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<h1 data-toc-skip>Model Building</h1>
<h4 data-toc-skip class="author">Jonas Förster
&amp; Jürgen Pahle</h4>
<small class="dont-index">Source: <a href="https://github.com/jpahle/CoRC/blob/HEAD/vignettes/model_building.Rmd" class="external-link"><code>vignettes/model_building.Rmd</code></a></small>
<div class="hidden name"><code>model_building.Rmd</code></div>
</div>
<div class="section level2">
<h2 id="initial-setup">Initial Setup<a class="anchor" aria-label="anchor" href="#initial-setup"></a>
</h2>
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://ggplot2.tidyverse.org" class="external-link">ggplot2</a></span><span class="op">)</span></span>
<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/jpahle/CoRC" class="external-link">CoRC</a></span><span class="op">)</span></span></code></pre></div>
</div>
<div class="section level2">
<h2 id="quick-model-building">Quick Model Building<a class="anchor" aria-label="anchor" href="#quick-model-building"></a>
</h2>
<p>Building a quick Michaelis-Menten reaction using COPASI’s
automatisms. Working with reaction equations automatically creates
required entities the same way the COPASI GUI does.</p>
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/newModel.html">newModel</a></span><span class="op">(</span><span class="op">)</span></span>
<span><span class="co">#&gt; # A COPASI model reference:</span></span>
<span><span class="co">#&gt; Model name: "New Model"</span></span>
<span><span class="co">#&gt; Number of compartments: 0</span></span>
<span><span class="co">#&gt; Number of species: 0</span></span>
<span><span class="co">#&gt; Number of reactions: 0</span></span>
<span></span>
<span><span class="fu"><a href="../reference/newReaction.html">newReaction</a></span><span class="op">(</span><span class="st">"a = b"</span>, fun <span class="op">=</span> <span class="st">"Reversible Michaelis-Menten"</span><span class="op">)</span></span>
<span><span class="co">#&gt; [1] "(a = b)"</span></span>
<span></span>
<span><span class="fu"><a href="../reference/getSpecies.html">getSpecies</a></span><span class="op">(</span><span class="op">)</span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2 × 13</span></span></span>
<span><span class="co">#&gt; key name compa…¹ type unit initi…² initi…³ conce…⁴ number rate numbe…⁵</span></span>
<span><span class="co">#&gt; <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">1</span> a{comp… a compar… reac… mol/l 1 6.02<span style="color: #949494;">e</span>23 <span style="color: #BB0000;">NaN</span> <span style="color: #BB0000;">NaN</span> 0 0</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">2</span> b{comp… b compar… reac… mol/l 1 6.02<span style="color: #949494;">e</span>23 <span style="color: #BB0000;">NaN</span> <span style="color: #BB0000;">NaN</span> 0 0</span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># … with 2 more variables: initial_expression &lt;chr&gt;, expression &lt;chr&gt;, and</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># abbreviated variable names ¹​compartment, ²​initial_concentration,</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ³​initial_number, ⁴​concentration, ⁵​number_rate</span></span></span>
<span><span class="fu"><a href="../reference/getReactions.html">getReactions</a></span><span class="op">(</span><span class="op">)</span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 1 × 6</span></span></span>
<span><span class="co">#&gt; key name reaction rate_law flux numbe…¹</span></span>
<span><span class="co">#&gt; <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">1</span> (a = b) a = b a = b FunctionDB.Functions[Reversible Michaeli… 0 0</span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># … with abbreviated variable name ¹​number_flux</span></span></span>
<span><span class="fu"><a href="../reference/getParameters.html">getParameters</a></span><span class="op">(</span><span class="op">)</span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 4 × 5</span></span></span>
<span><span class="co">#&gt; key name reaction value mapping</span></span>
<span><span class="co">#&gt; <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">1</span> (a = b).Kms Kms a = b 0.1 <span style="color: #BB0000;">NA</span> </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">2</span> (a = b).Kmp Kmp a = b 0.1 <span style="color: #BB0000;">NA</span> </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">3</span> (a = b).Vf Vf a = b 0.1 <span style="color: #BB0000;">NA</span> </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">4</span> (a = b).Vr Vr a = b 0.1 <span style="color: #BB0000;">NA</span></span></span>
<span></span>
<span><span class="fu"><a href="../reference/unloadModel.html">unloadModel</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
</div>
<div class="section level2">
<h2 id="more-detail">More Detail<a class="anchor" aria-label="anchor" href="#more-detail"></a>
</h2>
<p>Getting more detail in can be helpful. Here we create a global
quantity “substrate concentration” which applies a fixed value to
species “a”. This is achieved by assigning the <code>Value</code>
reference of the global quantity to species “a”.</p>
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/newModel.html">newModel</a></span><span class="op">(</span><span class="op">)</span></span>
<span><span class="co">#&gt; # A COPASI model reference:</span></span>
<span><span class="co">#&gt; Model name: "New Model"</span></span>
