<!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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