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<h1 data-toc-skip>Model Entity Management</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/entity_management.Rmd" class="external-link"><code>vignettes/entity_management.Rmd</code></a></small>
<div class="hidden name"><code>entity_management.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://github.com/jpahle/CoRC" class="external-link">CoRC</a></span><span class="op">)</span></span>
<span><span class="fu"><a href="../reference/loadExamples.html">loadExamples</a></span><span class="op">(</span><span class="fl">2</span><span class="op">)</span></span>
<span><span class="co">#&gt; [[1]]</span></span>
<span><span class="co">#&gt; # A COPASI model reference:</span></span>
<span><span class="co">#&gt; Model name: "Bacterial chemotaxis model"</span></span>
<span><span class="co">#&gt; Number of compartments: 1</span></span>
<span><span class="co">#&gt; Number of species: 21</span></span>
<span><span class="co">#&gt; Number of reactions: 14</span></span>
<span><span class="fu"><a href="../reference/entity_finders.html">species</a></span><span class="op">(</span><span class="op">)</span></span>
<span><span class="co">#&gt; [1] "CheA{compartment}" "CheAp{compartment}" "CheB{compartment}" </span></span>
<span><span class="co">#&gt; [4] "CheBp{compartment}" "CheY{compartment}" "CheYp{compartment}" </span></span>
<span><span class="co">#&gt; [7] "CheR{compartment}" "Tactive{compartment}" "CheZ{compartment}" </span></span>
<span><span class="co">#&gt; [10] "T0{compartment}" "T1{compartment}" "T2{compartment}" </span></span>
<span><span class="co">#&gt; [13] "T3{compartment}" "T4{compartment}" "L{compartment}" </span></span>
<span><span class="co">#&gt; [16] "Tactive0{compartment}" "Tactive1{compartment}" "Tactive2{compartment}"</span></span>
<span><span class="co">#&gt; [19] "Tactive3{compartment}" "Tactive4{compartment}" "Ttotal{compartment}"</span></span></code></pre></div>
</div>
<div class="section level2">
<h2 id="identifying-entities">Identifying entities<a class="anchor" aria-label="anchor" href="#identifying-entities"></a>
</h2>
<p>There are various types of model entities supported for
identification by a given string. The strings are matched against the
available names of e.g. species, compartments, or global quantities. The
fuctions are listed below and return entitiy <code>key</code>s when
entities are identified.</p>
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/entity_finders.html">species</a></span><span class="op">(</span><span class="st">"CheA"</span><span class="op">)</span></span>
<span><span class="co">#&gt; [1] "CheA{compartment}" "CheAp{compartment}"</span></span>
<span><span class="fu"><a href="../reference/entity_finders.html">compartment</a></span><span class="op">(</span><span class="st">"comp"</span><span class="op">)</span></span>
<span><span class="co">#&gt; [1] "Compartments[compartment]"</span></span>
<span><span class="fu"><a href="../reference/entity_finders.html">quantity</a></span><span class="op">(</span><span class="st">"a"</span><span class="op">)</span></span>
<span><span class="co">#&gt; character(0)</span></span>
<span><span class="fu"><a href="../reference/entity_finders.html">reaction</a></span><span class="op">(</span><span class="st">"Che B phosph"</span><span class="op">)</span></span>
<span><span class="co">#&gt; [1] "(Che B phosph)"</span></span>
<span><span class="fu"><a href="../reference/entity_finders.html">parameter</a></span><span class="op">(</span><span class="st">"4).kR"</span><span class="op">)</span></span>
