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diff --git a/docs/reference/index.html b/docs/reference/index.html index 6c05941d..5785b5aa 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -21,13 +21,19 @@ <!-- clipboard.js --> <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> +<!-- sticky kit --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> + <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> - - + + + <meta property="og:title" content="Function reference" /> + + + <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -50,8 +56,12 @@ <span class="icon-bar"></span> <span class="icon-bar"></span> </button> - <a class="navbar-brand" href="../index.html">mkin</a> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">mkin</a> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.1</span> + </span> </div> + <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> @@ -92,6 +102,7 @@ <ul class="nav navbar-nav navbar-right"> </ul> + </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -99,330 +110,326 @@ </header> - <div class="row"> - <div class="col-md-9"> +<div class="row"> + <div class="contents col-md-9"> <div class="page-header"> - <h1> - Reference - <small>version 0.9.47.1</small> - </h1> + <h1>Reference</h1> </div> - <div class="contents"> - <table class="ref-index"> + <table class="ref-index"> - <colgroup> - <col class="alias" /> - <col class="title" /> - </colgroup> + <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> - <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="Extract.mmkin.html">[.mmkin</a></code> </p> - </td> - <td><p>Subsetting method for mmkin objects</p></td> - </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">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="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.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="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">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="geometric_mean.html">geometric_mean</a></code> </p> - </td> - <td><p>Calculate the geometric mean</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="max_twa_parent.html">max_twa_parent</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="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="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="print.mkinmod.html">print</a></code> </p> - </td> - <td><p>Print mkinmod objects</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="sigma_rl.html">sigma_rl</a></code> </p> - </td> - <td><p>Two component error model of Rocke and Lorenzato</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> + <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(<i><mkinfit></i>)</a></code> <code><a href="plot.mkinfit.html">plot_sep()</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="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="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> + </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">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="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.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="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">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(<i><mkinds></i>)</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="geometric_mean.html">geometric_mean()</a></code> </p> + </td> + <td><p>Calculate the geometric mean</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="max_twa_parent.html">max_twa_parent()</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="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="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="print.mkinmod.html">print(<i><mkinmod></i>)</a></code> </p> + </td> + <td><p>Print mkinmod objects</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="sigma_rl.html">sigma_rl()</a></code> </p> + </td> + <td><p>Two component error model of Rocke and Lorenzato</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 class="col-md-3 hidden-xs hidden-sm" id="sidebar"> @@ -452,6 +459,8 @@ </footer> </div> + + </body> </html> |