="true"><msub><mi>p</mi><mi>S</mi></msub><mo>˙</mo></mover></mrow><annotation encoding="application/x-tex">\dot{p_G} = \kappa\dot{p_C} - \dot{p_S} </annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:0.8623000000000001em;vertical-align:-0.19444em;"></span><span class="mord accent"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.66786em;"><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="mord"><span class="mord mathnormal">p</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.32833099999999993em;"><span style="top:-2.5500000000000003em;margin-left:0em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight"><span class="mord mathnormal mtight">G</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.15em;"><span></span></span></span></span></span></span></span><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="accent-body" style="left:-0.13889em;"><span class="mord">˙</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.19444em;"><span></span></span></span></span></span><span class="mspace" style="margin-right:0.2777777777777778em;"></span><span class="mrel">=</span><span class="mspace" style="margin-right:0.2777777777777778em;"></span></span><span class="base"><span class="strut" style="height:0.8623000000000001em;vertical-align:-0.19444em;"></span><span class="mord mathnormal">κ</span><span class="mord accent"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.66786em;"><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="mord"><span class="mord mathnormal">p</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.32833099999999993em;"><span style="top:-2.5500000000000003em;margin-left:0em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight"><span class="mord mathnormal mtight" style="margin-right:0.07153em;">C</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.15em;"><span></span></span></span></span></span></span></span><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="accent-body" style="left:-0.13889em;"><span class="mord">˙</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.19444em;"><span></span></span></span></span></span><span class="mspace" style="margin-right:0.2222222222222222em;"></span><span class="mbin">−</span><span class="mspace" style="margin-right:0.2222222222222222em;"></span></span><span class="base"><span class="strut" style="height:0.8623000000000001em;vertical-align:-0.19444em;"></span><span class="mord accent"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.66786em;"><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="mord"><span class="mord mathnormal">p</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.32833099999999993em;"><span style="top:-2.5500000000000003em;margin-left:0em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight"><span class="mord mathnormal mtight" style="margin-right:0.05764em;">S</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.15em;"><span></span></span></span></span></span></span></span><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="accent-body" style="left:-0.13889em;"><span class="mord">˙</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.19444em;"><span></span></span></span></span></span></span></span></span></span></eqn></section></math>
<section><eqn><span class="katex-display"><span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML" display="block"><semantics><mrow><mover accent="true"><msub><mi>p</mi><mi>G</mi></msub><mo>˙</mo></mover><mo>=</mo><mo stretchy="false">[</mo><msub><mi>E</mi><mi>G</mi></msub><mo stretchy="false">]</mo><mfrac><mrow><mi>d</mi><mi>V</mi></mrow><mrow><mi>d</mi><mi>t</mi></mrow></mfrac></mrow><annotation encoding="application/x-tex">\dot{p_G} = [E_G] \frac{dV}{dt}</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:0.8623000000000001em;vertical-align:-0.19444em;"></span><span class="mord accent"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.66786em;"><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="mord"><span class="mord mathnormal">p</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.32833099999999993em;"><span style="top:-2.5500000000000003em;margin-left:0em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight"><span class="mord mathnormal mtight">G</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.15em;"><span></span></span></span></span></span></span></span><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="accent-body" style="left:-0.13889em;"><span class="mord">˙</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.19444em;"><span></span></span></span></span></span><span class="mspace" style="margin-right:0.2777777777777778em;"></span><span class="mrel">=</span><span class="mspace" style="margin-right:0.2777777777777778em;"></span></span><span class="base"><span class="strut" style="height:2.05744em;vertical-align:-0.686em;"></span><span class="mopen">[</span><span class="mord"><span class="mord mathnormal" style="margin-right:0.05764em;">E</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.32833099999999993em;"><span style="top:-2.5500000000000003em;margin-left:-0.05764em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight"><span class="mord mathnormal mtight">G</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.15em;"><span></span></span></span></span></span></span><span class="mclose">]</span><span class="mord"><span class="mopen nulldelimiter"></span><span class="mfrac"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:1.37144em;"><span style="top:-2.314em;"><span class="pstrut" style="height:3em;"></span><span class="mord"><span class="mord mathnormal">d</span><span class="mord mathnormal">t</span></span></span><span style="top:-3.23em;"><span class="pstrut" style="height:3em;"></span><span class="frac-line" style="border-bottom-width:0.04em;"></span></span><span style="top:-3.677em;"><span class="pstrut" style="height:3em;"></span><span class="mord"><span class="mord mathnormal">d</span><span class="mord mathnormal" style="margin-right:0.22222em;">V</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.686em;"><span></span></span></span></span></span><span class="mclose nulldelimiter"></span></span></span></span></span></span></eqn></section></math>
</li>
<li>
<p>specific growth rate <eq><span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mstyle mathcolor="blue"><mover accent="true"><mi>r</mi><mo>˙</mo></mover></mstyle></mrow><annotation encoding="application/x-tex">\color{blue}\dot{r}</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:0.66786em;vertical-align:0em;"></span><span class="mord accent" style="color:blue;"><span class="vlist-t"><span class="vlist-r"><span class="vlist" style="height:0.66786em;"><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="mord mathnormal" style="margin-right:0.02778em;color:blue;">r</span></span><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="accent-body" style="left:-0.08333000000000002em;"><span class="mord" style="color:blue;">˙</span></span></span></span></span></span></span></span></span></span></eq></p>
<section><eqn><span class="katex-display"><span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML" display="block"><semantics><mrow><mover accent="true"><mi>r</mi><mo>˙</mo></mover><mo>=</mo><mfrac><mn>1</mn><mi>V</mi></mfrac><mfrac><mrow><mi>d</mi><mi>V</mi></mrow><mrow><mi>d</mi><mi>t</mi></mrow></mfrac></mrow><annotation encoding="application/x-tex">\dot{r} = \frac{1}{V}\frac{dV}{dt}</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:0.66786em;vertical-align:0em;"></span><span class="mord accent"><span class="vlist-t"><span class="vlist-r"><span class="vlist" style="height:0.66786em;"><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="mord mathnormal" style="margin-right:0.02778em;">r</span></span><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="accent-body" style="left:-0.08333000000000002em;"><span class="mord">˙</span></span></span></span></span></span></span><span class="mspace" style="margin-right:0.2777777777777778em;"></span><span class="mrel">=</span><span class="mspace" style="margin-right:0.2777777777777778em;"></span></span><span class="base"><span class="strut" style="height:2.05744em;vertical-align:-0.686em;"></span><span class="mord"><span class="mopen nulldelimiter"></span><span class="mfrac"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:1.32144em;"><span style="top:-2.314em;"><span class="pstrut" style="height:3em;"></span><span class="mord"><span class="mord mathnormal" style="margin-right:0.22222em;">V</span></span></span><span style="top:-3.23em;"><span class="pstrut" style="height:3em;"></span><span class="frac-line" style="border-bottom-width:0.04em;"></span></span><span style="top:-3.677em;"><span class="pstrut" style="height:3em;"></span><span class="mord"><span class="mord">1</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.686em;"><span></span></span></span></span></span><span class="mclose nulldelimiter"></span></span><span class="mord"><span class="mopen nulldelimiter"></span><span class="mfrac"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:1.37144em;"><span style="top:-2.314em;"><span class="pstrut" style="height:3em;"></span><span class="mord"><span class="mord mathnormal">d</span><span class="mord mathnormal">t</span></span></span><span style="top:-3.23em;"><span class="pstrut" style="height:3em;"></span><span class="frac-line" style="border-bottom-width:0.04em;"></span></span><span style="top:-3.677em;"><span class="pstrut" style="height:3em;"></span><span class="mord"><span class="mord mathnormal">d</span><span class="mord mathnormal" style="margin-right:0.22222em;">V</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.686em;"><span></span></span></span></span></span><span class="mclose nulldelimiter"></span></span></span></span></span></span></eqn></section></math>
<p>OR?</p>
