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<a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
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<a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
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<h1>Reference</h1>
</div>
<table class="ref-index">
<colgroup>
<col class="alias" />
<col class="title" />
</colgroup>
<tbody>
<tr>
<th colspan="2">
<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>
</th>
</tr>
</tbody><tbody>
<tr>
<td>
<p><code><a href="mkinmod.html">mkinmod()</a></code> <code><a href="mkinmod.html">print(<i><mkinmod></i>)</a></code> <code><a href="mkinmod.html">mkinsub()</a></code> </p>
</td>
<td><p>Function to set up a kinetic model with one or more state variables</p></td>
</tr><tr>
<td>
<p><code><a href="mkinfit.html">mkinfit()</a></code> </p>
</td>
<td><p>Fit a kinetic model to data with one or more state variables</p></td>
</tr><tr>
<td>
<p><code><a href="mmkin.html">mmkin()</a></code> <code><a href="mmkin.html">print(<i><mmkin></i>)</a></code> </p>
</td>
<td><p>Fit one or more kinetic models with one or more state variables to one or
more datasets</p></td>
</tr><tr>
<td>
<p><code><a href="nafta.html">nafta()</a></code> <code><a href="nafta.html">print(<i><nafta></i>)</a></code> </p>
</td>
<td><p>Evaluate parent kinetics using the NAFTA guidance</p></td>
</tr>
</tbody><tbody>
<tr>
<th colspan="2">
<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>
</th>
</tr>
</tbody><tbody>
<tr>
<td>
<p><code><a href="plot.mkinfit.html">plot(<i><mkinfit></i>)</a></code> <code><a href="plot.mkinfit.html">plot_sep()</a></code> <code><a href="plot.mkinfit.html">plot_res()</a></code> <code><a href="plot.mkinfit.html">plot_err()</a></code> </p>
</td>
<td><p>Plot the observed data and the fitted model of an mkinfit object</p></td>
</tr><tr>
<td>
<p><code><a href="summary.mkinfit.html">summary(<i><mkinfit></i>)</a></code> <code><a href="summary.mkinfit.html">print(<i><summary.mkinfit></i>)</a></code> </p>
</td>
<td><p>Summary method for class "mkinfit"</p></td>
</tr><tr>
<td>
<p><code><a href="parms.html">parms()</a></code> </p>
</td>
<td><p>Extract model parameters from mkinfit models</p></td>
</tr><tr>
<td>
<p><code><a href="confint.mkinfit.html">confint(<i><mkinfit></i>)</a></code> </p>
</td>
<td><p>Confidence intervals for parameters of mkinfit objects</p></td>
</tr><tr>
<td>
<p><code><a href="update.mkinfit.html">update(<i><mkinfit></i>)</a></code> </p>
</td>
<td><p>Update an mkinfit model with different arguments</p></td>
</tr><tr>
<td>
<p><code><a href="lrtest.mkinfit.html">lrtest(<i><mkinfit></i>)</a></code> <code><a href="lrtest.mkinfit.html">lrtest(<i><mmkin></i>)</a></code> </p>
</td>
<td><p>Likelihood ratio test for mkinfit models</p></td>
</tr><tr>
<td>
<p><code><a href="loftest.html">loftest()</a></code> </p>
</td>
<td><p>Lack-of-fit test for models fitted to data with replicates</p></td>
</tr><tr>
<td>
<p><code><a href="mkinerrmin.html">mkinerrmin()</a></code> </p>
</td>
<td><p>Calculate the minimum error to assume in order to pass the variance test</p></td>
</tr><tr>
<td>
<p><code><a href="endpoints.html">endpoints()</a></code> </p>
