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diff --git a/docs/reference.html b/docs/reference.html deleted file mode 100644 index df1bd9a8..00000000 --- a/docs/reference.html +++ /dev/null @@ -1,288 +0,0 @@ -<!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<title>Function reference. mkin 0.9.44.9000</title> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> -<meta name="author" content=""> - -<link href="css/bootstrap.css" rel="stylesheet"> -<link href="css/bootstrap-responsive.css" rel="stylesheet"> -<link href="css/highlight.css" rel="stylesheet"> -<link href="css/staticdocs.css" rel="stylesheet"> - -<!--[if lt IE 9]> - <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script> -<![endif]--> - -<script type="text/x-mathjax-config"> - MathJax.Hub.Config({ - tex2jax: { - inlineMath: [ ['$','$'], ["\\(","\\)"] ], - processEscapes: true - } - }); -</script> -<script type="text/javascript" - src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"> -</script> - </head> - - <body> - <div class="navbar"> - <div class="navbar-inner"> - <div class="container"> - <a class="brand" href="index.html">mkin 0.9.44.9000</a> - <div class="nav"> - <ul class="nav"> - <li><a href="index.html">Home</a></li> - <li><a href="reference.html">Reference</a></li> - </ul> - </div> - </div> - </div> -</div> - - - <div class="container"> - <header> - - </header> - - <div class="row"> - <div class="span8"> - <h2>Function reference</h2> - - <h3>Main functions</h3> - <p>Essential functionality</p> - - - <ul class="index"> - - <li> - <code><a href="mkinmod.html">mkinmod</a></code><br /> - Function to set up a kinetic model with one or more state variables -</li> - - <li> - <code><a href="mkinfit.html">mkinfit</a></code><br /> - Fit a kinetic model to data with one or more state variables -</li> - - <li> - <code><a href="mmkin.html">mmkin</a></code><br /> - Fit one or more kinetic models with one or more state variables to one or more datasets -</li> - - </ul> - <h3>Show results</h3> - <p>Functions working on mkinfit objects</p> - - - <ul class="index"> - - <li> - <code><a href="plot.mkinfit.html">plot.mkinfit</a></code>(plot_sep)<br /> - Plot the observed data and the fitted model of an mkinfit object -</li> - - <li> - <code><a href="summary.mkinfit.html">summary.mkinfit</a></code>(print.summary.mkinfit)<br /> - Summary method for class "mkinfit" -</li> - - <li> - <code><a href="mkinresplot.html">mkinresplot</a></code><br /> - Function to plot residuals stored in an mkin object -</li> - - <li> - <code><a href="mkinparplot.html">mkinparplot</a></code><br /> - Function to plot the confidence intervals obtained using - <code><a href='mkinfit.html'>mkinfit</a></code> -</li> - - <li> - <code><a href="endpoints.html">endpoints</a></code><br /> -Function to calculate endpoints for further use from kinetic models fitted with mkinfit -</li> - - <li> - <code><a href="mkinerrmin.html">mkinerrmin</a></code><br /> -Calculate the minimum error to assume in order to pass the variance test -</li> - - </ul> - <h3>Work with mmkin objects</h3> - <p>Functions working with aggregated results</p> - - - <ul class="index"> - - <li> - <code><a href="Extract.mmkin.html">[.mmkin</a></code><br />Subsetting method for mmkin objects</li> - - <li> - <code><a href="plot.mmkin.html">plot.mmkin</a></code><br /> - Plot model fits (observed and fitted) and the residuals for a row or column of an mmkin object -</li> - - </ul> - <h3>Datasets and known results</h3> - - - <ul class="index"> - - <li> - <code><a href="FOCUS_2006_datasets.html">FOCUS_2006_datasets</a></code>(FOCUS_2006_A, FOCUS_2006_B, FOCUS_2006_C, FOCUS_2006_D, FOCUS_2006_E, FOCUS_2006_F)<br /> -Datasets A to F from the FOCUS Kinetics report from 2006 -</li> - - <li> - <code><a href="FOCUS_2006_SFO_ref_A_to_F.html">FOCUS_2006_SFO_ref_A_to_F</a></code><br /> -Results of fitting the SFO model to Datasets A to F of FOCUS (2006) -</li> - - <li> - <code><a href="FOCUS_2006_FOMC_ref_A_to_F.html">FOCUS_2006_FOMC_ref_A_to_F</a></code><br /> -Results of fitting the FOMC model to Datasets A to F of FOCUS (2006) -</li> - - <li> - <code><a href="FOCUS_2006_HS_ref_A_to_F.html">FOCUS_2006_HS_ref_A_to_F</a></code><br /> -Results of fitting the HS model to Datasets A to F of FOCUS (2006) -</li> - - <li> - <code><a href="FOCUS_2006_DFOP_ref_A_to_B.html">FOCUS_2006_DFOP_ref_A_to_B</a></code><br /> -Results of fitting the DFOP model to Datasets A to B of FOCUS (2006) -</li> - - <li> - <code><a href="mccall81_245T.html">mccall81_245T</a></code><br /> - Datasets on aerobic soil metabolism of 2,4,5-T in six soils -</li> - - <li> - <code><a href="schaefer07_complex_case.html">schaefer07_complex_case</a></code>(schaefer07_complex_results)<br /> - Metabolism data set used for checking the software quality of KinGUI -</li> - - <li> - <code><a href="synthetic_data_for_UBA.html">synthetic_data_for_UBA_2014</a></code><br /> - Synthetic datasets for one parent compound with two metabolites -</li> - - </ul> - <h3>Helper functions</h3> - - - <ul class="index"> - - <li> - <code><a href="mkin_wide_to_long.html">mkin_wide_to_long</a></code><br /> - Convert a dataframe with observations over time into long format -</li> - - <li> - <code><a href="mkin_long_to_wide.html">mkin_long_to_wide</a></code><br /> - Convert a dataframe from long to wide format -</li> - - <li> - <code><a href="mkinsub.html">mkinsub</a></code><br /> - Function to set up a kinetic submodel for one state variable -</li> - - <li> - <code><a href="mkinds.html">mkinds</a></code><br />A dataset class for mkin</li> - - <li> - <code><a href="print.mkinds.html">print.mkinds</a></code><br /> - Print mkinds objects -</li> - - <li> - <code><a href="print.mkinmod.html">print.mkinmod</a></code><br /> - Print mkinmod objects -</li> - - <li> - <code><a href="mkinpredict.html">mkinpredict</a></code><br /> - Produce predictions from a kinetic model using specific parameters -</li> - - <li> - <code><a href="transform_odeparms.html">transform_odeparms</a></code>(backtransform_odeparms)<br /> - Functions to transform and backtransform kinetic parameters for fitting -</li> - - <li> - <code><a href="ilr.html">ilr</a></code>(invilr)<br /> - Function to perform isometric log-ratio transformation -</li> - - <li> - <code><a href="geometric_mean.html">geometric_mean</a></code><br /> Calculate the geometric mean </li> - - </ul> - <h3>Analytical solutions</h3> - <p>Parent only model solutions</p> - - - <ul class="index"> - - <li> - <code><a href="SFO.solution.html">SFO.solution</a></code><br /> Single First-Order kinetics </li> - - <li> - <code><a href="FOMC.solution.html">FOMC.solution</a></code><br /> First-Order Multi-Compartment kinetics </li> - - <li> - <code><a href="DFOP.solution.html">DFOP.solution</a></code><br /> -Double First-Order in Parallel kinetics -</li> - - <li> - <code><a href="SFORB.solution.html">SFORB.solution</a></code><br /> Single First-Order Reversible Binding kinetics </li> - - <li> - <code><a href="HS.solution.html">HS.solution</a></code><br /> Hockey-Stick kinetics </li> - - <li> - <code><a href="IORE.solution.html">IORE.solution</a></code><br /> Indeterminate order rate equation kinetics </li> - - </ul> - <h3>Deprecated functions</h3> - <p>Functions that have been superseeded</p> - - - <ul class="index"> - - <li> - <code><a href="mkinplot.html">mkinplot</a></code><br /> - Plot the observed data and the fitted model of an mkinfit object -</li> - - </ul> - <h3>Other</h3> - - - <ul class="index"> - - <li> - <code><a href="add_err.html">add_err</a></code><br /> - Add normally distributed errors to simulated kinetic degradation data -</li> - - </ul> - </div> -</div> - - <footer> - <p class="pull-right"><a href="#">Back to top</a></p> -<p>Built by <a href="https://github.com/hadley/staticdocs">staticdocs</a>. Styled with <a href="https://getbootstrap.com/2.0.4/">bootstrap</a>.</p> - </footer> - </div> - </body> -</html>
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