<span><span class="co">#&gt; [1] "(Rm4).kR"</span></span>
<span><span class="fu"><a href="../reference/entity_finders.html">kinfunction</a></span><span class="op">(</span><span class="st">"Michaelis-Menten"</span><span class="op">)</span></span>
<span><span class="co">#&gt; [1] "FunctionDB.Functions[Henri-Michaelis-Menten (irreversible)]"</span></span>
<span><span class="co">#&gt; [2] "FunctionDB.Functions[Reversible Michaelis-Menten]"</span></span>
<span><span class="fu"><a href="../reference/entity_finders.html">event</a></span><span class="op">(</span><span class="op">)</span></span>
<span><span class="co">#&gt; character(0)</span></span></code></pre></div>
<p>There are <code>_strict</code> variants that will always return a
vector of <code>key</code>s of the same length as the input or throw an
error. Accordingly, the behavior for <code>NA</code> or non-uniquely
matching strings is to throw an error. This allows the
<code>_strict</code> variants to uniquely identify species by giving the
full name, when the other methods might then still return multiple
matches.</p>
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/entity_finders.html">species</a></span><span class="op">(</span><span class="st">"CheY"</span><span class="op">)</span></span>
<span><span class="co">#&gt; [1] "CheY{compartment}" "CheYp{compartment}"</span></span>
<span><span class="fu"><a href="../reference/entity_finders.html">species_strict</a></span><span class="op">(</span><span class="st">"CheY"</span><span class="op">)</span></span>
<span><span class="co">#&gt; [1] "CheY{compartment}"</span></span>
<span><span class="fu"><a href="../reference/entity_finders.html">species_strict</a></span><span class="op">(</span><span class="st">"CheYp"</span><span class="op">)</span></span>
<span><span class="co">#&gt; [1] "CheYp{compartment}"</span></span>
<span><span class="fu"><a href="../reference/entity_finders.html">species_strict</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"CheY"</span>, <span class="st">"CheYp"</span><span class="op">)</span><span class="op">)</span></span>
<span><span class="co">#&gt; [1] "CheY{compartment}" "CheYp{compartment}"</span></span>
<span><span class="fu"><a href="../reference/entity_finders.html">species_strict</a></span><span class="op">(</span><span class="st">"Che"</span><span class="op">)</span></span>
<span><span class="co">#&gt; <span style="color: #BBBB00; font-weight: bold;">Error</span><span style="font-weight: bold;"> in `map2()`:</span></span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> In index: 1.</span></span>
<span><span class="co">#&gt; <span style="font-weight: bold;">Caused by error:</span></span></span>
<span><span class="co">#&gt; <span style="color: #BBBB00;">!</span> "Che" matches species "CheA{compartment}", "CheAp{compartment}", "CheB{compartment}", "CheBp{compartment}", "CheY{compartment}", "CheYp{compartment}", "CheR{compartment}", "CheZ{compartment}".</span></span>
<span><span class="fu"><a href="../reference/entity_finders.html">species_strict</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="cn">NA</span>, <span class="st">"CheY"</span><span class="op">)</span><span class="op">)</span></span>
<span><span class="co">#&gt; Error: key contains 1 missing values</span></span>
<span><span class="fu"><a href="../reference/entity_finders.html">species_strict</a></span><span class="op">(</span><span class="st">"failure"</span><span class="op">)</span></span>
<span><span class="co">#&gt; Error: Couldn't match species "failure".</span></span></code></pre></div>
<p>CoRC makes use of the regex functionality of the ‘stringr’ R package.
