aboutsummaryrefslogblamecommitdiff
path: root/docs/reference/index.html
blob: 24f3df0ce3c454b4be26cb9e63303900225e2051 (plain) (tree)
1
2
3
4
5
6
7
8
9

                                                  
                




                                                                      
                                          

               
                                                                                                                                                                                 
                  
 

                                                                                                                                                                                                             

                           
                                                                                                                                                                                                           
 
                     
                                                                                                                                                                                          
 


                                                                                                                                                                                         


                                             


 
                                                         


 
                

                                                                                                                                                                                                    




                                                                               

 


         
                                                    
              
                                                                            

                               

                                                                                                                               



                                      

                                                            
                                                                                                                                        
             
          
 


                                                      
                                                          
     
















                                                                                                 
                                                                                                   

         
                                                                                                                             
         


                                                                                                      
       
     


                                       
           
      
                                              
        
           
      


                                
 


               

                                 
                             
                        

          
                             
 




                           
 
























                                                                                                                                    





                                                                         











































                                                                                                                                                                                       





                                                                                               



















                                                                                                                                                               





                                                                                     










































































































































                                                                                                                                                                        
                                                                               
             
                                                 




                                                                           
                                                                             











































                                                                                                                                                      





                                                                                       






























                                                                                                                                                                           
        





                                                                   



                                                                                           
                                                                                             
                                                                               

         


              
                             
                                     


                     
                                                                                
      


               

  

         
 
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
<html lang="en">
  <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://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->

<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>

<!-- Font Awesome icons -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous" />

<!-- clipboard.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" 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://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></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" aria-expanded="false">
        <span class="sr-only">Toggle navigation</span>
        <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="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.48.1</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/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
    </li>
    <li>
      <a href="../articles/web_only/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><tr>
        
        <td>
          <p><code><a href="nafta.html">nafta()</a></code> </p>
        </td>
        <td><p>Evaluate parent kinetics using the NAFTA guidance</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>&lt;mkinfit&gt;</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>&lt;mkinfit&gt;</i>)</a></code> <code><a href="summary.mkinfit.html">print(<i>&lt;summary.mkinfit&gt;</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><tr>
        
        <td>
          <p><code><a href="logLik.mkinfit.html">logLik(<i>&lt;mkinfit&gt;</i>)</a></code> </p>
        </td>
        <td><p>Calculated the log-likelihood of a fitted mkinfit object</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>&lt;mmkin&gt;</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>&lt;mmkin&gt;</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><tr>
        
        <td>
          <p><code><a href="AIC.mmkin.html">AIC(<i>&lt;mmkin&gt;</i>)</a></code> </p>
        </td>
        <td><p>Calculated the AIC for a 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>&lt;mkinds&gt;</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>&lt;mkinmod&gt;</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><tr>
        
        <td>
          <p><code><a href="CAKE_export.html">CAKE_export()</a></code> </p>
        </td>
        <td><p>Export a list of datasets format to a CAKE study file</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><tr>
        
        <td>
          <p><code><a href="logistic.solution.html">logistic.solution()</a></code> </p>
        </td>
        <td><p>Logistic 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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
      </footer>
   </div>

  

  </body>
</html>

Contact - Imprint