path: root/docs/reference/summary.mkinfit.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>Summary method for class "mkinfit" — summary.mkinfit • 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">


<!-- 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-topic">
      <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/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">
        <li>
  <a href="http://github.com/jranke/mkin">
    <span class="fa fa-github fa-lg"></span>
     
  </a>
</li>
      </ul>
    </div><!--/.nav-collapse -->
  </div><!--/.container -->
</div><!--/.navbar -->

      
      </header>

      <div class="row">
  <div class="col-md-9 contents">
    <div class="page-header">
    <h1>Summary method for class "mkinfit"</h1>
    </div>

    
    <p>Lists model equations, the summary as returned by <code>summary.modFit</code>,
  the chi2 error levels calculated according to FOCUS guidance (2006) as far
  as defined therein, and optionally the data, consisting of observed, predicted
  and residual values.</p>
    

    <pre class="usage"><span class='co'># S3 method for mkinfit</span>
<span class='fu'>summary</span>(<span class='no'>object</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>distimes</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='no'>...</span>)
<span class='co'># S3 method for summary.mkinfit</span>
<span class='fu'>print</span>(<span class='no'>x</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fu'>max</span>(<span class='fl'>3</span>, <span class='fu'>getOption</span>(<span class='st'>"digits"</span>) - <span class='fl'>3</span>), <span class='no'>...</span>)</pre>
    
    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
    <table class="ref-arguments">
    <colgroup><col class="name" /><col class="desc" /></colgroup>
    <tr>
      <th>object</th>
      <td><p>an object of class <code><a href='mkinfit.html'>mkinfit</a></code>.</p></td>
    </tr>
    <tr>
      <th>x</th>
      <td><p>an object of class <code>summary.mkinfit</code>.</p></td>
    </tr>
    <tr>
      <th>data</th>
      <td><p>logical, indicating whether the data should be included in the summary.</p></td>
    </tr>
    <tr>
      <th>distimes</th>
      <td><p>logical, indicating whether DT50 and DT90 values should be included.</p></td>
    </tr>
    <tr>
      <th>alpha</th>
      <td><p>error level for confidence interval estimation from t distribution</p></td>
    </tr>
    <tr>
      <th>digits</th>
      <td><p>Number of digits to use for printing</p></td>
    </tr>
    <tr>
      <th>&#8230;</th>
      <td><p>optional arguments passed to methods like <code>print</code>.</p></td>
    </tr>
    </table>
    
    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>

    <p>The summary function returns a list derived from
  <code>summary.modFit</code>, with components, among others</p>
<dt>version, Rversion</dt><dd><p>The mkin and R versions used</p></dd>
  <dt>date.fit, date.summary</dt><dd><p>The dates where the fit and the summary were produced</p></dd>
  <dt>use_of_ff</dt><dd><p>Was maximum or minimum use made of formation fractions</p></dd>
  <dt>residuals, residualVariance, sigma, modVariance, df</dt><dd><p>As in summary.modFit</p></dd>
  <dt>cov.unscaled, cov.scaled, info, niter, stopmess, par</dt><dd><p>As in summary.modFit</p></dd>
  <dt>bpar</dt><dd><p>Optimised and backtransformed parameters</p></dd>
  <dt>diffs </dt><dd><p>The differential equations used in the model</p></dd>
  <dt>data </dt><dd><p>The data (see Description above).</p></dd>
  <dt>start </dt><dd><p>The starting values and bounds, if applicable, for optimised parameters.</p></dd>
  <dt>fixed </dt><dd><p>The values of fixed parameters.</p></dd>
  <dt>errmin </dt><dd><p>The chi2 error levels for each observed variable.</p></dd>
  <dt>bparms.ode </dt><dd><p>All backtransformed ODE parameters, for use as starting parameters for
    related models.</p></dd>
  <dt>ff </dt><dd><p>The estimated formation fractions derived from the fitted model.</p></dd>
  <dt>distimes </dt><dd><p>The DT50 and DT90 values for each observed variable.</p></dd>
  <dt>SFORB</dt><dd><p>If applicable, eigenvalues of SFORB components of the model.</p></dd>
  The print method is called for its side effect, i.e. printing the summary.