<section><eqn><span class="katex-display"><span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML" display="block"><semantics><mrow><mover accent="true"><mi>r</mi><mo>˙</mo></mover><mo>=</mo><mfrac><mi>d</mi><mrow><mi>d</mi><mi>t</mi></mrow></mfrac><mi>l</mi><mi>n</mi><mi>V</mi></mrow><annotation encoding="application/x-tex">\dot{r} = \frac{d}{dt}lnV</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:0.66786em;vertical-align:0em;"></span><span class="mord accent"><span class="vlist-t"><span class="vlist-r"><span class="vlist" style="height:0.66786em;"><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="mord mathnormal" style="margin-right:0.02778em;">r</span></span><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="accent-body" style="left:-0.08333000000000002em;"><span class="mord">˙</span></span></span></span></span></span></span><span class="mspace" style="margin-right:0.2777777777777778em;"></span><span class="mrel">=</span><span class="mspace" style="margin-right:0.2777777777777778em;"></span></span><span class="base"><span class="strut" style="height:2.05744em;vertical-align:-0.686em;"></span><span class="mord"><span class="mopen nulldelimiter"></span><span class="mfrac"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:1.37144em;"><span style="top:-2.314em;"><span class="pstrut" style="height:3em;"></span><span class="mord"><span class="mord mathnormal">d</span><span class="mord mathnormal">t</span></span></span><span style="top:-3.23em;"><span class="pstrut" style="height:3em;"></span><span class="frac-line" style="border-bottom-width:0.04em;"></span></span><span style="top:-3.677em;"><span class="pstrut" style="height:3em;"></span><span class="mord"><span class="mord mathnormal">d</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.686em;"><span></span></span></span></span></span><span class="mclose nulldelimiter"></span></span><span class="mord mathnormal" style="margin-right:0.01968em;">l</span><span class="mord mathnormal" style="margin-right:0.22222em;">nV</span></span></span></span></span></eqn></section></math>
<p>OR?</p>
<section><eqn><span class="katex-display"><span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML" display="block"><semantics><mrow><mover accent="true"><mi>r</mi><mo>˙</mo></mover><mo>=</mo><mfrac><mover accent="true"><mrow><mo stretchy="false">[</mo><msub><mi>p</mi><mi>G</mi></msub><mo stretchy="false">]</mo></mrow><mo>˙</mo></mover><mrow><mo stretchy="false">[</mo><msub><mi>E</mi><mi>G</mi></msub><mo stretchy="false">]</mo></mrow></mfrac></mrow><annotation encoding="application/x-tex">\dot{r} = \frac{\dot{[p_G]}
}{[E_G]}</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:0.66786em;vertical-align:0em;"></span><span class="mord accent"><span class="vlist-t"><span class="vlist-r"><span class="vlist" style="height:0.66786em;"><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="mord mathnormal" style="margin-right:0.02778em;">r</span></span><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="accent-body" style="left:-0.08333000000000002em;"><span class="mord">˙</span></span></span></span></span></span></span><span class="mspace" style="margin-right:0.2777777777777778em;"></span><span class="mrel">=</span><span class="mspace" style="margin-right:0.2777777777777778em;"></span></span><span class="base"><span class="strut" style="height:2.59986em;vertical-align:-0.936em;"></span><span class="mord"><span class="mopen nulldelimiter"></span><span class="mfrac"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:1.6638600000000001em;"><span style="top:-2.314em;"><span class="pstrut" style="height:3em;"></span><span class="mord"><span class="mopen">[</span><span class="mord"><span class="mord mathnormal" style="margin-right:0.05764em;">E</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.32833099999999993em;"><span style="top:-2.5500000000000003em;margin-left:-0.05764em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight"><span class="mord mathnormal mtight">G</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.15em;"><span></span></span></span></span></span></span><span class="mclose">]</span></span></span><span style="top:-3.23em;"><span class="pstrut" style="height:3em;"></span><span class="frac-line" style="border-bottom-width:0.04em;"></span></span><span style="top:-3.677em;"><span class="pstrut" style="height:3em;"></span><span class="mord"><span class="mord accent"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.9868600000000001em;"><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="mord"><span class="mopen">[</span><span class="mord"><span class="mord mathnormal">p</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.32833099999999993em;"><span style="top:-2.5500000000000003em;margin-left:0em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight"><span class="mord mathnormal mtight">G</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.15em;"><span></span></span></span></span></span></span><span class="mclose">]</span></span></span><span style="top:-3.319em;"><span class="pstrut" style="height:3em;"></span><span class="accent-body" style="left:-0.13889em;"><span class="mord">˙</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.25em;"><span></span></span></span></span></span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.936em;"><span></span></span></span></span></span><span class="mclose nulldelimiter"></span></span></span></span></span></span></eqn></section></math>
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<li>
<p>maturity maintenance <eq><span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mstyle mathcolor="red"><mover accent="true"><msub><mi>p</mi><mi>J</mi></msub><mo>˙</mo></mover></mstyle></mrow><annotation encoding="application/x-tex">\color{red}\dot{p_J}</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:0.8623000000000001em;vertical-align:-0.19444em;"></span><span class="mord accent" style="color:red;"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.66786em;"><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="mord" style="color:red;"><span class="mord mathnormal" style="color:red;">p</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.32833099999999993em;"><span style="top:-2.5500000000000003em;margin-left:0em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight" style="color:red;"><span class="mord mathnormal mtight" style="margin-right:0.09618em;color:red;">J</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.15em;"><span></span></span></span></span></span></span></span><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="accent-body" style="left:-0.13889em;"><span class="mord" style="color:red;">˙</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.19444em;"><span></span></span></span></span></span></span></span></span></eq></p>
<section><eqn><span class="katex-display"><span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML" display="block"><semantics><mrow><mover accent="true"><msub><mi>p</mi><mi>J</mi></msub><mo>˙</mo></mover><mo>=</mo><mover accent="true"><msub><mi>k</mi><mi>J</mi></msub><mo>˙</mo></mover><mo>∗</mo><msub><mi>E</mi><mi>H</mi></msub></mrow><annotation encoding="application/x-tex">\dot{p_J} = \dot{k_J} * E_H</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:0.8623000000000001em;vertical-align:-0.19444em;"></span><span class="mord accent"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.66786em;"><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="mord"><span class="mord mathnormal">p</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.32833099999999993em;"><span style="top:-2.5500000000000003em;margin-left:0em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight"><span class="mord mathnormal mtight" style="margin-right:0.09618em;">J</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.15em;"><span></span></span></span></span></span></span></span><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="accent-body" style="left:-0.13889em;"><span class="mord">˙</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.19444em;"><span></span></span></span></span></span><span class="mspace" style="margin-right:0.2777777777777778em;"></span><span class="mrel">=</span><span class="mspace" style="margin-right:0.2777777777777778em;"></span></span><span class="base"><span class="strut" style="height:1.0813em;vertical-align:-0.15em;"></span><span class="mord accent"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.9313em;"><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="mord"><span class="mord mathnormal" style="margin-right:0.03148em;">k</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.32833099999999993em;"><span style="top:-2.5500000000000003em;margin-left:-0.03148em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight"><span class="mord mathnormal mtight" style="margin-right:0.09618em;">J</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.15em;"><span></span></span></span></span></span></span></span><span style="top:-3.26344em;"><span class="pstrut" style="height:3em;"></span><span class="accent-body" style="left:-0.13889em;"><span class="mord">˙</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.15em;"><span></span></span></span></span></span><span class="mspace" style="margin-right:0.2222222222222222em;"></span><span class="mbin">∗</span><span class="mspace" style="margin-right:0.2222222222222222em;"></span></span><span class="base"><span class="strut" style="height:0.83333em;vertical-align:-0.15em;"></span><span class="mord"><span class="mord mathnormal" style="margin-right:0.05764em;">E</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.32833099999999993em;"><span style="top:-2.5500000000000003em;margin-left:-0.05764em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight"><span class="mord mathnormal mtight" style="margin-right:0.08125em;">H</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.15em;"><span></span></span></span></span></span></span></span></span></span></span></eqn></section></math>
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<li>
