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| <h1 data-toc-skip>Model Entity Management</h1> | |
| <h4 data-toc-skip class="author">Jonas Förster | |
| & 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">#> [[1]]</span></span> | |
| <span><span class="co">#> # A COPASI model reference:</span></span> | |
| <span><span class="co">#> Model name: "Bacterial chemotaxis model"</span></span> | |
| <span><span class="co">#> Number of compartments: 1</span></span> | |
| <span><span class="co">#> Number of species: 21</span></span> | |
| <span><span class="co">#> 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">#> [1] "CheA{compartment}" "CheAp{compartment}" "CheB{compartment}" </span></span> | |
| <span><span class="co">#> [4] "CheBp{compartment}" "CheY{compartment}" "CheYp{compartment}" </span></span> | |
| <span><span class="co">#> [7] "CheR{compartment}" "Tactive{compartment}" "CheZ{compartment}" </span></span> | |
| <span><span class="co">#> [10] "T0{compartment}" "T1{compartment}" "T2{compartment}" </span></span> | |
| <span><span class="co">#> [13] "T3{compartment}" "T4{compartment}" "L{compartment}" </span></span> | |
| <span><span class="co">#> [16] "Tactive0{compartment}" "Tactive1{compartment}" "Tactive2{compartment}"</span></span> | |
| <span><span class="co">#> [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">#> [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">#> [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">#> 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">#> [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">#> [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">#> [1] "FunctionDB.Functions[Henri-Michaelis-Menten (irreversible)]"</span></span> | |
| <span><span class="co">#> [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">#> 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">#> [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">#> [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">#> [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">#> [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">#> <span style="color: #BBBB00; font-weight: bold;">Error</span><span style="font-weight: bold;"> in `map2()`:</span></span></span> | |
| <span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> In index: 1.</span></span> | |
| <span><span class="co">#> <span style="font-weight: bold;">Caused by error:</span></span></span> | |
| <span><span class="co">#> <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">#> 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">#> 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">#> [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">$</span><span class="va">name</span></span> | |
| <span><span class="co">#> [1] "CheY" "CheYp"</span></span> | |
| <span><span class="fu"><a href="../reference/getSpecies.html">getSpecies</a></span><span class="op">(</span>key <span class="op">=</span> <span class="fu"><a href="../reference/entity_finders.html">species_strict</a></span><span class="op">(</span><span class="st">"CheY"</span><span class="op">)</span><span class="op">)</span><span class="op">$</span><span class="va">name</span></span> | |
| <span><span class="co">#> [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">$</span><span class="va">name</span></span> | |
| <span><span class="co">#> [1] "CheY"</span></span> | |
| <span><span class="fu"><a href="../reference/getSpecies.html">getSpecies</a></span><span class="op">(</span><span class="st">"CheY"</span><span class="op">)</span><span class="op">$</span><span class="va">name</span></span> | |
| <span><span class="co">#> [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">$</span><span class="va">name</span></span> | |
| <span><span class="co">#> <span style="color: #BBBB00; font-weight: bold;">Error</span><span style="font-weight: bold;"> in `map2()`:</span></span></span> | |
| <span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> In index: 1.</span></span> | |
| <span><span class="co">#> <span style="font-weight: bold;">Caused by error:</span></span></span> | |
| <span><span class="co">#> <span style="color: #BBBB00;">!</span> "Che" matches species "CheA{compartment}", "CheAp{compartment}", "CheB{compartment}", "CheBp{compartment}", "CheY{compartment}", "CheYp{compartment}", "CheR{compartment}", "CheZ{compartment}".</span></span> | |
| <span><span class="fu"><a href="../reference/getSpecies.html">getSpecies</a></span><span class="op">(</span><span class="fu"><a href="../reference/entity_finders.html">species</a></span><span class="op">(</span><span class="fu"><a href="../reference/regex.html">regex</a></span><span class="op">(</span><span class="st">"Che.p"</span><span class="op">)</span><span class="op">)</span><span class="op">)</span><span class="op">$</span><span class="va">name</span></span> | |
| <span><span class="co">#> [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">#> [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">#> <span style="color: #BBBB00; font-weight: bold;">Error</span><span style="font-weight: bold;"> in `map2()`:</span></span></span> | |
