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diff --git a/docs/reference/index.html b/docs/reference/index.html index 2e997ef0..16280a9d 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -25,12 +25,14 @@ <script src="../pkgdown.js"></script> <!-- mathjax --> -<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> +<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> <!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> <![endif]--> + + </head> <body> @@ -70,6 +72,9 @@ <li> <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> + <li> + <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + </li> </ul> </li> <li> @@ -95,250 +100,302 @@ <div class="row"> <div class="col-md-9"> <div class="page-header"> - <h1>Function reference</h1> - <h4>version 0.9.45.1</h4> + <h1> + Reference + <small>version 0.9.45.2</small> + </h1> </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"> -</a></p> - <ul> - <li><code><a href="mkinmod.html">mkinmod</a></code></li> - </ul> - - <p><a href="mkinfit.html"> -</a></p> - <ul> - <li><code><a href="mkinfit.html">mkinfit</a></code></li> - </ul> - - <p><a href="mmkin.html"> -</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"> -</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"> -</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"> -</a></p> - <ul> - <li><code><a href="mkinresplot.html">mkinresplot</a></code></li> - </ul> - - <p><a href="mkinparplot.html"> -</a></p> - <ul> - <li><code><a href="mkinparplot.html">mkinparplot</a></code></li> - </ul> - - <p><a href="endpoints.html"> -</a></p> - <ul> - <li><code><a href="endpoints.html">endpoints</a></code></li> - </ul> - - <p><a href="mkinerrmin.html"> -</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"> -</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"> -</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"> -</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"> -</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"> -</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"> -</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"> -</a></p> - <ul> - <li><code><a href="mccall81_245T.html">mccall81_245T</a></code></li> - </ul> - - <p><a href="schaefer07_complex_case.html"> -</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"> -</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"> -</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"> -</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"> -</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"> -</a></p> - <ul> - <li><code><a href="mkinsub.html">mkinsub</a></code></li> - </ul> - - <p><a href="print.mkinmod.html"> -</a></p> - <ul> - <li><code><a href="print.mkinmod.html">print.mkinmod</a></code></li> - </ul> - - <p><a href="mkinpredict.html"> -</a></p> - <ul> - <li><code><a href="mkinpredict.html">mkinpredict</a></code></li> - </ul> - - <p><a href="transform_odeparms.html"> -</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"> -</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> + <table class="ref-index"> - - <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="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="DFOP.solution.html"> -</a></p> - <ul> - <li><code><a href="DFOP.solution.html">DFOP.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> - - <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> - <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> + <colgroup> + <col class="alias" /> + <col class="title" /> + </colgroup> - - <p><a href="add_err.html"> -</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"> -</a></p> - <ul> - <li><code><a href="mkinplot.html">mkinplot</a></code></li> - </ul> - + <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> + <tr> + <!-- --> + <td> + <p><code><a href="mkinmod.html">mkinmod</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> </p> + </td> + <td><p>Fit one or more kinetic models with one or more state variables to one or more datasets</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> + <tr> + <!-- --> + <td> + <p><code><a href="plot.mkinfit.html">plot.mkinfit</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</a></code> <code><a href="summary.mkinfit.html">print</a></code> </p> + </td> + <td><p>Summary method for class "mkinfit"</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="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="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> + </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> + <tr> + <!-- --> + <td> + <p><code><a href="plot.mmkin.html">plot</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> + </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> + <tr> + <!-- --> + <td> + <p><code><a href="FOCUS_2006_datasets.html">FOCUS_2006_datasets</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">data</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">data</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">data</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">data</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="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">data</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.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="mkinds.html">mkinds</a></code> </p> + </td> + <td><p>A dataset class for mkin</p></td> + </tr><tr> + <!-- --> + <td> + <p><code><a href="print.mkinds.html">print</a></code> </p> + </td> + <td><p>Print mkinds objects</p></td> + </tr> + </tbody><tbody> + <tr> + <th colspan="2"> + <h2 id="section-helper-functions" class="hasAnchor"><a href="#section-helper-functions" class="anchor"></a>Helper functions</h2> + <p class="section-desc"></p> + </th> + </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><tr> + <!-- --> + <td> + <p><code><a href="mkinsub.html">mkinsub</a></code> </p> + </td> + <td><p>Function to set up a kinetic submodel for one state variable</p></td> + </tr><tr> + <!-- --> + <td> + <p><code><a href="print.mkinmod.html">print</a></code> </p> + </td> + <td><p>Print mkinmod objects</p></td> + </tr><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="geometric_mean.html">geometric_mean</a></code> </p> + </td> + <td><p>Calculate the geometric mean</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> + <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> + </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> + <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> + </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 superseeded</p></p> + </th> + </tr> + <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> </div> </div> |