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<h1>Define a parameter estimation experiment</h1>
<small class="dont-index">Source: <a href="https://github.com/jpahle/CoRC/blob/HEAD/R/task_parameterestimation.R" class="external-link"><code>R/task_parameterestimation.R</code></a></small>
<div class="hidden name"><code>defineExperiments.Rd</code></div>
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<div class="ref-description">
<p><code>defineExperiments</code> defines a set of experiments given as tidy data frame to the given model.</p>
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<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">defineExperiments</span><span class="op">(</span></span>
<span> experiment_type <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">"time_course"</span>, <span class="st">"steady_state"</span><span class="op">)</span>,</span>
<span> data <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> types <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> mappings <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> weights <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> weight_method <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> normalize_weights_per_experiment <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span> filename <span class="op">=</span> <span class="cn">NULL</span></span>
<span><span class="op">)</span></span></code></pre></div>
</div>
<div id="arguments">
<h2>Arguments</h2>
<dl><dt>experiment_type</dt>
<dd><p>string</p></dd>
<dt>data</dt>
<dd><p>list of tidy data frames</p></dd>
<dt>types</dt>
<dd><p>data column types as character vector</p>
<p>Allowed types of columns are: 'time', 'independent', 'dependent', 'ignore'.</p>
<p>Type 'time' is only allowed for time course experiments.</p>
<p>Can be a named vector to only specify for a subset of data columns.</p></dd>
<dt>mappings</dt>
<dd><p>data column mappings as character vector</p>
<p>Expects value references.</p>
<p>If no mappings are given, column names can serve as mappings.</p>
<p>Can be a named vector to only specify for a subset of data columns.</p></dd>
<dt>weights</dt>
<dd><p>data column weights as numeric vector</p>
<p>`NaN` corresponds to automatic weight.</p>
<p>Can be a named vector to only specify for a subset of data columns.</p></dd>
<dt>weight_method</dt>
<dd><p>string</p>
<p>Allowed methods: 'mean', 'mean_square', 'sd', 'value_scaling'.</p></dd>
<dt>normalize_weights_per_experiment</dt>
<dd><p>flag</p></dd>
<dt>filename</dt>
<dd><p>optional string</p>
<p>When adding the experiments to a COPASI model, this filename will be used.
In use cases, where experiments are only used temporarily, the filename is ignored.</p></dd>
</dl></div>
<div id="value">
<h2>Value</h2>
<p>copasi_exp object for input into related functions</p>
</div>
<div id="details">
<h2>Details</h2>
<p>CoRC uses it's own methodology for defining experimental data for use with a COPASI model.
To this end it is required that experimental data be imported to R by the user and transformed to tidy data.
For help on data import and tidying see: <code><a href="https://tidyr.tidyverse.org/articles/tidy-data.html" class="external-link">vignette("tidy-data", "tidyr")</a></code>.
This function adds required metadata to experimental data for use with CoRC.</p>
</div>
<div id="see-also">
<h2>See also</h2>
<div class="dont-index"><p><code><a href="addExperiments.html">addExperiments</a></code> <code><a href="clearExperiments.html">clearExperiments</a></code></p>
<p>Other parameter estimation:
<code><a href="addExperiments.html">addExperiments</a>()</code>,
<code><a href="addParameterEstimationParameter.html">addParameterEstimationParameter</a>()</code>,
<code><a href="clearExperiments.html">clearExperiments</a>()</code>,
<code><a href="clearParameterEstimationParameters.html">clearParameterEstimationParameters</a>()</code>,
<code><a href="clearValidations.html">clearValidations</a>()</code>,
<code><a href="getParameterEstimationSettings.html">getParameterEstimationSettings</a>()</code>,
<code><a href="runParameterEstimation.html">runParameterEstimation</a>()</code>,
<code><a href="setParameterEstimationSettings.html">setParameterEstimationSettings</a>()</code></p></div>
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