| <span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> In index: 1.</span></span> | |
| <span><span class="co">#> <span style="font-weight: bold;">Caused by error:</span></span></span> | |
| <span><span class="co">#> <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">#> tibble [1 × 13] (S3: tbl_df/tbl/data.frame)</span></span> | |
| <span><span class="co">#> $ key : chr "CheY{compartment}"</span></span> | |
| <span><span class="co">#> $ name : chr "CheY"</span></span> | |
| <span><span class="co">#> $ compartment : chr "compartment"</span></span> | |
| <span><span class="co">#> $ type : chr "reactions"</span></span> | |
| <span><span class="co">#> $ unit : chr "µmol/l"</span></span> | |
| <span><span class="co">#> $ initial_concentration: num 9.7</span></span> | |
| <span><span class="co">#> $ initial_number : num 8178</span></span> | |
| <span><span class="co">#> $ concentration : num NaN</span></span> | |
| <span><span class="co">#> $ number : num NaN</span></span> | |
| <span><span class="co">#> $ rate : num 0</span></span> | |
| <span><span class="co">#> $ number_rate : num 0</span></span> | |
| <span><span class="co">#> $ initial_expression : chr ""</span></span> | |
| <span><span class="co">#> $ 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">#> tibble [1 × 13] (S3: tbl_df/tbl/data.frame)</span></span> | |
| <span><span class="co">#> $ key : chr "CheY{compartment}"</span></span> | |
| <span><span class="co">#> $ name : chr "CheY"</span></span> | |
| <span><span class="co">#> $ compartment : chr "compartment"</span></span> | |
| <span><span class="co">#> $ type : chr "reactions"</span></span> | |
| <span><span class="co">#> $ unit : chr "µmol/l"</span></span> | |
| <span><span class="co">#> $ initial_concentration: chr "{[CheY]_0}"</span></span> | |
| <span><span class="co">#> $ initial_number : chr "{CheY.InitialParticleNumber}"</span></span> | |
| <span><span class="co">#> $ concentration : chr "{[CheY]}"</span></span> | |
| <span><span class="co">#> $ number : chr "{CheY.ParticleNumber}"</span></span> | |
| <span><span class="co">#> $ rate : chr "{CheY.Rate}"</span></span> | |
| <span><span class="co">#> $ number_rate : chr "{CheY.ParticleNumberRate}"</span></span> | |
| <span><span class="co">#> $ initial_expression : chr NA</span></span> | |
| <span><span class="co">#> $ 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"><-</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">#> [1] "{[T0]_0}" "{[T1]_0}" "{[T2]_0}" "{[T3]_0}" "{[T4]_0}"</span></span> | |
| <span><span class="va">expression</span> <span class="op"><-</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">#> [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">#> [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">#> [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">$</span><span class="va">name</span></span> | |
| <span><span class="co">#> [1] "CheY"</span></span></code></pre></div> | |
| <p>It is under consideration to allow for a simpler method:</p> | |
| <div class="sourceCode" id="cb11"><pre class="downlit sourceCode r"> | |
| <code class="sourceCode R"><span><span class="fu"><a href="../reference/entity_finders.html">species</a></span><span class="op">(</span><span class="fl">5</span><span class="op">)</span></span> | |
| <span><span class="co">#> Error: key is not a string (a length one character vector).</span></span> | |
| <span><span class="fu"><a href="../reference/entity_finders.html">species_strict</a></span><span class="op">(</span><span class="fl">5</span><span class="op">)</span></span> | |
| <span><span class="co">#> Error: key is not a character vector</span></span> | |
| <span><span class="fu"><a href="../reference/getSpecies.html">getSpecies</a></span><span class="op">(</span><span class="fl">5</span><span class="op">)</span><span class="op">$</span><span class="va">name</span></span> | |
| <span><span class="co">#> 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">$</span><span class="va">initial_concentration</span></span> | |
| <span><span class="co">#> [1] 0</span></span> | |
| <span></span> | |
| <span><span class="fu"><a href="../reference/setSpecies.html">setSpecies</a></span><span class="op">(</span><span class="st">"CheYp"</span>, initial_concentration <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span> | |
| <span><span class="fu"><a href="../reference/getSpecies.html">getSpecies</a></span><span class="op">(</span><span class="st">"CheYp"</span><span class="op">)</span><span class="op">$</span><span class="va">initial_concentration</span></span> | |
| <span><span class="co">#> [1] 1</span></span> | |
| <span></span> | |
| <span><span class="va">yp_init_expression</span> <span class="op"><-</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">#> [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">#> [1] 1</span></span></code></pre></div> | |
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