<p>maturation (embryo-juvenile) <eq><span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mstyle mathcolor="red"><mover accent="true"><msub><mi>p</mi><mi>R</mi></msub><mo>˙</mo></mover></mstyle></mrow><annotation encoding="application/x-tex">\color{red}\dot{p_R}</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:0.8623000000000001em;vertical-align:-0.19444em;"></span><span class="mord accent" style="color:red;"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.66786em;"><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="mord" style="color:red;"><span class="mord mathnormal" style="color:red;">p</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.32833099999999993em;"><span style="top:-2.5500000000000003em;margin-left:0em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight" style="color:red;"><span class="mord mathnormal mtight" style="margin-right:0.00773em;color:red;">R</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.15em;"><span></span></span></span></span></span></span></span><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="accent-body" style="left:-0.13889em;"><span class="mord" style="color:red;">˙</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.19444em;"><span></span></span></span></span></span></span></span></span></eq></p>
<section><eqn><span class="katex-display"><span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML" display="block"><semantics><mrow><mover accent="true"><msub><mi>p</mi><mi>R</mi></msub><mo>˙</mo></mover><mo>=</mo><mo stretchy="false">(</mo><mn>1</mn><mo>−</mo><mi>κ</mi><mo stretchy="false">)</mo><mover accent="true"><msub><mi>p</mi><mi>C</mi></msub><mo>˙</mo></mover><mo>−</mo><mover accent="true"><msub><mi>p</mi><mi>J</mi></msub><mo>˙</mo></mover></mrow><annotation encoding="application/x-tex">\dot{p_R} = (1 - \kappa) \dot{p_C} - \dot{p_J} </annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:0.8623000000000001em;vertical-align:-0.19444em;"></span><span class="mord accent"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.66786em;"><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="mord"><span class="mord mathnormal">p</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.32833099999999993em;"><span style="top:-2.5500000000000003em;margin-left:0em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight"><span class="mord mathnormal mtight" style="margin-right:0.00773em;">R</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.15em;"><span></span></span></span></span></span></span></span><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="accent-body" style="left:-0.13889em;"><span class="mord">˙</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.19444em;"><span></span></span></span></span></span><span class="mspace" style="margin-right:0.2777777777777778em;"></span><span class="mrel">=</span><span class="mspace" style="margin-right:0.2777777777777778em;"></span></span><span class="base"><span class="strut" style="height:1em;vertical-align:-0.25em;"></span><span class="mopen">(</span><span class="mord">1</span><span class="mspace" style="margin-right:0.2222222222222222em;"></span><span class="mbin">−</span><span class="mspace" style="margin-right:0.2222222222222222em;"></span></span><span class="base"><span class="strut" style="height:1em;vertical-align:-0.25em;"></span><span class="mord mathnormal">κ</span><span class="mclose">)</span><span class="mord accent"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.66786em;"><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="mord"><span class="mord mathnormal">p</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.32833099999999993em;"><span style="top:-2.5500000000000003em;margin-left:0em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight"><span class="mord mathnormal mtight" style="margin-right:0.07153em;">C</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.15em;"><span></span></span></span></span></span></span></span><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="accent-body" style="left:-0.13889em;"><span class="mord">˙</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.19444em;"><span></span></span></span></span></span><span class="mspace" style="margin-right:0.2222222222222222em;"></span><span class="mbin">−</span><span class="mspace" style="margin-right:0.2222222222222222em;"></span></span><span class="base"><span class="strut" style="height:0.8623000000000001em;vertical-align:-0.19444em;"></span><span class="mord accent"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.66786em;"><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="mord"><span class="mord mathnormal">p</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.32833099999999993em;"><span style="top:-2.5500000000000003em;margin-left:0em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight"><span class="mord mathnormal mtight" style="margin-right:0.09618em;">J</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.15em;"><span></span></span></span></span></span></span></span><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="accent-body" style="left:-0.13889em;"><span class="mord">˙</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.19444em;"><span></span></span></span></span></span></span></span></span></span></eqn></section></math>
<section><eqn><span class="katex-display"><span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML" display="block"><semantics><mrow><mfrac><mrow><mi>d</mi><msub><mi>E</mi><mi>H</mi></msub></mrow><mrow><mi>d</mi><mi>t</mi></mrow></mfrac><mo>=</mo><mover accent="true"><msub><mi>p</mi><mi>R</mi></msub><mo>˙</mo></mover></mrow><annotation encoding="application/x-tex">\frac{dE_H}{dt} = \dot{p_R}</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:2.05744em;vertical-align:-0.686em;"></span><span class="mord"><span class="mopen nulldelimiter"></span><span class="mfrac"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:1.37144em;"><span style="top:-2.314em;"><span class="pstrut" style="height:3em;"></span><span class="mord"><span class="mord mathnormal">d</span><span class="mord mathnormal">t</span></span></span><span style="top:-3.23em;"><span class="pstrut" style="height:3em;"></span><span class="frac-line" style="border-bottom-width:0.04em;"></span></span><span style="top:-3.677em;"><span class="pstrut" style="height:3em;"></span><span class="mord"><span class="mord mathnormal">d</span><span class="mord"><span class="mord mathnormal" style="margin-right:0.05764em;">E</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.32833099999999993em;"><span style="top:-2.5500000000000003em;margin-left:-0.05764em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight"><span class="mord mathnormal mtight" style="margin-right:0.08125em;">H</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.15em;"><span></span></span></span></span></span></span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.686em;"><span></span></span></span></span></span><span class="mclose nulldelimiter"></span></span><span class="mspace" style="margin-right:0.2777777777777778em;"></span><span class="mrel">=</span><span class="mspace" style="margin-right:0.2777777777777778em;"></span></span><span class="base"><span class="strut" style="height:0.8623000000000001em;vertical-align:-0.19444em;"></span><span class="mord accent"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.66786em;"><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="mord"><span class="mord mathnormal">p</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.32833099999999993em;"><span style="top:-2.5500000000000003em;margin-left:0em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight"><span class="mord mathnormal mtight" style="margin-right:0.00773em;">R</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.15em;"><span></span></span></span></span></span></span></span><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="accent-body" style="left:-0.13889em;"><span class="mord">˙</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.19444em;"><span></span></span></span></span></span></span></span></span></span></eqn></section></math>
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<li>
<p>reproduction (adult) <eq><span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mstyle mathcolor="red"><mover accent="true"><msub><mi>p</mi><mi>R</mi></msub><mo>˙</mo></mover></mstyle></mrow><annotation encoding="application/x-tex">\color{red}\dot{p_R}</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:0.8623000000000001em;vertical-align:-0.19444em;"></span><span class="mord accent" style="color:red;"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.66786em;"><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="mord" style="color:red;"><span class="mord mathnormal" style="color:red;">p</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.32833099999999993em;"><span style="top:-2.5500000000000003em;margin-left:0em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight" style="color:red;"><span class="mord mathnormal mtight" style="margin-right:0.00773em;color:red;">R</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.15em;"><span></span></span></span></span></span></span></span><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="accent-body" style="left:-0.13889em;"><span class="mord" style="color:red;">˙</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.19444em;"><span></span></span></span></span></span></span></span></span></eq></p>