<span><span class="co">#&gt; Number of compartments: 0</span></span>
<span><span class="co">#&gt; Number of species: 0</span></span>
<span><span class="co">#&gt; Number of reactions: 0</span></span>
<span></span>
<span><span class="va">subs_quant</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/newGlobalQuantity.html">newGlobalQuantity</a></span><span class="op">(</span><span class="st">"substrate concentration"</span>, initial_value <span class="op">=</span> <span class="fl">10</span><span class="op">)</span></span>
<span><span class="va">subs_value</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/entity_finders.html">quantity</a></span><span class="op">(</span><span class="va">subs_quant</span>, reference <span class="op">=</span> <span class="st">"Value"</span><span class="op">)</span></span>
<span><span class="va">subs_value</span></span>
<span><span class="co">#&gt; [1] "{Values[substrate concentration]}"</span></span>
<span></span>
<span><span class="fu"><a href="../reference/newSpecies.html">newSpecies</a></span><span class="op">(</span><span class="st">"a"</span>, type <span class="op">=</span> <span class="st">"assignment"</span>, expression <span class="op">=</span> <span class="va">subs_value</span><span class="op">)</span></span>
<span><span class="co">#&gt; Warning: No compartment exists. Created default compartment.</span></span>
<span><span class="co">#&gt; [1] "a{compartment}"</span></span>
<span><span class="fu"><a href="../reference/newReaction.html">newReaction</a></span><span class="op">(</span><span class="st">"a = b"</span>, fun <span class="op">=</span> <span class="st">"Reversible Michaelis-Menten"</span><span class="op">)</span></span>
<span><span class="co">#&gt; [1] "(a = b)"</span></span>
<span></span>
<span><span class="fu"><a href="../reference/getGlobalQuantities.html">getGlobalQuantities</a></span><span class="op">(</span><span class="op">)</span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 1 × 9</span></span></span>
<span><span class="co">#&gt; key name type unit initi…¹ value rate initi…² expre…³</span></span>
<span><span class="co">#&gt; <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">1</span> Values[substrate concen… subs… fixed <span style="color: #949494;">""</span> 10 <span style="color: #BB0000;">NaN</span> 0 <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> </span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># … with abbreviated variable names ¹​initial_value, ²​initial_expression,</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ³​expression</span></span></span>
<span><span class="fu"><a href="../reference/getSpecies.html">getSpecies</a></span><span class="op">(</span><span class="op">)</span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2 × 13</span></span></span>
<span><span class="co">#&gt; key name compa…¹ type unit initi…² initi…³ conce…⁴ number rate numbe…⁵</span></span>
<span><span class="co">#&gt; <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">1</span> a{comp… a compar… assi… mol/l 10 6.02<span style="color: #949494;">e</span>24 <span style="color: #BB0000;">NaN</span> <span style="color: #BB0000;">NaN</span> <span style="color: #BB0000;">NaN</span> <span style="color: #BB0000;">NaN</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">2</span> b{comp… b compar… reac… mol/l 1 6.02<span style="color: #949494;">e</span>23 <span style="color: #BB0000;">NaN</span> <span style="color: #BB0000;">NaN</span> 0 0</span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># … with 2 more variables: initial_expression &lt;chr&gt;, expression &lt;chr&gt;, and</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># abbreviated variable names ¹​compartment, ²​initial_concentration,</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ³​initial_number, ⁴​concentration, ⁵​number_rate</span></span></span>
<span><span class="fu"><a href="../reference/getReactions.html">getReactions</a></span><span class="op">(</span><span class="op">)</span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 1 × 6</span></span></span>
<span><span class="co">#&gt; key name reaction rate_law flux numbe…¹</span></span>
<span><span class="co">#&gt; <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">1</span> (a = b) a = b a = b FunctionDB.Functions[Reversible Michaeli… 0 0</span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># … with abbreviated variable name ¹​number_flux</span></span></span>
<span><span class="fu"><a href="../reference/getParameters.html">getParameters</a></span><span class="op">(</span><span class="op">)</span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 4 × 5</span></span></span>
<span><span class="co">#&gt; key name reaction value mapping</span></span>
<span><span class="co">#&gt; <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">1</span> (a = b).Kms Kms a = b 0.1 <span style="color: #BB0000;">NA</span> </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">2</span> (a = b).Kmp Kmp a = b 0.1 <span style="color: #BB0000;">NA</span> </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">3</span> (a = b).Vf Vf a = b 0.1 <span style="color: #BB0000;">NA</span> </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">4</span> (a = b).Vr Vr a = b 0.1 <span style="color: #BB0000;">NA</span></span></span>
<span></span>
<span><span class="va">timecourse</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/runTimeCourse.html">runTimeCourse</a></span><span class="op">(</span><span class="fl">1000</span><span class="op">)</span></span>
