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<h1>Function reference</h1>
<h4>version 0.9.44.9000</h4>
</div>
<div class="contents">
<h2 id="section-main-functions" class="hasAnchor"><a href="#section-main-functions" class="anchor"></a>Main functions</h2>
<p class="section-desc"><p>Essential functionality</p></p>
<p><a href="mkinmod.html">Function to set up a kinetic model with one or more state variables</a></p>
<ul>
<li><code><a href="mkinmod.html">mkinmod</a></code></li>
</ul>
<p><a href="mkinfit.html">Fit a kinetic model to data with one or more state variables</a></p>
<ul>
<li><code><a href="mkinfit.html">mkinfit</a></code></li>
</ul>
<p><a href="mmkin.html">Fit one or more kinetic models with one or more state variables to one or more datasets</a></p>
<ul>
<li><code><a href="mmkin.html">mmkin</a></code></li>
</ul>
<h2 id="section-show-results" class="hasAnchor"><a href="#section-show-results" class="anchor"></a>Show results</h2>
<p class="section-desc"><p>Functions working with mkinfit objects</p></p>
<p><a href="plot.mkinfit.html">Plot the observed data and the fitted model of an mkinfit object</a></p>
<ul>
<li><code><a href="plot.mkinfit.html">plot.mkinfit</a></code></li><li><code><a href="plot.mkinfit.html">plot_sep</a></code></li>
</ul>
<p><a href="summary.mkinfit.html">Summary method for class "mkinfit"</a></p>
<ul>
<li><code><a href="summary.mkinfit.html">summary.mkinfit</a></code></li><li><code><a href="summary.mkinfit.html">print.summary.mkinfit</a></code></li>
</ul>
<p><a href="mkinresplot.html">Function to plot residuals stored in an mkin object</a></p>
<ul>
<li><code><a href="mkinresplot.html">mkinresplot</a></code></li>
</ul>
<p><a href="mkinparplot.html">Function to plot the confidence intervals obtained using
list(list("mkinfit"))</a></p>
<ul>
<li><code><a href="mkinparplot.html">mkinparplot</a></code></li>
</ul>
<p><a href="endpoints.html">Function to calculate endpoints for further use from kinetic models fitted with mkinfit</a></p>
<ul>
<li><code><a href="endpoints.html">endpoints</a></code></li>
</ul>
<p><a href="mkinerrmin.html">Calculate the minimum error to assume in order to pass the variance test</a></p>
<ul>
<li><code><a href="mkinerrmin.html">mkinerrmin</a></code></li>
</ul>
<h2 id="section-work-with-mmkin-objects" class="hasAnchor"><a href="#section-work-with-mmkin-objects" class="anchor"></a>Work with mmkin objects</h2>
<p class="section-desc"><p>Functions working with aggregated results</p></p>
<p><a href="Extract.mmkin.html">Subsetting method for mmkin objects</a></p>
<ul>
<li><code><a href="Extract.mmkin.html">[.mmkin</a></code></li>
</ul>
<p><a href="plot.mmkin.html">Plot model fits (observed and fitted) and the residuals for a row or column of an mmkin object</a></p>
<ul>
<li><code><a href="plot.mmkin.html">plot.mmkin</a></code></li>
</ul>
<h2 id="section-datasets-and-known-results" class="hasAnchor"><a href="#section-datasets-and-known-results" class="anchor"></a>Datasets and known results</h2>
<p class="section-desc"></p>
<p><a href="FOCUS_2006_datasets.html">Datasets A to F from the FOCUS Kinetics report from 2006</a></p>
<ul>
<li><code><a href="FOCUS_2006_datasets.html">FOCUS_2006_A</a></code></li><li><code><a href="FOCUS_2006_datasets.html">FOCUS_2006_B</a></code></li><li><code><a href="FOCUS_2006_datasets.html">FOCUS_2006_C</a></code></li><li><code><a href="FOCUS_2006_datasets.html">FOCUS_2006_D</a></code></li><li><code><a href="FOCUS_2006_datasets.html">FOCUS_2006_E</a></code></li><li><code><a href="FOCUS_2006_datasets.html">FOCUS_2006_F</a></code></li>
</ul>
<p><a href="FOCUS_2006_SFO_ref_A_to_F.html">Results of fitting the SFO model to Datasets A to F of FOCUS (2006)</a></p>
<ul>
<li><code><a href="FOCUS_2006_SFO_ref_A_to_F.html">FOCUS_2006_SFO_ref_A_to_F</a></code></li>
</ul>
<p><a href="FOCUS_2006_FOMC_ref_A_to_F.html">Results of fitting the FOMC model to Datasets A to F of FOCUS (2006)</a></p>
<ul>
<li><code><a href="FOCUS_2006_FOMC_ref_A_to_F.html">FOCUS_2006_FOMC_ref_A_to_F</a></code></li>
</ul>
<p><a href="FOCUS_2006_HS_ref_A_to_F.html">Results of fitting the HS model to Datasets A to F of FOCUS (2006)</a></p>
<ul>
<li><code><a href="FOCUS_2006_HS_ref_A_to_F.html">FOCUS_2006_HS_ref_A_to_F</a></code></li>
</ul>
<p><a href="FOCUS_2006_DFOP_ref_A_to_B.html">Results of fitting the DFOP model to Datasets A to B of FOCUS (2006)</a></p>
<ul>
<li><code><a href="FOCUS_2006_DFOP_ref_A_to_B.html">FOCUS_2006_DFOP_ref_A_to_B</a></code></li>
</ul>
<p><a href="mccall81_245T.html">Datasets on aerobic soil metabolism of 2,4,5-T in six soils</a></p>
<ul>
<li><code><a href="mccall81_245T.html">mccall81_245T</a></code></li>
</ul>
<p><a href="schaefer07_complex_case.html">Metabolism data set used for checking the software quality of KinGUI</a></p>
<ul>