<section><eqn><span class="katex-display"><span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML" display="block"><semantics><mrow><mover accent="true"><msub><mi>p</mi><mi>R</mi></msub><mo>˙</mo></mover><mo>=</mo><mo stretchy="false">(</mo><mn>1</mn><mo>−</mo><mi>κ</mi><mo stretchy="false">)</mo><mover accent="true"><msub><mi>p</mi><mi>C</mi></msub><mo>˙</mo></mover><mo>−</mo><mover accent="true"><msub><mi>p</mi><mi>J</mi></msub><mo>˙</mo></mover></mrow><annotation encoding="application/x-tex">\dot{p_R} = (1 - \kappa) \dot{p_C} - \dot{p_J}</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:0.8623000000000001em;vertical-align:-0.19444em;"></span><span class="mord accent"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.66786em;"><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="mord"><span class="mord mathnormal">p</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.32833099999999993em;"><span style="top:-2.5500000000000003em;margin-left:0em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight"><span class="mord mathnormal mtight" style="margin-right:0.00773em;">R</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.15em;"><span></span></span></span></span></span></span></span><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="accent-body" style="left:-0.13889em;"><span class="mord">˙</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.19444em;"><span></span></span></span></span></span><span class="mspace" style="margin-right:0.2777777777777778em;"></span><span class="mrel">=</span><span class="mspace" style="margin-right:0.2777777777777778em;"></span></span><span class="base"><span class="strut" style="height:1em;vertical-align:-0.25em;"></span><span class="mopen">(</span><span class="mord">1</span><span class="mspace" style="margin-right:0.2222222222222222em;"></span><span class="mbin">−</span><span class="mspace" style="margin-right:0.2222222222222222em;"></span></span><span class="base"><span class="strut" style="height:1em;vertical-align:-0.25em;"></span><span class="mord mathnormal">κ</span><span class="mclose">)</span><span class="mord accent"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.66786em;"><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="mord"><span class="mord mathnormal">p</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.32833099999999993em;"><span style="top:-2.5500000000000003em;margin-left:0em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight"><span class="mord mathnormal mtight" style="margin-right:0.07153em;">C</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.15em;"><span></span></span></span></span></span></span></span><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="accent-body" style="left:-0.13889em;"><span class="mord">˙</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.19444em;"><span></span></span></span></span></span><span class="mspace" style="margin-right:0.2222222222222222em;"></span><span class="mbin">−</span><span class="mspace" style="margin-right:0.2222222222222222em;"></span></span><span class="base"><span class="strut" style="height:0.8623000000000001em;vertical-align:-0.19444em;"></span><span class="mord accent"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.66786em;"><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="mord"><span class="mord mathnormal">p</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.32833099999999993em;"><span style="top:-2.5500000000000003em;margin-left:0em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight"><span class="mord mathnormal mtight" style="margin-right:0.09618em;">J</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.15em;"><span></span></span></span></span></span></span></span><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="accent-body" style="left:-0.13889em;"><span class="mord">˙</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.19444em;"><span></span></span></span></span></span></span></span></span></span></eqn></section></math>
<section><eqn><span class="katex-display"><span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML" display="block"><semantics><mrow><mfrac><mrow><mi>d</mi><msub><mi>E</mi><mi>R</mi></msub></mrow><mrow><mi>d</mi><mi>t</mi></mrow></mfrac><mo>=</mo><msub><mi>κ</mi><mi>R</mi></msub><mover accent="true"><msub><mi>p</mi><mi>R</mi></msub><mo>˙</mo></mover></mrow><annotation encoding="application/x-tex">\frac{dE_R}{dt} = \kappa_R \dot{p_R}</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:2.05744em;vertical-align:-0.686em;"></span><span class="mord"><span class="mopen nulldelimiter"></span><span class="mfrac"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:1.37144em;"><span style="top:-2.314em;"><span class="pstrut" style="height:3em;"></span><span class="mord"><span class="mord mathnormal">d</span><span class="mord mathnormal">t</span></span></span><span style="top:-3.23em;"><span class="pstrut" style="height:3em;"></span><span class="frac-line" style="border-bottom-width:0.04em;"></span></span><span style="top:-3.677em;"><span class="pstrut" style="height:3em;"></span><span class="mord"><span class="mord mathnormal">d</span><span class="mord"><span class="mord mathnormal" style="margin-right:0.05764em;">E</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.32833099999999993em;"><span style="top:-2.5500000000000003em;margin-left:-0.05764em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight"><span class="mord mathnormal mtight" style="margin-right:0.00773em;">R</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.15em;"><span></span></span></span></span></span></span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.686em;"><span></span></span></span></span></span><span class="mclose nulldelimiter"></span></span><span class="mspace" style="margin-right:0.2777777777777778em;"></span><span class="mrel">=</span><span class="mspace" style="margin-right:0.2777777777777778em;"></span></span><span class="base"><span class="strut" style="height:0.8623000000000001em;vertical-align:-0.19444em;"></span><span class="mord"><span class="mord mathnormal">κ</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.32833099999999993em;"><span style="top:-2.5500000000000003em;margin-left:0em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight"><span class="mord mathnormal mtight" style="margin-right:0.00773em;">R</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.15em;"><span></span></span></span></span></span></span><span class="mord accent"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.66786em;"><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="mord"><span class="mord mathnormal">p</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.32833099999999993em;"><span style="top:-2.5500000000000003em;margin-left:0em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight"><span class="mord mathnormal mtight" style="margin-right:0.00773em;">R</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.15em;"><span></span></span></span></span></span></span></span><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="accent-body" style="left:-0.13889em;"><span class="mord">˙</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.19444em;"><span></span></span></span></span></span></span></span></span></span></eqn></section></math>
</li>
</ul>
<blockquote>
<p><a href="DEB_derivations/derivations.md">MORE DERIVATIONS</a> for equations</p>
</blockquote>
<h1 id="existing-models">Existing models</h1>
<p>some of these packages are required to run the scripts in <code>code_pu</code> (or <code>src</code>)</p>
<h2 id="matlab-tools-original-deb">MATLAB tools (original DEB)</h2>
<p><a href="https://debtool.debtheory.org/docs/index.html">DEBtool</a></p>
<blockquote>
<p><em>DEBtool illustrate some implications of the DEB theory</em></p>
</blockquote>
<p><a href="https://amptool.debtheory.org/docs/index.html">AmPtool</a></p>
<blockquote>
<p><em>AmPtool analyses patterns in DEB parameters</em></p>
</blockquote>
<blockquote>
<p><strong>install and configuration:</strong>
Need MATLAB. In MATLAB, <code>Home</code> >> <code>set path</code> and direct to the source code</p>
</blockquote>
<h2 id="nichemapr-habitat-modeling">NicheMapR (Habitat modeling)</h2>
<p><a href="https://mrke.github.io/getting_started/">NicheMapR package</a></p>
<blockquote>
<p><em>NicheMapR is written by Michael Kearney. It includes Microclimates, Ectotherms, Endotherms, Plants, Dynamic Energy Budgets modules that can be coupled together to do habitat and behavioral modeling</em></p>
</blockquote>
<blockquote>
<p><strong>install and configuration:</strong>
<a href="https://cran.r-project.org/web/packages/githubinstall/vignettes/githubinstall.html">install package from github tutorial</a></p>
</blockquote>
<h2 id="fabm-fabm-deb-hydrodynamic-coupling">FABM, FABM-DEB (Hydrodynamic coupling)</h2>
<p><a href="https://github.com/fabm-model/fabm">FABM</a></p>
<p><a href="https://github.com/jornbr/fabm-deb">FABM-DEB</a> (it is a population model)</p>
<blockquote>
<p><em>FABM couples hydrodynamic models with biogeochemical models. There is a FABM-DEB model constructed by
Jorn Bruggeman</em></p>
</blockquote>
<blockquote>
<p><strong>installation and configuration</strong></p>
</blockquote>
<pre><code class="language-shell"><span class="hljs-meta prompt_"># </span><span class="language-bash">>>>>>> install and compile FABM-DEB with 0d driver</span>
FABMDIR="~/src/fabm" # Path to FABM source code
GOTMDIR="~/src/GOTM6" # Path to GOTM source code
compiler="/opt/homebrew/bin/gfortran" # fortran compiler on this computer
mkdir -p ~/build/fabm-0d && cd ~/build/fabm-0d
cmake $FABMDIR/src/drivers/0d -DGOTM_BASE=$GOTMDIR -DCMAKE_Fortran_COMPILER=$compiler -DFABM_INSTITUTES="akvaplan;au;bb;csiro;ersem;examples;gotm;iow;jrc;msi;niva;pclake;pml;selma;su;uhh;deb" -DFABM_DEB_BASE=~/src/fabm-deb
make install
<span class="hljs-meta prompt_">
# </span><span class="language-bash">>>>>>> generate yaml files >>>>>>></span>
https://github.com/fabm-model/fabm/wiki/Setting-up-a-simulation
<span class="hljs-meta prompt_">
# </span><span class="language-bash">>>>>>> run fabm0d coupled with deb >>>>>>></span>
cd /Users/tongyaop/test_funcs_local/fabm-deb/0d_deb_test
~/local/fabm/0d/bin/fabm0d -y ./fabm-deb.yaml
</code></pre>
<p>Or use <a href="https://github.com/jornbr/pydeb">pydeb</a>:</p>
<pre><code class="language-shell"><span class="hljs-meta prompt_"># </span><span class="language-bash">>>>>>> run deb <span class="hljs-keyword">in</span> pydeb >>>>>>></span>
<span class="hljs-meta prompt_">
# </span><span class="language-bash">python packages : NumPy, Python, Jupyter, plotly</span>
<span class="hljs-meta prompt_">
# </span><span class="language-bash">install pydeb:</span>
PYDEB_DIR=~/src/pydeb
python -m pip install $PYDEB_DIR --user
<span class="hljs-meta prompt_">
# </span><span class="language-bash">run a deb model:</span>
<span class="hljs-meta prompt_"># </span><span class="language-bash">go to <span class="hljs-variable">$PYDEB_DIR</span>/examples</span>
</code></pre>