</td>
<td><p>Function to calculate endpoints for further use from kinetic models fitted
with mkinfit</p></td>
</tr><tr>
<td>
<p><code><a href="aw.html">aw()</a></code> </p>
</td>
<td><p>Calculate Akaike weights for model averaging</p></td>
</tr><tr>
<td>
<p><code><a href="CAKE_export.html">CAKE_export()</a></code> </p>
</td>
<td><p>Export a list of datasets format to a CAKE study file</p></td>
</tr>
</tbody><tbody>
<tr>
<th colspan="2">
<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>
</th>
</tr>
</tbody><tbody>
<tr>
<td>
<p><code><a href="Extract.mmkin.html">`[`(<i><mmkin></i>)</a></code> </p>
</td>
<td><p>Subsetting method for mmkin objects</p></td>
</tr><tr>
<td>
<p><code><a href="plot.mmkin.html">plot(<i><mmkin></i>)</a></code> </p>
</td>
<td><p>Plot model fits (observed and fitted) and the residuals for a row or column
of an mmkin object</p></td>
</tr><tr>
<td>
<p><code><a href="AIC.mmkin.html">AIC(<i><mmkin></i>)</a></code> <code><a href="AIC.mmkin.html">BIC(<i><mmkin></i>)</a></code> </p>
</td>
<td><p>Calculate the AIC for a column of an mmkin object</p></td>
</tr>
</tbody><tbody>
<tr>
<th colspan="2">
<h2 id="section-mixed-models" class="hasAnchor"><a href="#section-mixed-models" class="anchor"></a>Mixed models</h2>
<p class="section-desc"><p>Create and work with nonlinear mixed effects models</p></p>
</th>
</tr>
</tbody><tbody>
<tr>
<td>
<p><code><a href="nlme.mmkin.html">nlme(<i><mmkin></i>)</a></code> <code><a href="nlme.mmkin.html">print(<i><nlme.mmkin></i>)</a></code> <code><a href="nlme.mmkin.html">update(<i><nlme.mmkin></i>)</a></code> </p>
</td>
<td><p>Create an nlme model for an mmkin row object</p></td>
</tr><tr>
<td>
<p><code><a href="saem.html">saem()</a></code> <code><a href="saem.html">print(<i><saem.mmkin></i>)</a></code> <code><a href="saem.html">saemix_model()</a></code> <code><a href="saem.html">saemix_data()</a></code> </p>
</td>
<td><p>Fit nonlinear mixed models with SAEM</p></td>
</tr><tr>
<td>
<p><code><a href="plot.mixed.mmkin.html">plot(<i><mixed.mmkin></i>)</a></code> </p>
</td>
<td><p>Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object</p></td>
</tr><tr>
<td>
<p><code><a href="summary.nlme.mmkin.html">summary(<i><nlme.mmkin></i>)</a></code> <code><a href="summary.nlme.mmkin.html">print(<i><summary.nlme.mmkin></i>)</a></code> </p>
</td>
<td><p>Summary method for class "nlme.mmkin"</p></td>
</tr><tr>
<td>
<p><code><a href="summary.saem.mmkin.html">summary(<i><saem.mmkin></i>)</a></code> <code><a href="summary.saem.mmkin.html">print(<i><summary.saem.mmkin></i>)</a></code> </p>
</td>
<td><p>Summary method for class "saem.mmkin"</p></td>
</tr><tr>
<td>
<p><code><a href="nlme.html">nlme_function()</a></code> <code><a href="nlme.html">mean_degparms()</a></code> <code><a href="nlme.html">nlme_data()</a></code> </p>
</td>
<td><p>Helper functions to create nlme models from mmkin row objects</p></td>
</tr><tr>
<td>
<p><code><a href="get_deg_func.html">get_deg_func()</a></code> </p>
</td>
<td><p>Retrieve a degradation function from the mmkin namespace</p></td>
</tr><tr>
<td>
<p><code><a href="mixed.html">mixed()</a></code> <code><a href="mixed.html">print(<i><mixed.mmkin></i>)</a></code> </p>
