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diff --git a/docs/reference.html b/docs/reference.html new file mode 100644 index 00000000..df1bd9a8 --- /dev/null +++ b/docs/reference.html @@ -0,0 +1,288 @@ +<!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>. 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