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authorJohannes Ranke <jranke@uni-bremen.de>2020-11-30 16:05:10 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2020-11-30 16:05:10 +0100
commit524a8bba89b95840b4e9215c403947a8bb76d7b2 (patch)
treef28717d46b0ac95bd56d4b84ee4fb770364b91ba /docs/dev/reference/mkinsub.html
parent78884beed74c18c99521b9ceeaa643e13cf94c06 (diff)
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- <h1>Function to set up a kinetic submodel for one state variable</h1>
- <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/mkinsub.R'><code>R/mkinsub.R</code></a></small>
- <div class="hidden name"><code>mkinsub.Rd</code></div>
- </div>
-
- <div class="ref-description">
- <p>This is a convenience function to set up the lists used as arguments for
-<code><a href='mkinmod.html'>mkinmod</a></code>.</p>
- </div>
-
- <pre class="usage"><span class='fu'>mkinsub</span><span class='op'>(</span><span class='va'>submodel</span>, to <span class='op'>=</span> <span class='cn'>NULL</span>, sink <span class='op'>=</span> <span class='cn'>TRUE</span>, full_name <span class='op'>=</span> <span class='cn'>NA</span><span class='op'>)</span></pre>
-
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
- <table class="ref-arguments">
- <colgroup><col class="name" /><col class="desc" /></colgroup>
- <tr>
- <th>submodel</th>
- <td><p>Character vector of length one to specify the submodel type.
-See <code><a href='mkinmod.html'>mkinmod</a></code> for the list of allowed submodel names.</p></td>
- </tr>
- <tr>
- <th>to</th>
- <td><p>Vector of the names of the state variable to which a
-transformation shall be included in the model.</p></td>
- </tr>
- <tr>
- <th>sink</th>
- <td><p>Should a pathway to sink be included in the model in addition to
-the pathways to other state variables?</p></td>
- </tr>
- <tr>
- <th>full_name</th>
- <td><p>An optional name to be used e.g. for plotting fits
-performed with the model. You can use non-ASCII characters here, but then
-your R code will not be portable, <em>i.e.</em> may produce unintended plot
-results on other operating systems or system configurations.</p></td>
- </tr>
- </table>
-
- <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
- <p>A list for use with <code><a href='mkinmod.html'>mkinmod</a></code>.</p>
- <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2>
-
- <p>Johannes Ranke</p>
-
- <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'>
-<span class='co'># One parent compound, one metabolite, both single first order.</span>
-<span class='va'>SFO_SFO</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>
- parent <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"m1"</span><span class='op'>)</span>,
- m1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
-<span class='co'># The same model using mkinsub</span>
-<span class='va'>SFO_SFO.2</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>
- parent <span class='op'>=</span> <span class='fu'>mkinsub</span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"m1"</span><span class='op'>)</span>,
- m1 <span class='op'>=</span> <span class='fu'>mkinsub</span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
-<span class='co'># \dontrun{</span>
- <span class='co'># Now supplying full names</span>
- <span class='va'>SFO_SFO.2</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>
- parent <span class='op'>=</span> <span class='fu'>mkinsub</span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"m1"</span>, full_name <span class='op'>=</span> <span class='st'>"Test compound"</span><span class='op'>)</span>,
- m1 <span class='op'>=</span> <span class='fu'>mkinsub</span><span class='op'>(</span><span class='st'>"SFO"</span>, full_name <span class='op'>=</span> <span class='st'>"Metabolite M1"</span><span class='op'>)</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> <span class='co'># }</span>
-</div></pre>
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