</td>
<td><p>Create a mixed effects model from an mmkin row object</p></td>
</tr>
</tbody><tbody>
<tr>
<th colspan="2">
<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>
</th>
</tr>
</tbody><tbody>
<tr>
<td>
<p><code><a href="focus_soil_moisture.html">focus_soil_moisture</a></code> </p>
</td>
<td><p>FOCUS default values for soil moisture contents at field capacity, MWHC and 1/3 bar</p></td>
</tr><tr>
<td>
<p><code><a href="D24_2014.html">D24_2014</a></code> </p>
</td>
<td><p>Aerobic soil degradation data on 2,4-D from the EU assessment in 2014</p></td>
</tr><tr>
<td>
<p><code><a href="dimethenamid_2018.html">dimethenamid_2018</a></code> </p>
</td>
<td><p>Aerobic soil degradation data on dimethenamid and dimethenamid-P from the EU assessment in 2018</p></td>
</tr><tr>
<td>
<p><code><a href="FOCUS_2006_datasets.html">FOCUS_2006_A</a></code> <code><a href="FOCUS_2006_datasets.html">FOCUS_2006_B</a></code> <code><a href="FOCUS_2006_datasets.html">FOCUS_2006_C</a></code> <code><a href="FOCUS_2006_datasets.html">FOCUS_2006_D</a></code> <code><a href="FOCUS_2006_datasets.html">FOCUS_2006_E</a></code> <code><a href="FOCUS_2006_datasets.html">FOCUS_2006_F</a></code> </p>
</td>
<td><p>Datasets A to F from the FOCUS Kinetics report from 2006</p></td>
</tr><tr>
<td>
<p><code><a href="FOCUS_2006_SFO_ref_A_to_F.html">FOCUS_2006_SFO_ref_A_to_F</a></code> </p>
</td>
<td><p>Results of fitting the SFO model to Datasets A to F of FOCUS (2006)</p></td>
</tr><tr>
<td>
<p><code><a href="FOCUS_2006_FOMC_ref_A_to_F.html">FOCUS_2006_FOMC_ref_A_to_F</a></code> </p>
</td>
<td><p>Results of fitting the FOMC model to Datasets A to F of FOCUS (2006)</p></td>
</tr><tr>
<td>
<p><code><a href="FOCUS_2006_HS_ref_A_to_F.html">FOCUS_2006_HS_ref_A_to_F</a></code> </p>
</td>
<td><p>Results of fitting the HS model to Datasets A to F of FOCUS (2006)</p></td>
</tr><tr>
<td>
<p><code><a href="FOCUS_2006_DFOP_ref_A_to_B.html">FOCUS_2006_DFOP_ref_A_to_B</a></code> </p>
</td>
<td><p>Results of fitting the DFOP model to Datasets A to B of FOCUS (2006)</p></td>
</tr><tr>
<td>
<p><code><a href="NAFTA_SOP_2015.html">NAFTA_SOP_Appendix_B</a></code> <code><a href="NAFTA_SOP_2015.html">NAFTA_SOP_Appendix_D</a></code> </p>
</td>
<td><p>Example datasets from the NAFTA SOP published 2015</p></td>
</tr><tr>
<td>
<p><code><a href="NAFTA_SOP_Attachment.html">NAFTA_SOP_Attachment</a></code> </p>
</td>
<td><p>Example datasets from Attachment 1 to the NAFTA SOP published 2015</p></td>
</tr><tr>
<td>
<p><code><a href="mccall81_245T.html">mccall81_245T</a></code> </p>
</td>
<td><p>Datasets on aerobic soil metabolism of 2,4,5-T in six soils</p></td>
</tr><tr>
<td>
<p><code><a href="schaefer07_complex_case.html">schaefer07_complex_case</a></code> </p>
</td>
<td><p>Metabolism data set used for checking the software quality of KinGUI</p></td>
</tr><tr>
<td>
<p><code><a href="synthetic_data_for_UBA_2014.html">synthetic_data_for_UBA_2014</a></code> </p>
</td>
<td><p>Synthetic datasets for one parent compound with two metabolites</p></td>
</tr><tr>
<td>
<p><code><a href="experimental_data_for_UBA.html">experimental_data_for_UBA_2019</a></code> </p>
</td>