You can therefore wrap any string via <code>regex(string)</code> to
enable regex matching.</p>
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/entity_finders.html">species</a></span><span class="op">(</span><span class="fu"><a href="../reference/regex.html">regex</a></span><span class="op">(</span><span class="st">"Che.p"</span><span class="op">)</span><span class="op">)</span></span>
<span><span class="co">#&gt; [1] "CheAp{compartment}" "CheBp{compartment}" "CheYp{compartment}"</span></span></code></pre></div>
<p>In cases, where a function argument <code>key</code> is clear to
always expect the same kind of entity, identification can also be
handled by the function itself. These methods will always use the
<code>_strict</code> variants to reliably match species.</p>
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/getSpecies.html">getSpecies</a></span><span class="op">(</span>key <span class="op">=</span> <span class="fu"><a href="../reference/entity_finders.html">species</a></span><span class="op">(</span><span class="st">"CheY"</span><span class="op">)</span><span class="op">)</span><span class="op">$</span><span class="va">name</span></span>
<span><span class="co">#&gt; [1] "CheY" "CheYp"</span></span>
<span><span class="fu"><a href="../reference/getSpecies.html">getSpecies</a></span><span class="op">(</span>key <span class="op">=</span> <span class="fu"><a href="../reference/entity_finders.html">species_strict</a></span><span class="op">(</span><span class="st">"CheY"</span><span class="op">)</span><span class="op">)</span><span class="op">$</span><span class="va">name</span></span>
<span><span class="co">#&gt; [1] "CheY"</span></span>
<span><span class="fu"><a href="../reference/getSpecies.html">getSpecies</a></span><span class="op">(</span>key <span class="op">=</span> <span class="st">"CheY"</span><span class="op">)</span><span class="op">$</span><span class="va">name</span></span>
<span><span class="co">#&gt; [1] "CheY"</span></span>
<span><span class="fu"><a href="../reference/getSpecies.html">getSpecies</a></span><span class="op">(</span><span class="st">"CheY"</span><span class="op">)</span><span class="op">$</span><span class="va">name</span></span>
<span><span class="co">#&gt; [1] "CheY"</span></span>
<span><span class="fu"><a href="../reference/getSpecies.html">getSpecies</a></span><span class="op">(</span><span class="st">"Che"</span><span class="op">)</span><span class="op">$</span><span class="va">name</span></span>
<span><span class="co">#&gt; <span style="color: #BBBB00; font-weight: bold;">Error</span><span style="font-weight: bold;"> in `map2()`:</span></span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> In index: 1.</span></span>
<span><span class="co">#&gt; <span style="font-weight: bold;">Caused by error:</span></span></span>
<span><span class="co">#&gt; <span style="color: #BBBB00;">!</span> "Che" matches species "CheA{compartment}", "CheAp{compartment}", "CheB{compartment}", "CheBp{compartment}", "CheY{compartment}", "CheYp{compartment}", "CheR{compartment}", "CheZ{compartment}".</span></span>
<span><span class="fu"><a href="../reference/getSpecies.html">getSpecies</a></span><span class="op">(</span><span class="fu"><a href="../reference/entity_finders.html">species</a></span><span class="op">(</span><span class="fu"><a href="../reference/regex.html">regex</a></span><span class="op">(</span><span class="st">"Che.p"</span><span class="op">)</span><span class="op">)</span><span class="op">)</span><span class="op">$</span><span class="va">name</span></span>
<span><span class="co">#&gt; [1] "CheAp" "CheBp" "CheYp"</span></span></code></pre></div>
</div>
<div class="section level2">
<h2 id="using-references">Using References<a class="anchor" aria-label="anchor" href="#using-references"></a>
</h2>
<p>The identifying functions can also return value references if
specified. Such references identify specific values, of which most
COPASI entities can have multiple. This allows to differentiate for
example between ‘Concentration’ and ‘Initial Concentration’ of a
species. References are needed e.g. for definition of optimization task
parameters. They also allow for building expressions, which are needed
e.g. in value assignments and the optimization task. Expressions in CoRC
behave similar to how they work in COPASI.</p>
