blob: af7642e67363c631281d6a543b78e2cc7ef592e4 (
plain) (
tree)
|
|
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Function reference • mkin</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
<!-- 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="../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>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
<![endif]-->
</head>
<body>
<div class="container template-reference-index">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<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">0.9.47.3</span>
</span>
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
<a href="../reference/index.html">Functions and data</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
Articles
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="../articles/mkin.html">Introduction to mkin</a>
</li>
<li>
<a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a>
</li>
<li>
<a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
</li>
<li>
<a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
</li>
<li>
<a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
</li>
<li>
<a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
</li>
</ul>
</li>
<li>
<a href="../news/index.html">News</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
</header>
<div class="row">
<div class="contents col-md-9">
<div class="page-header">
<h1>Reference</h1>
</div>
<table class="ref-index">
<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(<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_twocomp.html">sigma_twocomp()</a></code> </p>
</td>
<td><p>Two component error model</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">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#section-main-functions">Main functions</a></li>
<li><a href="#section-show-results">Show results</a></li>
<li><a href="#section-work-with-mmkin-objects">Work with mmkin objects</a></li>
<li><a href="#section-datasets-and-known-results">Datasets and known results</a></li>
<li><a href="#section-helper-functions">Helper functions</a></li>
<li><a href="#section-analytical-solutions">Analytical solutions</a></li>
<li><a href="#section-generate-synthetic-datasets">Generate synthetic datasets</a></li>
<li><a href="#section-deprecated-functions">Deprecated functions</a></li>
</ul>
</div>
</div>
<footer>
<div class="copyright">
<p>Developed by Johannes Ranke.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
</div>
</footer>
</div>
</body>
</html>
|