<td><p>Experimental datasets used for development and testing of error models</p></td>
</tr><tr>
<td>
<p><code><a href="test_data_from_UBA_2014.html">test_data_from_UBA_2014</a></code> </p>
</td>
<td><p>Three experimental datasets from two water sediment systems and one soil</p></td>
</tr><tr>
<td>
<p><code><a href="mkinds.html">print(<i><mkinds></i>)</a></code> </p>
</td>
<td><p>A dataset class for mkin</p></td>
</tr><tr>
<td>
<p><code><a href="mkindsg.html">print(<i><mkindsg></i>)</a></code> </p>
</td>
<td><p>A class for dataset groups for mkin</p></td>
</tr>
</tbody><tbody>
<tr>
<th colspan="2">
<h2 id="section-nafta-guidance" class="hasAnchor"><a href="#section-nafta-guidance" class="anchor"></a>NAFTA guidance</h2>
<p class="section-desc"></p>
</th>
</tr>
</tbody><tbody>
<tr>
<td>
<p><code><a href="nafta.html">nafta()</a></code> <code><a href="nafta.html">print(<i><nafta></i>)</a></code> </p>
</td>
<td><p>Evaluate parent kinetics using the NAFTA guidance</p></td>
</tr><tr>
<td>
<p><code><a href="plot.nafta.html">plot(<i><nafta></i>)</a></code> </p>
</td>
<td><p>Plot the results of the three models used in the NAFTA scheme.</p></td>
</tr>
</tbody><tbody>
<tr>
<th colspan="2">
<h2 id="section-utility-functions" class="hasAnchor"><a href="#section-utility-functions" class="anchor"></a>Utility functions</h2>
<p class="section-desc"></p>
</th>
</tr>
</tbody><tbody>
<tr>
<td>
<p><code><a href="f_time_norm_focus.html">f_time_norm_focus()</a></code> </p>
</td>
<td><p>Normalisation factors for aerobic soil degradation according to FOCUS guidance</p></td>
</tr><tr>
<td>
<p><code><a href="max_twa_parent.html">max_twa_parent()</a></code> <code><a href="max_twa_parent.html">max_twa_sfo()</a></code> <code><a href="max_twa_parent.html">max_twa_fomc()</a></code> <code><a href="max_twa_parent.html">max_twa_dfop()</a></code> <code><a href="max_twa_parent.html">max_twa_hs()</a></code> </p>
</td>
<td><p>Function to calculate maximum time weighted average concentrations from
kinetic models fitted with mkinfit</p></td>
</tr><tr>
<td>
<p><code><a href="mkin_wide_to_long.html">mkin_wide_to_long()</a></code> </p>
</td>
<td><p>Convert a dataframe with observations over time into long format</p></td>
</tr><tr>
<td>
<p><code><a href="mkin_long_to_wide.html">mkin_long_to_wide()</a></code> </p>
</td>
<td><p>Convert a dataframe from long to wide format</p></td>
</tr>
</tbody><tbody>
<tr>
<th colspan="2">
<h2 id="section-helper-functions-mainly-used-internally" class="hasAnchor"><a href="#section-helper-functions-mainly-used-internally" class="anchor"></a>Helper functions mainly used internally</h2>
<p class="section-desc"></p>
</th>
</tr>
</tbody><tbody>
<tr>
<td>
<p><code><a href="mkinpredict.html">mkinpredict()</a></code> </p>
</td>
<td><p>Produce predictions from a kinetic model using specific parameters</p></td>
</tr><tr>
<td>
<p><code><a href="transform_odeparms.html">transform_odeparms()</a></code> <code><a href="transform_odeparms.html">backtransform_odeparms()</a></code> </p>
</td>
<td><p>Functions to transform and backtransform kinetic parameters for fitting</p></td>
</tr><tr>
<td>
<p><code><a href="ilr.html">ilr()</a></code> <code><a href="ilr.html">invilr()</a></code> </p>