<h2 id="population-models">Population models</h2>
<p><img src="./DEB_figures/popModels.png" alt="DEB concept -Tongyao"></p>
<h3 id="ibm-individual-based-model">IBM (Individual-Based-Model)</h3>
<blockquote>
<p><strong>installation and configuration</strong></p>
</blockquote>
<ol>
<li>
<p>Install <code>NetLogo</code></p>
</li>
<li>
<p>set path in <code>.bash_profile</code> for MacOS</p>
</li>
</ol>
<pre><code class="language-shell">cd
vim .bash_profile
export JAVA_HOME=/Library/Internet\ Plug-Ins/JavaAppletPlugin.plugin/Contents/Home
export EBTPATH=/Applications/EBTtool.app/Contents/Resources
export PATH=${JAVA_HOME}/bin:/Applications/NetLogo\ 6.2.0/app:/Applications/EBTtool.app/Contents/MacOs:$PATH
</code></pre>
<ol start="3">
<li>To run: use <code>IBM()</code> function in MATLAB (from <code>DEBtool</code>)</li>
</ol>
<pre><code> [txNL23W, info] = IBM('Daphnia_magna', [], [], [], [], [], [], 80, 1);
</code></pre>
<h3 id="ebt">EBT</h3>
<blockquote>
<p><strong>installation and configuration</strong> Need fortran compiler and MATLAB</p>
</blockquote>
<p>To run: use <code>EBT()</code> function in MATLAB (from <code>DEBtool</code>).</p>
<pre><code>[txNL23W, info] = EBT('Daphnia_magna', [], [], [], [], [], 80);
</code></pre>
<h3 id="cpm">CPM</h3>
<blockquote>
<p>EXPLAIN</p>
</blockquote>
<h1 id="useful-web-interfaces">Useful web interfaces</h1>
<ul>
<li>
<p><a href="https://www.bio.vu.nl/thb/deb/deblab/add_my_pet/">AmP (Add my pet) portal</a></p>
</li>
<li>
<p><a href="https://mrke.github.io/">NicheMapR shiny apps</a>: Online habitat and DEB modeling</p>
</li>
<li>
<p><a href="https://deb.bolding-bruggeman.com/">Debber</a>: Estimates DEB parameters and provide confidence interval ranges.</p>
</li>
</ul>
<blockquote>
<p>This could be a documentation for the DEBtool github. Instead of just linking https://bio.vu.nl/thb/deb/deblab/ in the github readme file (That's could be where the frustrating, because you are getting back to where you came from), maybe explain a little bit about how to work with the code.</p>
</blockquote>
<h1 id="acquire-parameters">Acquire parameters</h1>
<h2 id="from-amp-collection">From AmP collection</h2>
<p><em>Even a species exist in the collection, it can be improved</em></p>
<p><a href="https://www.bio.vu.nl/thb/deb/deblab/add_my_pet/">AmP website</a></p>
<blockquote>
<p>This website should get a top-left figure to click on to go back to the home page</p>
</blockquote>
<p><code>COLLECTION</code> > <code>AmPdata.zip</code></p>
<h3 id="in-matlab">In MATLAB</h3>
<ol>
<li>Put <code>AmPdata</code> to MATLAB path</li>
<li>In MATLAB,</li>
</ol>
<pre><code class="language-MATLAB">load AmPdata
</code></pre>
<h3 id="in-r">In R</h3>
<p>(copied from <a href="https://mrke.github.io/NicheMapR/inst/doc/deb-model-tutorial">NicheMapR tutorial</a>)</p>
<pre><code class="language-R">install.packages<span class="hljs-punctuation">(</span><span class="hljs-string">'R.matlab'</span><span class="hljs-punctuation">)</span>
library<span class="hljs-punctuation">(</span>R.matlab<span class="hljs-punctuation">)</span>
allStat <span class="hljs-operator"><-</span> readMat<span class="hljs-punctuation">(</span><span class="hljs-string">'allStat.mat'</span><span class="hljs-punctuation">)</span> <span class="hljs-comment"># this will take a few minutes</span>
save<span class="hljs-punctuation">(</span>allStat<span class="hljs-punctuation">,</span> file <span class="hljs-operator">=</span> <span class="hljs-string">'allstat.Rda'</span><span class="hljs-punctuation">)</span> <span class="hljs-comment"># save it as an R data file for faster future loading</span>
library<span class="hljs-punctuation">(</span>knitr<span class="hljs-punctuation">)</span> <span class="hljs-comment"># this packages has a function for producing formatted tables.</span>
load<span class="hljs-punctuation">(</span><span class="hljs-string">'allStat.Rda'</span><span class="hljs-punctuation">)</span>
allDEB.species<span class="hljs-operator"><-</span>unlist<span class="hljs-punctuation">(</span>labels<span class="hljs-punctuation">(</span>allStat<span class="hljs-operator">$</span>allStat<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span> <span class="hljs-comment"># get all the species names</span>
allDEB.species<span class="hljs-operator"><-</span>allDEB.species<span class="hljs-punctuation">[</span><span class="hljs-number">1</span><span class="hljs-operator">:</span><span class="hljs-punctuation">(</span><span class="hljs-built_in">length</span><span class="hljs-punctuation">(</span>allDEB.species<span class="hljs-punctuation">)</span><span class="hljs-operator">-</span><span class="hljs-number">2</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span> <span class="hljs-comment"># last two elements are not species names</span>
kable<span class="hljs-punctuation">(</span>head<span class="hljs-punctuation">(</span>allDEB.species<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span>
Nspecies <span class="hljs-operator"><-</span> <span class="hljs-built_in">length</span><span class="hljs-punctuation">(</span>allStat<span class="hljs-operator">$</span>allStat<span class="hljs-punctuation">)</span>
Nspecies
species <span class="hljs-operator"><-</span> <span class="hljs-string">"Eulamprus.quoyii"</span>
species.slot <span class="hljs-operator"><-</span> which<span class="hljs-punctuation">(</span>allDEB.species <span class="hljs-operator">==</span> species<span class="hljs-punctuation">)</span>
par.names <span class="hljs-operator"><-</span> unlist<span class="hljs-punctuation">(</span>labels<span class="hljs-punctuation">(</span>allStat<span class="hljs-operator">$</span>allStat<span class="hljs-punctuation">[[</span>species.slot<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span>
<span class="hljs-keyword">for</span><span class="hljs-punctuation">(</span>i <span class="hljs-keyword">in</span> <span class="hljs-number">1</span><span class="hljs-operator">:</span><span class="hljs-built_in">length</span><span class="hljs-punctuation">(</span>par.names<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">{</span>
assign<span class="hljs-punctuation">(</span>par.names<span class="hljs-punctuation">[</span>i<span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> unlist<span class="hljs-punctuation">(</span>allStat<span class="hljs-operator">$</span>allStat<span class="hljs-punctuation">[[</span>species.slot<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">[</span>i<span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span>
<span class="hljs-punctuation">}</span>
</code></pre>
<h2 id="parameter-estimation-with-literatureexperimental-data">Parameter estimation with literature/experimental data</h2>
<h3 id="better-to-have-data">Better-to-have data</h3>
<table>
<thead>
<tr>
<th>Data to be collected</th>
<th>Common symbol</th>
</tr>
</thead>
<tbody>
<tr>
<td>length-weight relationship</td>
<td></td>
</tr>
<tr>
<td>length at first feeding (birth)</td>
<td><eq><span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><msub><mi>L</mi><mi>b</mi></msub></mrow><annotation encoding="application/x-tex">L_b</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:0.83333em;vertical-align:-0.15em;"></span><span class="mord"><span class="mord mathnormal">L</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.33610799999999996em;"><span style="top:-2.5500000000000003em;margin-left:0em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight"><span class="mord mathnormal mtight">b</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.15em;"><span></span></span></span></span></span></span></span></span></span></eq></td>
</tr>
<tr>
<td>length at puberty</td>
<td><eq><span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><msub><mi>L</mi><mi>p</mi></msub></mrow><annotation encoding="application/x-tex">L_p</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:0.969438em;vertical-align:-0.286108em;"></span><span class="mord"><span class="mord mathnormal">L</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.15139200000000003em;"><span style="top:-2.5500000000000003em;margin-left:0em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight"><span class="mord mathnormal mtight">p</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.286108em;"><span></span></span></span></span></span></span></span></span></span></eq></td>
</tr>
<tr>
<td>max mass</td>
<td><eq><span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><msub><mi>L</mi><mi>m</mi></msub></mrow><annotation encoding="application/x-tex">L_m</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:0.83333em;vertical-align:-0.15em;"></span><span class="mord"><span class="mord mathnormal">L</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.151392em;"><span style="top:-2.5500000000000003em;margin-left:0em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight"><span class="mord mathnormal mtight">m</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.15em;"><span></span></span></span></span></span></span></span></span></span></eq></td>
</tr>
<tr>
<td>max reproduction rate</td>
<td><eq><span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><msub><mi>R</mi><mi>i</mi></msub></mrow><annotation encoding="application/x-tex">R_i</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:0.83333em;vertical-align:-0.15em;"></span><span class="mord"><span class="mord mathnormal" style="margin-right:0.00773em;">R</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.31166399999999994em;"><span style="top:-2.5500000000000003em;margin-left:-0.00773em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight"><span class="mord mathnormal mtight">i</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.15em;"><span></span></span></span></span></span></span></span></span></span></eq></td>
</tr>
<tr>
<td>time from conception to first feeding (birth)</td>
