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<title>summary.mkinfit. mkin 0.9-41</title>
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  Johannes Ranke
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      <h1>
  Summary method for class "mkinfit"
</h1>

<div class="row">
  <div class="span8">
    <h2>Usage</h2>
    <pre><div>"summary"(object, data&nbsp;=&nbsp;TRUE, distimes&nbsp;=&nbsp;TRUE, alpha&nbsp;=&nbsp;0.05, ...)
"print"(x, digits&nbsp;=&nbsp;max(3, getOption("digits") - 3), ...)</div></pre>
    
    <h2>Arguments</h2>
    <dl>
      <dt>object</dt>
      <dd>
  an object of class <code><a href='mkinfit.html'>mkinfit</a></code>.
</dd>
      <dt>x</dt>
      <dd>
  an object of class <code>summary.mkinfit</code>.
</dd>
      <dt>data</dt>
      <dd>
  logical, indicating whether the data should be included in the summary. 
</dd>
      <dt>distimes</dt>
      <dd>
  logical, indicating whether DT50 and DT90 values should be included.
</dd>
      <dt>alpha</dt>
      <dd>
  error level for confidence interval estimation from t distribution
</dd>
      <dt>digits</dt>
      <dd>
  Number of digits to use for printing
</dd>
      <dt>...</dt>
      <dd>
  optional arguments passed to methods like <code>print</code>.
</dd>
    </dl>
    
    <div class="Description">
      <h2>Description</h2>

      <p>Lists model equations, the summary as returned by <code><a href='http://www.inside-r.org/packages/cran/FME/docs/modFit'>summary.modFit</a></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>
  
    </div>

    <div class="Value">
      <h2>Value</h2>

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

    <div class="References">
      <h2>References</h2>

      <p>FOCUS (2006) &#147;Guidance Document on Estimating Persistence and
  Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
  Registration&#148; Report of the FOCUS Work Group on Degradation Kinetics,
  EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
  <a href = 'http://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p>
  
    </div>
    
    <h2 id="examples">Examples</h2>
    <pre class="examples"><div class='input'>  summary(mkinfit(mkinmod(parent = list(type = &quot;SFO&quot;)), FOCUS_2006_A, quiet = TRUE))
</div>
<div class='output'>mkin version:    0.9.41 
R version:       3.2.2 
Date of fit:     Mon Nov  9 09:06:13 2015 
Date of summary: Mon Nov  9 09:06:13 2015 

Equations:
d_parent = - k_parent_sink * parent

Model predictions using solution type analytical 

Fitted with method Port using 35 model solutions performed in 0.1 s

Weighting: none

Starting values for parameters to be optimised:
               value   type
parent_0      101.24  state
k_parent_sink   0.10 deparm

Starting values for the transformed parameters actually optimised:
                       value lower upper
parent_0          101.240000  -Inf   Inf
log_k_parent_sink  -2.302585  -Inf   Inf

Fixed parameter values:
None

Optimised, transformed parameters with symmetric confidence intervals:
                  Estimate Std. Error  Lower   Upper
parent_0           109.200     4.3910 98.410 119.900
log_k_parent_sink   -3.291     0.1152 -3.573  -3.009

Parameter correlation:
                  parent_0 log_k_parent_sink
parent_0             1.000             0.575
log_k_parent_sink    0.575             1.000

Residual standard error: 6.08 on 6 degrees of freedom

Backtransformed parameters:
Confidence intervals for internally transformed parameters are asymmetric.
t-test (unrealistically) based on the assumption of normal distribution
for estimators of untransformed parameters.
               Estimate t value    Pr(&gt;t)    Lower     Upper
parent_0      109.20000  24.860 1.394e-07 98.41000 119.90000
k_parent_sink   0.03722   8.679 6.457e-05  0.02807   0.04934

Chi2 error levels in percent:
         err.min n.optim df
All data   8.385       2  6
parent     8.385       2  6

Resulting formation fractions:
            ff
parent_sink  1

Estimated disappearance times:
        DT50  DT90
parent 18.62 61.87

Data:
 time variable observed predicted residual
    0   parent   101.24   109.153  -7.9132
    3   parent    99.27    97.622   1.6484
    7   parent    90.11    84.119   5.9913
   14   parent    72.19    64.826   7.3641
   30   parent    29.71    35.738  -6.0283
   62   parent     5.98    10.862  -4.8818
   90   parent     1.54     3.831  -2.2911
  118   parent     0.39     1.351  -0.9613
</div></pre>
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    <!-- <ul>
      <li>summary.mkinfit</li><li>print.summary.mkinfit</li>
    </ul>
    <ul>
      <li> utilities </li>
    </ul> -->
      
    
    <h2>Author</h2>
    
  Johannes Ranke

    
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