</td>
<td><p>Function to perform isometric log-ratio transformation</p></td>
</tr><tr>
<td>
<p><code><a href="logLik.mkinfit.html">logLik(<i><mkinfit></i>)</a></code> </p>
</td>
<td><p>Calculated the log-likelihood of a fitted mkinfit object</p></td>
</tr><tr>
<td>
<p><code><a href="residuals.mkinfit.html">residuals(<i><mkinfit></i>)</a></code> </p>
</td>
<td><p>Extract residuals from an mkinfit model</p></td>
</tr><tr>
<td>
<p><code><a href="nobs.mkinfit.html">nobs(<i><mkinfit></i>)</a></code> </p>
</td>
<td><p>Number of observations on which an mkinfit object was fitted</p></td>
</tr><tr>
<td>
<p><code><a href="mkinresplot.html">mkinresplot()</a></code> </p>
</td>
<td><p>Function to plot residuals stored in an mkin object</p></td>
</tr><tr>
<td>
<p><code><a href="mkinparplot.html">mkinparplot()</a></code> </p>
</td>
<td><p>Function to plot the confidence intervals obtained using mkinfit</p></td>
</tr><tr>
<td>
<p><code><a href="mkinerrplot.html">mkinerrplot()</a></code> </p>
</td>
<td><p>Function to plot squared residuals and the error model for an mkin object</p></td>
</tr><tr>
<td>
<p><code><a href="create_deg_func.html">create_deg_func()</a></code> </p>
</td>
<td><p>Create degradation functions for known analytical solutions</p></td>
</tr>
</tbody><tbody>
<tr>
<th colspan="2">
<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>
</th>
</tr>
</tbody><tbody>
<tr>
<td>
<p><code><a href="SFO.solution.html">SFO.solution()</a></code> </p>
</td>
<td><p>Single First-Order kinetics</p></td>
</tr><tr>
<td>
<p><code><a href="FOMC.solution.html">FOMC.solution()</a></code> </p>
</td>
<td><p>First-Order Multi-Compartment kinetics</p></td>
</tr><tr>
<td>
<p><code><a href="DFOP.solution.html">DFOP.solution()</a></code> </p>
</td>
<td><p>Double First-Order in Parallel kinetics</p></td>
</tr><tr>
<td>
<p><code><a href="SFORB.solution.html">SFORB.solution()</a></code> </p>
</td>
<td><p>Single First-Order Reversible Binding kinetics</p></td>
</tr><tr>
<td>
<p><code><a href="HS.solution.html">HS.solution()</a></code> </p>
</td>
<td><p>Hockey-Stick kinetics</p></td>
</tr><tr>
<td>
<p><code><a href="IORE.solution.html">IORE.solution()</a></code> </p>
</td>
<td><p>Indeterminate order rate equation kinetics</p></td>
</tr><tr>
<td>
<p><code><a href="logistic.solution.html">logistic.solution()</a></code> </p>
</td>
<td><p>Logistic kinetics</p></td>
</tr>
</tbody><tbody>
<tr>
<th colspan="2">
<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>
</th>
</tr>
</tbody><tbody>
<tr>
<td>
<p><code><a href="add_err.html">add_err()</a></code> </p>
</td>
<td><p>Add normally distributed errors to simulated kinetic degradation data</p></td>
</tr><tr>
<td>
<p><code><a href="sigma_twocomp.html">sigma_twocomp()</a></code> </p>
</td>
<td><p>Two-component error model</p></td>
</tr>
</tbody><tbody>
<tr>
<th colspan="2">
<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 superseded</p></p>
</th>
</tr>
</tbody><tbody>
<tr>
<td>
<p><code><a href="mkinplot.html">mkinplot()</a></code> </p>
</td>
<td><p>Plot the observed data and the fitted model of an mkinfit object</p></td>
</tr>
</tbody>
</table>
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