<!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>