<td><eq><span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><msub><mi>a</mi><mi>b</mi></msub></mrow><annotation encoding="application/x-tex">a_b</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:0.58056em;vertical-align:-0.15em;"></span><span class="mord"><span class="mord mathnormal">a</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.33610799999999996em;"><span style="top:-2.5500000000000003em;margin-left:0em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight"><span class="mord mathnormal mtight">b</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.15em;"><span></span></span></span></span></span></span></span></span></span></eq></td>
</tr>
<tr>
<td>time from first feeding (birth) to puberty</td>
<td><eq><span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><msub><mi>a</mi><mi>p</mi></msub></mrow><annotation encoding="application/x-tex">a_p</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:0.716668em;vertical-align:-0.286108em;"></span><span class="mord"><span class="mord mathnormal">a</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.15139200000000003em;"><span style="top:-2.5500000000000003em;margin-left:0em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight"><span class="mord mathnormal mtight">p</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.286108em;"><span></span></span></span></span></span></span></span></span></span></eq></td>
</tr>
<tr>
<td>life span</td>
<td><eq><span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><msub><mi>a</mi><mi>m</mi></msub></mrow><annotation encoding="application/x-tex">a_m</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:0.58056em;vertical-align:-0.15em;"></span><span class="mord"><span class="mord mathnormal">a</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.151392em;"><span style="top:-2.5500000000000003em;margin-left:0em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight"><span class="mord mathnormal mtight">m</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.15em;"><span></span></span></span></span></span></span></span></span></span></eq></td>
</tr>
<tr>
<td>*metamorphasis info</td>
<td></td>
</tr>
<tr>
<td>*other types of weight</td>
<td></td>
</tr>
<tr>
<td>*growth data from birth to death</td>
<td></td>
</tr>
<tr>
<td>*any forms of rate</td>
<td></td>
</tr>
<tr>
<td>*reproduction</td>
<td></td>
</tr>
<tr>
<td>*temperature dependence</td>
<td></td>
</tr>
</tbody>
</table>
<p><em>Better to be under known constant temperature, saturated food conditions (f = 1). This is not a hard requirement.</em></p>
<p><em>Start working on all the available data and then reduce the weight of some data if they are uncertain and provides bad estimations</em></p>
<blockquote>
<p>❗ Provide an univariate dataset here in txt/xlsx file form.</p>
</blockquote>
<h3 id="parameter-estimation-preparation">parameter estimation preparation</h3>
<ol>
<li>
<p>Create directory <code>Taeniopygia_guttata_test</code></p>
</li>
<li>
<p>In MATLAB, change directory to <code>Taeniopygia_guttata_test</code>, then run <code>AmPeps</code> in the command window. The following window will pop up</p>
<img src="./DEB_figures/AmPeps_popup.png" width="200" height="250" />
</li>
<li>
<p>Type in corresponding information:</p>
<table>
<thead>
<tr>
<th></th>
<th></th>
</tr>
</thead>
<tbody>
<tr>
<td>species</td>
<td>Taeniopygia_guttata_test</td>
</tr>
<tr>
<td>ecoCode</td>
<td>climate: Af</td>
</tr>
<tr>
<td></td>
<td>ecozone: TPi, TA</td>
</tr>
<tr>
<td></td>
<td>habitat: 0iTh, 0iTi, 0iTs, 0iTg, 0iTa</td>
</tr>
<tr>
<td></td>
<td>embryo: Tnsf, Tnpf</td>
</tr>
<tr>
<td></td>
<td>migrate:</td>
</tr>
<tr>
<td></td>
<td>food: biCi, biHs</td>
</tr>
<tr>
<td></td>
<td>gender: Dg</td>
</tr>
<tr>
<td></td>
<td>reprod: O</td>
</tr>
<tr>
<td>T_typical</td>
<td>42°C</td>
</tr>
</tbody>
</table>
<p>Add to <code>0-var data</code></p>
<table>
<thead>
<tr>
<th></th>
<th>Value</th>
<th>Reference</th>
</tr>
</thead>
<tbody>
<tr>
<td>age at birth</td>
<td>15 d</td>
<td>Wiki</td>
</tr>
<tr>
<td>time since birth at puberty</td>
<td>300 d</td>
<td>Wiki</td>
</tr>
<tr>
<td>life span</td>
<td>4360 d</td>
<td>voliere</td>
</tr>
<tr>
<td>wet weight at birth</td>
<td>0.8 g</td>
<td>Wiki</td>
</tr>
<tr>
<td>ultimate wet weight</td>
<td>11.7 g</td>
<td>AnAge</td>
</tr>
<tr>
<td>maximum reproduction rate</td>
<td>0.0137</td>
<td>Wiki</td>
</tr>
</tbody>
</table>
<p>You can also add to <code>1-var data</code></p>
<p>Add the reference list to biblist</p>
<p>Add author (your name)</p>
<p>Add curator (this will not send the information directly)</p>
<p>Add data completeness</p>
<p>If finishes, click <code>pause/save</code> > <code>quit AmPgui, continue with AmPeps</code></p>
</li>
<li>
<p><code>AmPeps</code> will then generate four MATLAB scripts. Edit accordingly</p>
<ul>
<li><code>mydata_*.m</code> includes observational data you just typed in. You can add to this by typing or using MATLAB functions (e.g. <code>load</code>, <code>readmatrix</code>). Code up corresponding temperature/food if they vary with time.</li>
<li><code>pars_init_*.m</code> don't need to be edited at this stage.</li>
<li><code>predict_*.m</code> includes prediction models for observational data. Add in your own model if the auto-generated one is not ideal.</li>
<li><code>run_*.m</code> specifies estimation options and run the parameter estimation process.</li>
</ul>
</li>
</ol>
<p><em>predict model examples can be searched in <a href="https://www.bio.vu.nl/thb/deb/deblab/add_my_pet/">AmP website</a> > COLLECTION > search for relevant models (e.g. t-L (time-length), T-F(temperature-filtration rate)), click into the species with these models, look at their <code>predict_</code> file and get inspired</em></p>
<h3 id="parameter-estimation-procedure">Parameter estimation procedure</h3>
<p><a href="https://debportal.debtheory.org/docs/AmPestimation.html">AmPestimation</a></p>
<p>Open the <code>run_*.m</code> script, you will see:</p>
<pre><code class="language-MATLAB">close all;
<span class="hljs-keyword">global</span> pets
pets = {<span class="hljs-string">'Taeniopygia_guttata'</span>};
check_my_pet(pets);
estim_options(<span class="hljs-string">'default'</span>); <span class="hljs-comment">% initialize estimation options</span>
estim_options(<span class="hljs-string">'max_step_number'</span>, <span class="hljs-number">5e2</span>); <span class="hljs-comment">% maximum </span>
estim_options(<span class="hljs-string">'max_fun_evals'</span>, <span class="hljs-number">5e3</span>);
estim_options(<span class="hljs-string">'pars_init_method'</span>, <span class="hljs-number">2</span>);
estim_options(<span class="hljs-string">'results_output'</span>, <span class="hljs-number">3</span>);
estim_options(<span class="hljs-string">'method'</span>, <span class="hljs-string">'no'</span>);
estim_pars;
</code></pre>
<p>The parameter estimation procedure compares observational data in <code>mydata_*.m</code> with DEB model described in <code>predict_*.m</code> using parameters defined in <code>pars_init_*.m</code></p>
<p>The comparison result is evaluated with loss function.</p>
<p>By running <code>run_*.m</code> in MATLAB, this procedure is repeated for many times (until <code>max_step_number</code>), or until the minimum of the loss function is found.</p>
<p>If the minimum of loss function is not found (did not converge), edit <code>pars_init_method</code> to <code>1</code> (now reading parameters from previous-procedure-generated <code>results_*.mat</code>); then run <code>run_*.m</code> again in MATLAB until convergence is reached.</p>
<p>In the MATLAB command window, type <code>mat2pars_init</code>. This will rewrite the estimated parameter sets to the <code>pars_init_*.m</code> file.</p>
<p>❗ Make sure to look at the generated .html page, evaluate if the predicted data is physical, and look at if MRE is small. If not, you might want to fix a certain parameter or set less weight to the questionable observational dataset.</p>
<p>To fix a parameter: open <code>pars_init_*.m</code>, change <code>par.**</code> based on your best guess, and set <code>free.**</code> = 0.</p>
<p>To set dataset weight, open <code>mydata_*.m</code>, in the <code>%% set weights for all real data</code> section, change/type <code>weights.** = 0</code> if you don't want this data to affect parameter estimation, or <code>weights.** = 5</code> if you feel the dataset is of great importance.</p>
<h1 id="further-deb-modeling">Further DEB modeling</h1>
<p>Extract the estimated parameters, and use that in a designated models (e.g. self-coded DEB model, NicheMapR, other coupling modules, population models). Sometimes a full-set of ODE (ordinary differential equation) is needed to simulate the influence of time-varying temperature or food concentration.</p>
<h4 id="state-variables">State Variables</h4>
<p>Variables to be modeled. Typical DEB state variables:</p>
<table>
<thead>
<tr>
<th></th>
<th>Variable</th>
<th>Dynamics</th>
</tr>
</thead>
<tbody>
<tr>
<td>Reserve</td>
<td><eq><span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mi>E</mi></mrow><annotation encoding="application/x-tex">E</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:0.68333em;vertical-align:0em;"></span><span class="mord mathnormal" style="margin-right:0.05764em;">E</span></span></span></span></eq></td>
