path: root/docs/reference/index.html



<!-- 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>

<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
  
  
<!-- 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>
      <a class="navbar-brand" href="../index.html">mkin</a>
    </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="col-md-9">
    <div class="page-header">
      <h1>
        Reference
        <small>version&nbsp;0.9.47.1</small>
      </h1>
    </div>

    <div class="contents">
      <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.mkinfit</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</a></code> <code><a href="summary.mkinfit.html">print</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">[.mmkin</a></code> </p>
          </td>
          <td><p>Subsetting method for mmkin objects</p></td>
        </tr><tr>
          <!--  -->
          <td>
            <p><code><a href="plot.mmkin.html">plot</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</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</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_rl.html">sigma_rl</a></code> </p>
          </td>
          <td><p>Two component error model of Rocke and Lorenzato</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>

  <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>