<li><code><a href="schaefer07_complex_case.html">schaefer07_complex_case</a></code></li><li><code><a href="schaefer07_complex_case.html">schaefer07_complex_results</a></code></li>
</ul>
<p><a href="synthetic_data_for_UBA.html">Synthetic datasets for one parent compound with two metabolites</a></p>
<ul>
<li><code><a href="synthetic_data_for_UBA.html">synthetic_data_for_UBA_2014</a></code></li>
</ul>
<p><a href="mkinds.html">A dataset class for mkin</a></p>
<ul>
<li><code><a href="mkinds.html">mkinds</a></code></li>
</ul>
<p><a href="print.mkinds.html">Print mkinds objects</a></p>
<ul>
<li><code><a href="print.mkinds.html">print.mkinds</a></code></li>
</ul>
<h2 id="section-helper-functions" class="hasAnchor"><a href="#section-helper-functions" class="anchor"></a>Helper functions</h2>
<p class="section-desc"></p>
<p><a href="mkin_wide_to_long.html">Convert a dataframe with observations over time into long format</a></p>
<ul>
<li><code><a href="mkin_wide_to_long.html">mkin_wide_to_long</a></code></li>
</ul>
<p><a href="mkin_long_to_wide.html">Convert a dataframe from long to wide format</a></p>
<ul>
<li><code><a href="mkin_long_to_wide.html">mkin_long_to_wide</a></code></li>
</ul>
<p><a href="mkinsub.html">Function to set up a kinetic submodel for one state variable</a></p>
<ul>
<li><code><a href="mkinsub.html">mkinsub</a></code></li>
</ul>
<p><a href="print.mkinmod.html">Print mkinmod objects</a></p>
<ul>
<li><code><a href="print.mkinmod.html">print.mkinmod</a></code></li>
</ul>
<p><a href="mkinpredict.html">Produce predictions from a kinetic model using specific parameters</a></p>
<ul>
<li><code><a href="mkinpredict.html">mkinpredict</a></code></li>
</ul>
<p><a href="transform_odeparms.html">Functions to transform and backtransform kinetic parameters for fitting</a></p>
<ul>
<li><code><a href="transform_odeparms.html">transform_odeparms</a></code></li><li><code><a href="transform_odeparms.html">backtransform_odeparms</a></code></li>
</ul>
<p><a href="ilr.html">Function to perform isometric log-ratio transformation</a></p>
<ul>
<li><code><a href="ilr.html">ilr</a></code></li><li><code><a href="ilr.html">invilr</a></code></li>
</ul>
<p><a href="geometric_mean.html">Calculate the geometric mean</a></p>
<ul>
<li><code><a href="geometric_mean.html">geometric_mean</a></code></li>
</ul>
<h2 id="section-analytical-solutions" class="hasAnchor"><a href="#section-analytical-solutions" class="anchor"></a>Analytical solutions</h2>
<p class="section-desc"><p>Parent only model solutions</p></p>
<p><a href="DFOP.solution.html">Double First-Order in Parallel kinetics</a></p>
<ul>
<li><code><a href="DFOP.solution.html">DFOP.solution</a></code></li>
</ul>
<p><a href="FOMC.solution.html">First-Order Multi-Compartment kinetics</a></p>
<ul>
<li><code><a href="FOMC.solution.html">FOMC.solution</a></code></li>
</ul>
<p><a href="HS.solution.html">Hockey-Stick kinetics</a></p>
<ul>
<li><code><a href="HS.solution.html">HS.solution</a></code></li>
</ul>
<p><a href="IORE.solution.html">Indeterminate order rate equation kinetics</a></p>
<ul>
<li><code><a href="IORE.solution.html">IORE.solution</a></code></li>
</ul>
<p><a href="SFO.solution.html">Single First-Order kinetics</a></p>
<ul>
<li><code><a href="SFO.solution.html">SFO.solution</a></code></li>
</ul>
<p><a href="SFORB.solution.html">Single First-Order Reversible Binding kinetics</a></p>
<ul>
<li><code><a href="SFORB.solution.html">SFORB.solution</a></code></li>
</ul>
<h2 id="section-generate-synthetic-datasets" class="hasAnchor"><a href="#section-generate-synthetic-datasets" class="anchor"></a>Generate synthetic datasets</h2>
<p class="section-desc"></p>
<p><a href="add_err.html">Add normally distributed errors to simulated kinetic degradation data</a></p>
<ul>
<li><code><a href="add_err.html">add_err</a></code></li>
</ul>
<h2 id="section-deprecated-functions" class="hasAnchor"><a href="#section-deprecated-functions" class="anchor"></a>Deprecated functions</h2>
<p class="section-desc"><p>Functions that have been superseeded</p></p>
<p><a href="mkinplot.html">Plot the observed data and the fitted model of an mkinfit object</a></p>
<ul>
<li><code><a href="mkinplot.html">mkinplot</a></code></li>
</ul>
</div>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#section-main-functions">Main functions</a></li>
<li><a href="#section-show-results">Show results</a></li>
<li><a href="#section-work-with-mmkin-objects">Work with mmkin objects</a></li>
<li><a href="#section-datasets-and-known-results">Datasets and known results</a></li>
<li><a href="#section-helper-functions">Helper functions</a></li>
<li><a href="#section-analytical-solutions">Analytical solutions</a></li>
<li><a href="#section-generate-synthetic-datasets">Generate synthetic datasets</a></li>
<li><a href="#section-deprecated-functions">Deprecated functions</a></li>
</ul>
</div>
</div>
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