<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/entity_finders.html">species</a></span><span class="op">(</span><span class="st">"CheY"</span>, reference <span class="op">=</span> <span class="st">"InitialConcentration"</span><span class="op">)</span></span>
<span><span class="co">#&gt; [1] "{[CheY]_0}" "{[CheYp]_0}"</span></span></code></pre></div>
<p>These functions however can not give any clues about what references
are available.</p>
<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/entity_finders.html">species</a></span><span class="op">(</span><span class="st">"CheY"</span>, reference <span class="op">=</span> <span class="st">"failure"</span><span class="op">)</span></span>
<span><span class="co">#&gt; <span style="color: #BBBB00; font-weight: bold;">Error</span><span style="font-weight: bold;"> in `map2()`:</span></span></span>
<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> In index: 1.</span></span>
<span><span class="co">#&gt; <span style="font-weight: bold;">Caused by error:</span></span></span>
<span><span class="co">#&gt; <span style="color: #BBBB00;">!</span> Failed to gather reference "failure".</span></span></code></pre></div>
<p>To help with this, functions implemented to get model values have
similar functions that return references instead of values.</p>
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/str.html" class="external-link">str</a></span><span class="op">(</span><span class="fu"><a href="../reference/getSpecies.html">getSpecies</a></span><span class="op">(</span><span class="st">"CheY"</span><span class="op">)</span><span class="op">)</span></span>
<span><span class="co">#&gt; tibble [1 × 13] (S3: tbl_df/tbl/data.frame)</span></span>
<span><span class="co">#&gt; $ key : chr "CheY{compartment}"</span></span>
<span><span class="co">#&gt; $ name : chr "CheY"</span></span>
<span><span class="co">#&gt; $ compartment : chr "compartment"</span></span>
<span><span class="co">#&gt; $ type : chr "reactions"</span></span>
<span><span class="co">#&gt; $ unit : chr "µmol/l"</span></span>
<span><span class="co">#&gt; $ initial_concentration: num 9.7</span></span>
<span><span class="co">#&gt; $ initial_number : num 8178</span></span>
<span><span class="co">#&gt; $ concentration : num NaN</span></span>
<span><span class="co">#&gt; $ number : num NaN</span></span>
<span><span class="co">#&gt; $ rate : num 0</span></span>
<span><span class="co">#&gt; $ number_rate : num 0</span></span>
<span><span class="co">#&gt; $ initial_expression : chr ""</span></span>
<span><span class="co">#&gt; $ expression : chr ""</span></span>
<span><span class="fu"><a href="https://rdrr.io/r/utils/str.html" class="external-link">str</a></span><span class="op">(</span><span class="fu"><a href="../reference/getSpeciesReferences.html">getSpeciesReferences</a></span><span class="op">(</span><span class="st">"CheY"</span><span class="op">)</span><span class="op">)</span></span>
<span><span class="co">#&gt; tibble [1 × 13] (S3: tbl_df/tbl/data.frame)</span></span>
<span><span class="co">#&gt; $ key : chr "CheY{compartment}"</span></span>
<span><span class="co">#&gt; $ name : chr "CheY"</span></span>
<span><span class="co">#&gt; $ compartment : chr "compartment"</span></span>
<span><span class="co">#&gt; $ type : chr "reactions"</span></span>
<span><span class="co">#&gt; $ unit : chr "µmol/l"</span></span>
<span><span class="co">#&gt; $ initial_concentration: chr "{[CheY]_0}"</span></span>
<span><span class="co">#&gt; $ initial_number : chr "{CheY.InitialParticleNumber}"</span></span>
<span><span class="co">#&gt; $ concentration : chr "{[CheY]}"</span></span>
<span><span class="co">#&gt; $ number : chr "{CheY.ParticleNumber}"</span></span>
<span><span class="co">#&gt; $ rate : chr "{CheY.Rate}"</span></span>
<span><span class="co">#&gt; $ number_rate : chr "{CheY.ParticleNumberRate}"</span></span>
<span><span class="co">#&gt; $ initial_expression : chr NA</span></span>
<span><span class="co">#&gt; $ expression : chr NA</span></span></code></pre></div>
</div>
<div class="section level2">
<h2 id="building-expressions">Building expressions<a class="anchor" aria-label="anchor" href="#building-expressions"></a>
</h2>
<p>Any expression can easily be built as a string. In the following
example, several related species are selected via a REGEX rule and the
reference to their initial concentration is requested. The expression is
then built by concatenating these references with a plus sign.