<td><eq><span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mfrac><mrow><mi>d</mi><mi>E</mi></mrow><mrow><mi>d</mi><mi>t</mi></mrow></mfrac><mo>=</mo><mover accent="true"><msub><mi>p</mi><mi>A</mi></msub><mo>˙</mo></mover><mo>−</mo><mover accent="true"><msub><mi>p</mi><mi>C</mi></msub><mo>˙</mo></mover></mrow><annotation encoding="application/x-tex">\frac{dE}{dt} = \dot{p_A} - \dot{p_C}</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:1.2251079999999999em;vertical-align:-0.345em;"></span><span class="mord"><span class="mopen nulldelimiter"></span><span class="mfrac"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.8801079999999999em;"><span style="top:-2.6550000000000002em;"><span class="pstrut" style="height:3em;"></span><span class="sizing reset-size6 size3 mtight"><span class="mord mtight"><span class="mord mathnormal mtight">d</span><span class="mord mathnormal mtight">t</span></span></span></span><span style="top:-3.23em;"><span class="pstrut" style="height:3em;"></span><span class="frac-line" style="border-bottom-width:0.04em;"></span></span><span style="top:-3.394em;"><span class="pstrut" style="height:3em;"></span><span class="sizing reset-size6 size3 mtight"><span class="mord mtight"><span class="mord mathnormal mtight">d</span><span class="mord mathnormal mtight" style="margin-right:0.05764em;">E</span></span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.345em;"><span></span></span></span></span></span><span class="mclose nulldelimiter"></span></span><span class="mspace" style="margin-right:0.2777777777777778em;"></span><span class="mrel">=</span><span class="mspace" style="margin-right:0.2777777777777778em;"></span></span><span class="base"><span class="strut" style="height:0.8623000000000001em;vertical-align:-0.19444em;"></span><span class="mord accent"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.66786em;"><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="mord"><span class="mord mathnormal">p</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.32833099999999993em;"><span style="top:-2.5500000000000003em;margin-left:0em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight"><span class="mord mathnormal mtight">A</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.15em;"><span></span></span></span></span></span></span></span><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="accent-body" style="left:-0.13889em;"><span class="mord">˙</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.19444em;"><span></span></span></span></span></span><span class="mspace" style="margin-right:0.2222222222222222em;"></span><span class="mbin">−</span><span class="mspace" style="margin-right:0.2222222222222222em;"></span></span><span class="base"><span class="strut" style="height:0.8623000000000001em;vertical-align:-0.19444em;"></span><span class="mord accent"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.66786em;"><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="mord"><span class="mord mathnormal">p</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.32833099999999993em;"><span style="top:-2.5500000000000003em;margin-left:0em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight"><span class="mord mathnormal mtight" style="margin-right:0.07153em;">C</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.15em;"><span></span></span></span></span></span></span></span><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="accent-body" style="left:-0.13889em;"><span class="mord">˙</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.19444em;"><span></span></span></span></span></span></span></span></span></eq></td>
</tr>
<tr>
<td>Structure</td>
<td><eq><span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mi>V</mi></mrow><annotation encoding="application/x-tex">V</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:0.68333em;vertical-align:0em;"></span><span class="mord mathnormal" style="margin-right:0.22222em;">V</span></span></span></span></eq></td>
<td><eq><span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mfrac><mrow><mi>d</mi><mi>V</mi></mrow><mrow><mi>d</mi><mi>t</mi></mrow></mfrac><mo>=</mo><mfrac><mover accent="true"><msub><mi>p</mi><mi>G</mi></msub><mo>˙</mo></mover><mrow><mo stretchy="false">[</mo><msub><mi>E</mi><mi>G</mi></msub><mo stretchy="false">]</mo></mrow></mfrac></mrow><annotation encoding="application/x-tex">\frac{dV}{dt} = \frac{\dot{p_G}}{[E_G]}</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:1.2251079999999999em;vertical-align:-0.345em;"></span><span class="mord"><span class="mopen nulldelimiter"></span><span class="mfrac"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.8801079999999999em;"><span style="top:-2.6550000000000002em;"><span class="pstrut" style="height:3em;"></span><span class="sizing reset-size6 size3 mtight"><span class="mord mtight"><span class="mord mathnormal mtight">d</span><span class="mord mathnormal mtight">t</span></span></span></span><span style="top:-3.23em;"><span class="pstrut" style="height:3em;"></span><span class="frac-line" style="border-bottom-width:0.04em;"></span></span><span style="top:-3.394em;"><span class="pstrut" style="height:3em;"></span><span class="sizing reset-size6 size3 mtight"><span class="mord mtight"><span class="mord mathnormal mtight">d</span><span class="mord mathnormal mtight" style="margin-right:0.22222em;">V</span></span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.345em;"><span></span></span></span></span></span><span class="mclose nulldelimiter"></span></span><span class="mspace" style="margin-right:0.2777777777777778em;"></span><span class="mrel">=</span><span class="mspace" style="margin-right:0.2777777777777778em;"></span></span><span class="base"><span class="strut" style="height:1.43361em;vertical-align:-0.52em;"></span><span class="mord"><span class="mopen nulldelimiter"></span><span class="mfrac"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.91361em;"><span style="top:-2.655em;"><span class="pstrut" style="height:3em;"></span><span class="sizing reset-size6 size3 mtight"><span class="mord mtight"><span class="mopen mtight">[</span><span class="mord mtight"><span class="mord mathnormal mtight" style="margin-right:0.05764em;">E</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.3448em;"><span style="top:-2.3567071428571427em;margin-left:-0.05764em;margin-right:0.07142857142857144em;"><span class="pstrut" style="height:2.5em;"></span><span class="sizing reset-size3 size1 mtight"><span class="mord mathnormal mtight">G</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.14329285714285717em;"><span></span></span></span></span></span></span><span class="mclose mtight">]</span></span></span></span><span style="top:-3.23em;"><span class="pstrut" style="height:3em;"></span><span class="frac-line" style="border-bottom-width:0.04em;"></span></span><span style="top:-3.446108em;"><span class="pstrut" style="height:3em;"></span><span class="sizing reset-size6 size3 mtight"><span class="mord mtight"><span class="mord accent mtight"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.66786em;"><span style="top:-2.7em;"><span class="pstrut" style="height:2.7em;"></span><span class="mord mtight"><span class="mord mathnormal mtight">p</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.3448em;"><span style="top:-2.3567071428571427em;margin-left:0em;margin-right:0.07142857142857144em;"><span class="pstrut" style="height:2.5em;"></span><span class="sizing reset-size3 size1 mtight"><span class="mord mathnormal mtight">G</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.14329285714285717em;"><span></span></span></span></span></span></span></span><span style="top:-2.7em;"><span class="pstrut" style="height:2.7em;"></span><span class="accent-body" style="left:-0.13889em;"><span class="mord mtight">˙</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.19444em;"><span></span></span></span></span></span></span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.52em;"><span></span></span></span></span></span><span class="mclose nulldelimiter"></span></span></span></span></span></eq></td>
</tr>
<tr>
<td>Maturity</td>
<td><eq><span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><msub><mi>E</mi><mi>H</mi></msub></mrow><annotation encoding="application/x-tex">E_H</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:0.83333em;vertical-align:-0.15em;"></span><span class="mord"><span class="mord mathnormal" style="margin-right:0.05764em;">E</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.32833099999999993em;"><span style="top:-2.5500000000000003em;margin-left:-0.05764em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight"><span class="mord mathnormal mtight" style="margin-right:0.08125em;">H</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.15em;"><span></span></span></span></span></span></span></span></span></span></eq></td>
<td><eq><span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mfrac><mrow><mi>d</mi><msub><mi>E</mi><mi>H</mi></msub></mrow><mrow><mi>d</mi><mi>t</mi></mrow></mfrac><mo>=</mo><mover accent="true"><msub><mi>p</mi><mi>R</mi></msub><mo>˙</mo></mover></mrow><annotation encoding="application/x-tex">\frac{dE_H}{dt} = \dot{p_R}</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:1.2414129999999999em;vertical-align:-0.345em;"></span><span class="mord"><span class="mopen nulldelimiter"></span><span class="mfrac"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.8964129999999999em;"><span style="top:-2.6550000000000002em;"><span class="pstrut" style="height:3em;"></span><span class="sizing reset-size6 size3 mtight"><span class="mord mtight"><span class="mord mathnormal mtight">d</span><span class="mord mathnormal mtight">t</span></span></span></span><span style="top:-3.23em;"><span class="pstrut" style="height:3em;"></span><span class="frac-line" style="border-bottom-width:0.04em;"></span></span><span style="top:-3.410305em;"><span class="pstrut" style="height:3em;"></span><span class="sizing reset-size6 size3 mtight"><span class="mord mtight"><span class="mord mathnormal mtight">d</span><span class="mord mtight"><span class="mord mathnormal mtight" style="margin-right:0.05764em;">E</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.3448em;"><span style="top:-2.3567071428571427em;margin-left:-0.05764em;margin-right:0.07142857142857144em;"><span class="pstrut" style="height:2.5em;"></span><span class="sizing reset-size3 size1 mtight"><span class="mord mathnormal mtight" style="margin-right:0.08125em;">H</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.14329285714285717em;"><span></span></span></span></span></span></span></span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.345em;"><span></span></span></span></span></span><span class="mclose nulldelimiter"></span></span><span class="mspace" style="margin-right:0.2777777777777778em;"></span><span class="mrel">=</span><span class="mspace" style="margin-right:0.2777777777777778em;"></span></span><span class="base"><span class="strut" style="height:0.8623000000000001em;vertical-align:-0.19444em;"></span><span class="mord accent"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.66786em;"><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="mord"><span class="mord mathnormal">p</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.32833099999999993em;"><span style="top:-2.5500000000000003em;margin-left:0em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight"><span class="mord mathnormal mtight" style="margin-right:0.00773em;">R</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.15em;"><span></span></span></span></span></span></span></span><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="accent-body" style="left:-0.13889em;"><span class="mord">˙</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.19444em;"><span></span></span></span></span></span></span></span></span></eq> (before maturation)</td>