<span></span>
<span><span class="fu"><a href="../reference/autoplot.copasi_ts.html">autoplot.copasi_ts</a></span><span class="op">(</span><span class="va">timecourse</span><span class="op">)</span></span></code></pre></div>
<p><img src="model_building_files/figure-html/unnamed-chunk-3-1.png" width="100%"></p>
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span></span>
<span><span class="fu"><a href="../reference/unloadModel.html">unloadModel</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
</div>
<div class="section level2">
<h2 id="defining-reaction-kinetics-manually">Defining Reaction Kinetics Manually<a class="anchor" aria-label="anchor" href="#defining-reaction-kinetics-manually"></a>
</h2>
<p>In previous examples, we used the predefined “Reversible
Michaelis-Menten” kinetic functions. In this example we create an
equivalent function manually to achieve the same result.</p>
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/newModel.html">newModel</a></span><span class="op">(</span><span class="op">)</span></span>
<span><span class="co">#&gt; # A COPASI model reference:</span></span>
<span><span class="co">#&gt; Model name: "New Model"</span></span>
<span><span class="co">#&gt; Number of compartments: 0</span></span>
<span><span class="co">#&gt; Number of species: 0</span></span>
<span><span class="co">#&gt; Number of reactions: 0</span></span>
<span></span>
<span><span class="fu"><a href="../reference/newCompartment.html">newCompartment</a></span><span class="op">(</span><span class="st">"compartment"</span><span class="op">)</span></span>
<span><span class="co">#&gt; [1] "Compartments[compartment]"</span></span>
<span><span class="fu"><a href="../reference/newSpecies.html">newSpecies</a></span><span class="op">(</span><span class="st">"a"</span>, type <span class="op">=</span> <span class="st">"fixed"</span>, initial_concentration <span class="op">=</span> <span class="fl">10</span><span class="op">)</span></span>
<span><span class="co">#&gt; [1] "a{compartment}"</span></span>
<span><span class="fu"><a href="../reference/newSpecies.html">newSpecies</a></span><span class="op">(</span><span class="st">"b"</span><span class="op">)</span></span>
<span><span class="co">#&gt; [1] "b{compartment}"</span></span>
<span><span class="fu"><a href="../reference/newKineticFunction.html">newKineticFunction</a></span><span class="op">(</span></span>
<span> <span class="st">"manual MM"</span>,</span>
<span> <span class="st">"((Vf * substrate) / Kms - Vr * product / Kmp) / (1 + substrate / Kms + product / Kms)"</span>,</span>
<span> parameters <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>substrate <span class="op">=</span> <span class="st">"substrate"</span>, product <span class="op">=</span> <span class="st">"product"</span><span class="op">)</span></span>
<span><span class="op">)</span></span>
<span><span class="co">#&gt; [1] "FunctionDB.Functions[manual MM]"</span></span>
<span><span class="fu"><a href="../reference/newReaction.html">newReaction</a></span><span class="op">(</span></span>
<span> <span class="st">"a = b"</span>,</span>
<span> fun <span class="op">=</span> <span class="st">"manual MM"</span>,</span>
<span> mapping <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span></span>
<span> substrate <span class="op">=</span> <span class="st">"a"</span>,</span>
<span> product <span class="op">=</span> <span class="st">"b"</span>,</span>
<span> Vf <span class="op">=</span> <span class="fl">0.1</span>,</span>
<span> Kms <span class="op">=</span> <span class="fl">0.1</span>,</span>
<span> Vr <span class="op">=</span> <span class="fl">0.1</span>,</span>
<span> Kmp <span class="op">=</span> <span class="fl">0.1</span></span>
<span> <span class="op">)</span></span>
<span><span class="op">)</span></span>
<span><span class="co">#&gt; [1] "(a = b)"</span></span>
<span></span>
<span><span class="va">timecourse</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/runTimeCourse.html">runTimeCourse</a></span><span class="op">(</span><span class="fl">1000</span><span class="op">)</span></span>
<span></span>
<span><span class="fu"><a href="../reference/autoplot.copasi_ts.html">autoplot.copasi_ts</a></span><span class="op">(</span><span class="va">timecourse</span><span class="op">)</span></span></code></pre></div>
<p><img src="model_building_files/figure-html/unnamed-chunk-4-1.png" width="100%"></p>
<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span></span>
<span><span class="fu"><a href="../reference/unloadModel.html">unloadModel</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
</div>
<div class="section level2">
<h2 id="quantities-as-proxy-for-time-course-output">Quantities as Proxy for Time Course Output<a class="anchor" aria-label="anchor" href="#quantities-as-proxy-for-time-course-output"></a>
</h2>
<p>The <code>runTimeCourse</code> function only returns data for actual
defined entities of the model. Auxiliarry information like reaction
rates can be missing and needs to be added via global quantity
assignments. This example creates a global quantity “reaction rate” to
generate data for the main reaction’s flux.</p>
<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/newModel.html">newModel</a></span><span class="op">(</span><span class="op">)</span></span>
<span><span class="co">#&gt; # A COPASI model reference:</span></span>