<code>getValue</code> calculates this expressions value and thereby the
sum of the individual species.</p>
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">matching_init_conc</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/entity_finders.html">species</a></span><span class="op">(</span><span class="fu"><a href="../reference/regex.html">regex</a></span><span class="op">(</span><span class="st">"^T[0-4]"</span><span class="op">)</span>, reference <span class="op">=</span> <span class="st">"InitialConcentration"</span><span class="op">)</span></span>
<span><span class="va">matching_init_conc</span></span>
<span><span class="co">#&gt; [1] "{[T0]_0}" "{[T1]_0}" "{[T2]_0}" "{[T3]_0}" "{[T4]_0}"</span></span>
<span><span class="va">expression</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="va">matching_init_conc</span>, collapse <span class="op">=</span> <span class="st">" + "</span><span class="op">)</span></span>
<span><span class="va">expression</span></span>
<span><span class="co">#&gt; [1] "{[T0]_0} + {[T1]_0} + {[T2]_0} + {[T3]_0} + {[T4]_0}"</span></span>
<span><span class="fu"><a href="../reference/getValue.html">getValue</a></span><span class="op">(</span><span class="va">expression</span><span class="op">)</span></span>
<span><span class="co">#&gt; [1] 5.3</span></span></code></pre></div>
</div>
<div class="section level2">
<h2 id="using-numbers-for-referencing">Using numbers for referencing<a class="anchor" aria-label="anchor" href="#using-numbers-for-referencing"></a>
</h2>
<p>Numbers can in principle be used by getting all entities and picking
an index from that vector:</p>
<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/entity_finders.html">species</a></span><span class="op">(</span><span class="op">)</span><span class="op">[</span><span class="fl">5</span><span class="op">]</span></span>
<span><span class="co">#&gt; [1] "CheY{compartment}"</span></span>
<span><span class="fu"><a href="../reference/getSpecies.html">getSpecies</a></span><span class="op">(</span><span class="fu"><a href="../reference/entity_finders.html">species</a></span><span class="op">(</span><span class="op">)</span><span class="op">[</span><span class="fl">5</span><span class="op">]</span><span class="op">)</span><span class="op">$</span><span class="va">name</span></span>
<span><span class="co">#&gt; [1] "CheY"</span></span></code></pre></div>
<p>It is under consideration to allow for a simpler method:</p>
<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/entity_finders.html">species</a></span><span class="op">(</span><span class="fl">5</span><span class="op">)</span></span>
<span><span class="co">#&gt; Error: key is not a string (a length one character vector).</span></span>
<span><span class="fu"><a href="../reference/entity_finders.html">species_strict</a></span><span class="op">(</span><span class="fl">5</span><span class="op">)</span></span>
<span><span class="co">#&gt; Error: key is not a character vector</span></span>
<span><span class="fu"><a href="../reference/getSpecies.html">getSpecies</a></span><span class="op">(</span><span class="fl">5</span><span class="op">)</span><span class="op">$</span><span class="va">name</span></span>
<span><span class="co">#&gt; Error: key is not a character vector</span></span></code></pre></div>
</div>
<div class="section level2">
<h2 id="entity-modification">Entity modification<a class="anchor" aria-label="anchor" href="#entity-modification"></a>
</h2>
<p>For most kinds of entities there is a finder function
(e.g. <code>species</code>), a getter function
(e.g. <code>getSpecies</code>) and a setter function
(e.g. <code>setSpecies</code>).</p>
<p>Another way to access model values is by evaluating expressions
(e.g. <code>getValue</code>):</p>
<div class="sourceCode" id="cb12"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/getSpecies.html">getSpecies</a></span><span class="op">(</span><span class="st">"CheYp"</span><span class="op">)</span><span class="op">$</span><span class="va">initial_concentration</span></span>
<span><span class="co">#&gt; [1] 0</span></span>
<span></span>
<span><span class="fu"><a href="../reference/setSpecies.html">setSpecies</a></span><span class="op">(</span><span class="st">"CheYp"</span>, initial_concentration <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span>
<span><span class="fu"><a href="../reference/getSpecies.html">getSpecies</a></span><span class="op">(</span><span class="st">"CheYp"</span><span class="op">)</span><span class="op">$</span><span class="va">initial_concentration</span></span>
<span><span class="co">#&gt; [1] 1</span></span>
<span></span>
<span><span class="va">yp_init_expression</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/entity_finders.html">species</a></span><span class="op">(</span><span class="st">"CheYp"</span>, reference <span class="op">=</span> <span class="st">"InitialConcentration"</span><span class="op">)</span></span>
<span><span class="va">yp_init_expression</span></span>
<span><span class="co">#&gt; [1] "{[CheYp]_0}"</span></span>
<span><span class="fu"><a href="../reference/getValue.html">getValue</a></span><span class="op">(</span><span class="va">yp_init_expression</span><span class="op">)</span></span>
<span><span class="co">#&gt; [1] 1</span></span></code></pre></div>
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