    
    <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>

    <p>FOCUS (2006) &#8220;Guidance Document on Estimating Persistence and
  Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
  Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
  EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
  <a href = 'http://esdac.jrc.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.europa.eu/projects/degradation-kinetics</a></p>
    

    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
    <pre class="examples"><div class='input'>  <span class='fu'>summary</span>(<span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>)), <span class='no'>FOCUS_2006_A</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#&gt; mkin version:    0.9.45.2 
#&gt; R version:       3.4.0 
#&gt; Date of fit:     Fri May  5 12:46:20 2017 
#&gt; Date of summary: Fri May  5 12:46:20 2017 
#&gt; 
#&gt; Equations:
#&gt; d_parent/dt = - k_parent_sink * parent
#&gt; 
#&gt; Model predictions using solution type analytical 
#&gt; 
#&gt; Fitted with method Port using 35 model solutions performed in 0.082 s
#&gt; 
#&gt; Weighting: none
#&gt; 
#&gt; Starting values for parameters to be optimised:
#&gt;                value   type
#&gt; parent_0      101.24  state
#&gt; k_parent_sink   0.10 deparm
#&gt; 
#&gt; Starting values for the transformed parameters actually optimised:
#&gt;                        value lower upper
#&gt; parent_0          101.240000  -Inf   Inf
#&gt; log_k_parent_sink  -2.302585  -Inf   Inf
#&gt; 
#&gt; Fixed parameter values:
#&gt; None
#&gt; 
#&gt; Optimised, transformed parameters with symmetric confidence intervals:
#&gt;                   Estimate Std. Error  Lower   Upper
#&gt; parent_0           109.200     4.3910 98.410 119.900
#&gt; log_k_parent_sink   -3.291     0.1152 -3.573  -3.009
#&gt; 
#&gt; Parameter correlation:
#&gt;                   parent_0 log_k_parent_sink
#&gt; parent_0             1.000             0.575
#&gt; log_k_parent_sink    0.575             1.000
#&gt; 
#&gt; Residual standard error: 6.08 on 6 degrees of freedom
#&gt; 
#&gt; Backtransformed parameters:
#&gt; Confidence intervals for internally transformed parameters are asymmetric.
#&gt; t-test (unrealistically) based on the assumption of normal distribution
#&gt; for estimators of untransformed parameters.
#&gt;                Estimate t value    Pr(&gt;t)    Lower     Upper
#&gt; parent_0      109.20000  24.860 1.394e-07 98.41000 119.90000
#&gt; k_parent_sink   0.03722   8.679 6.457e-05  0.02807   0.04934
#&gt; 
#&gt; Chi2 error levels in percent:
#&gt;          err.min n.optim df
#&gt; All data   8.385       2  6
#&gt; parent     8.385       2  6
#&gt; 
#&gt; Resulting formation fractions:
#&gt;             ff
#&gt; parent_sink  1
#&gt; 
#&gt; Estimated disappearance times:
#&gt;         DT50  DT90
#&gt; parent 18.62 61.87
#&gt; 
#&gt; Data:
#&gt;  time variable observed predicted residual
#&gt;     0   parent   101.24   109.153  -7.9132
#&gt;     3   parent    99.27    97.622   1.6484
#&gt;     7   parent    90.11    84.119   5.9913
#&gt;    14   parent    72.19    64.826   7.3641
#&gt;    30   parent    29.71    35.738  -6.0283
#&gt;    62   parent     5.98    10.862  -4.8818
#&gt;    90   parent     1.54     3.831  -2.2911
#&gt;   118   parent     0.39     1.351  -0.9613</div></pre>
  </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="#arguments">Arguments</a></li>
      
      <li><a href="#value">Value</a></li>

      <li><a href="#references">References</a></li>
      
      <li><a href="#examples">Examples</a></li>
    </ul>

    <h2>Author</h2>
    
  Johannes Ranke

  </div>
</div>

      <footer>
      <div class="copyright">
  <p>Developed by Johannes Ranke.</p>
</div>

<div class="pkgdown">
  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
</div>

      </footer>
   </div>

  </body>
</html>