<span><span class="co">#&gt; Model name: "New Model"</span></span>
<span><span class="co">#&gt; Number of compartments: 0</span></span>
<span><span class="co">#&gt; Number of species: 0</span></span>
<span><span class="co">#&gt; Number of reactions: 0</span></span>
<span></span>
<span><span class="va">subs_quant</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/newGlobalQuantity.html">newGlobalQuantity</a></span><span class="op">(</span><span class="st">"substrate concentration"</span>, initial_value <span class="op">=</span> <span class="fl">10</span><span class="op">)</span></span>
<span><span class="va">subs_value</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/entity_finders.html">quantity</a></span><span class="op">(</span><span class="va">subs_quant</span>, reference <span class="op">=</span> <span class="st">"Value"</span><span class="op">)</span></span>
<span></span>
<span><span class="fu"><a href="../reference/newSpecies.html">newSpecies</a></span><span class="op">(</span><span class="st">"a"</span>, type <span class="op">=</span> <span class="st">"assignment"</span>, expression <span class="op">=</span> <span class="va">subs_value</span><span class="op">)</span></span>
<span><span class="co">#&gt; Warning: No compartment exists. Created default compartment.</span></span>
<span><span class="co">#&gt; [1] "a{compartment}"</span></span>
<span><span class="fu"><a href="../reference/newReaction.html">newReaction</a></span><span class="op">(</span><span class="st">"a = b"</span>, fun <span class="op">=</span> <span class="st">"Reversible Michaelis-Menten"</span><span class="op">)</span></span>
<span><span class="co">#&gt; [1] "(a = b)"</span></span>
<span></span>
<span><span class="fu"><a href="../reference/runTimeCourse.html">runTC</a></span><span class="op">(</span><span class="fl">1000</span><span class="op">)</span><span class="op">$</span><span class="va">result</span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 101 × 3</span></span></span>
<span><span class="co">#&gt; Time b a</span></span>
<span><span class="co">#&gt; <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> 0 1 10</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 2</span> 10 1.75 10</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 3</span> 20 2.40 10</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 4</span> 30 2.97 10</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 5</span> 40 3.48 10</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 6</span> 50 3.94 10</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 7</span> 60 4.35 10</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> 70 4.72 10</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> 80 5.06 10</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> 90 5.37 10</span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># … with 91 more rows</span></span></span>
<span></span>
<span><span class="fu"><a href="../reference/newGlobalQuantity.html">newGlobalQuantity</a></span><span class="op">(</span></span>
<span> <span class="st">"reaction rate"</span>,</span>
<span> type <span class="op">=</span> <span class="st">"assignment"</span>,</span>
<span> expression <span class="op">=</span> <span class="fu"><a href="../reference/entity_finders.html">reaction</a></span><span class="op">(</span><span class="st">"a = b"</span>, reference <span class="op">=</span> <span class="st">"Flux"</span><span class="op">)</span></span>
<span><span class="op">)</span></span>
<span><span class="co">#&gt; [1] "Values[reaction rate]"</span></span>
<span></span>
<span><span class="fu"><a href="../reference/runTimeCourse.html">runTimeCourse</a></span><span class="op">(</span><span class="fl">1000</span><span class="op">)</span><span class="op">$</span><span class="va">result</span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 101 × 4</span></span></span>
<span><span class="co">#&gt; Time b a `Values[reaction rate]`</span></span>
<span><span class="co">#&gt; <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> 0 1 10 0.081<span style="text-decoration: underline;">1</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 2</span> 10 1.75 10 0.069<span style="text-decoration: underline;">6</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 3</span> 20 2.40 10 0.060<span style="text-decoration: underline;">8</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 4</span> 30 2.97 10 0.053<span style="text-decoration: underline;">8</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 5</span> 40 3.48 10 0.048<span style="text-decoration: underline;">0</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 6</span> 50 3.94 10 0.043<span style="text-decoration: underline;">2</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 7</span> 60 4.35 10 0.039<span style="text-decoration: underline;">1</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> 70 4.72 10 0.035<span style="text-decoration: underline;">6</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> 80 5.06 10 0.032<span style="text-decoration: underline;">6</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> 90 5.37 10 0.029<span style="text-decoration: underline;">9</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># … with 91 more rows</span></span></span>
<span></span>
<span><span class="fu"><a href="../reference/unloadModel.html">unloadModel</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
</div>
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