</tr>
<tr>
<td>Reproduction</td>
<td><eq><span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><msub><mi>E</mi><mi>R</mi></msub></mrow><annotation encoding="application/x-tex">E_R</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:0.83333em;vertical-align:-0.15em;"></span><span class="mord"><span class="mord mathnormal" style="margin-right:0.05764em;">E</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.32833099999999993em;"><span style="top:-2.5500000000000003em;margin-left:-0.05764em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight"><span class="mord mathnormal mtight" style="margin-right:0.00773em;">R</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.15em;"><span></span></span></span></span></span></span></span></span></span></eq></td>
<td><eq><span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mfrac><mrow><mi>d</mi><msub><mi>E</mi><mi>R</mi></msub></mrow><mrow><mi>d</mi><mi>t</mi></mrow></mfrac><mo>=</mo><mover accent="true"><msub><mi>p</mi><mi>R</mi></msub><mo>˙</mo></mover></mrow><annotation encoding="application/x-tex">\frac{dE_R}{dt} = \dot{p_R}</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:1.2414129999999999em;vertical-align:-0.345em;"></span><span class="mord"><span class="mopen nulldelimiter"></span><span class="mfrac"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.8964129999999999em;"><span style="top:-2.6550000000000002em;"><span class="pstrut" style="height:3em;"></span><span class="sizing reset-size6 size3 mtight"><span class="mord mtight"><span class="mord mathnormal mtight">d</span><span class="mord mathnormal mtight">t</span></span></span></span><span style="top:-3.23em;"><span class="pstrut" style="height:3em;"></span><span class="frac-line" style="border-bottom-width:0.04em;"></span></span><span style="top:-3.410305em;"><span class="pstrut" style="height:3em;"></span><span class="sizing reset-size6 size3 mtight"><span class="mord mtight"><span class="mord mathnormal mtight">d</span><span class="mord mtight"><span class="mord mathnormal mtight" style="margin-right:0.05764em;">E</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.3448em;"><span style="top:-2.3567071428571427em;margin-left:-0.05764em;margin-right:0.07142857142857144em;"><span class="pstrut" style="height:2.5em;"></span><span class="sizing reset-size3 size1 mtight"><span class="mord mathnormal mtight" style="margin-right:0.00773em;">R</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.14329285714285717em;"><span></span></span></span></span></span></span></span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.345em;"><span></span></span></span></span></span><span class="mclose nulldelimiter"></span></span><span class="mspace" style="margin-right:0.2777777777777778em;"></span><span class="mrel">=</span><span class="mspace" style="margin-right:0.2777777777777778em;"></span></span><span class="base"><span class="strut" style="height:0.8623000000000001em;vertical-align:-0.19444em;"></span><span class="mord accent"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.66786em;"><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="mord"><span class="mord mathnormal">p</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.32833099999999993em;"><span style="top:-2.5500000000000003em;margin-left:0em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight"><span class="mord mathnormal mtight" style="margin-right:0.00773em;">R</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.15em;"><span></span></span></span></span></span></span></span><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="accent-body" style="left:-0.13889em;"><span class="mord">˙</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.19444em;"><span></span></span></span></span></span></span></span></span></eq> (after maturation)</td>
</tr>
</tbody>
</table>
<p>Where <eq><span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mover accent="true"><msub><mi>p</mi><mi>A</mi></msub><mo>˙</mo></mover></mrow><annotation encoding="application/x-tex">\dot{p_A}</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:0.8623000000000001em;vertical-align:-0.19444em;"></span><span class="mord accent"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.66786em;"><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="mord"><span class="mord mathnormal">p</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.32833099999999993em;"><span style="top:-2.5500000000000003em;margin-left:0em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight"><span class="mord mathnormal mtight">A</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.15em;"><span></span></span></span></span></span></span></span><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="accent-body" style="left:-0.13889em;"><span class="mord">˙</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.19444em;"><span></span></span></span></span></span></span></span></span></eq> is assimilation flux. <eq><span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mover accent="true"><msub><mi>p</mi><mi>C</mi></msub><mo>˙</mo></mover></mrow><annotation encoding="application/x-tex">\dot{p_C}</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:0.8623000000000001em;vertical-align:-0.19444em;"></span><span class="mord accent"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.66786em;"><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="mord"><span class="mord mathnormal">p</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.32833099999999993em;"><span style="top:-2.5500000000000003em;margin-left:0em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight"><span class="mord mathnormal mtight" style="margin-right:0.07153em;">C</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.15em;"><span></span></span></span></span></span></span></span><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="accent-body" style="left:-0.13889em;"><span class="mord">˙</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.19444em;"><span></span></span></span></span></span></span></span></span></eq>, <eq><span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mover accent="true"><msub><mi>p</mi><mi>G</mi></msub><mo>˙</mo></mover></mrow><annotation encoding="application/x-tex">\dot{p_G}</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:0.8623000000000001em;vertical-align:-0.19444em;"></span><span class="mord accent"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.66786em;"><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="mord"><span class="mord mathnormal">p</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.32833099999999993em;"><span style="top:-2.5500000000000003em;margin-left:0em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight"><span class="mord mathnormal mtight">G</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.15em;"><span></span></span></span></span></span></span></span><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="accent-body" style="left:-0.13889em;"><span class="mord">˙</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.19444em;"><span></span></span></span></span></span></span></span></span></eq>, and <eq><span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mover accent="true"><msub><mi>p</mi><mi>R</mi></msub><mo>˙</mo></mover></mrow><annotation encoding="application/x-tex">\dot{p_R}</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:0.8623000000000001em;vertical-align:-0.19444em;"></span><span class="mord accent"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.66786em;"><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="mord"><span class="mord mathnormal">p</span><span class="msupsub"><span class="vlist-t vlist-t2"><span class="vlist-r"><span class="vlist" style="height:0.32833099999999993em;"><span style="top:-2.5500000000000003em;margin-left:0em;margin-right:0.05em;"><span class="pstrut" style="height:2.7em;"></span><span class="sizing reset-size6 size3 mtight"><span class="mord mathnormal mtight" style="margin-right:0.00773em;">R</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.15em;"><span></span></span></span></span></span></span></span><span style="top:-3em;"><span class="pstrut" style="height:3em;"></span><span class="accent-body" style="left:-0.13889em;"><span class="mord">˙</span></span></span></span><span class="vlist-s"></span></span><span class="vlist-r"><span class="vlist" style="height:0.19444em;"><span></span></span></span></span></span></span></span></span></eq> are fluxes, all links to the reserve dynamics which can be expressed explicitly. Since all the dynamics of the state variables can be expressed explicitly, the dynamics can be solved with ODE (ordinary differential equation) solver.</p>
<h4 id="ode-in-standard-deb-model-std">ODE In standard DEB model (std)</h4>
<p>The ODEs are constructed by the dynamic equations above. Here is one coding example. This pieces of code generates 4-vector with state variabels <code>ELHR</code>, correspond to time <code>t</code></p>
<pre><code class="language-MATLAB">GIVE A CODING EXAMPLE, Maybe AmPtools/trajectory/>std model
</code></pre>
<h4 id="deb-model-can-be-coupled">DEB model can be coupled</h4>
<p>DEB has the potential to be coupled with physical environmental models, population dynamic models, ecological models etc.</p>
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