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<title>Summary method for class "mkinfit" — summary.mkinfit • mkin</title>
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<meta property="og:description" content="Lists model equations, the summary as returned by summary.modFit,
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<h1>Summary method for class "mkinfit"</h1>
<div class="hidden name"><code>summary.mkinfit.Rd</code></div>
</div>
<div class="ref-description">
<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>
</div>
<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>…</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) “Guidance Document on Estimating Persistence and
Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
Registration” 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.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.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'>#> mkin version used for fitting: 0.9.47.5
#> R version used for fitting: 3.5.1
#> Date of fit: Fri Sep 14 16:54:36 2018
#> Date of summary: Fri Sep 14 16:54:36 2018
#>
#> Equations:
#> d_parent/dt = - k_parent_sink * parent
#>
#> Model predictions using solution type analytical
#>
#> Fitted with method Port using 35 model solutions performed in 0.077 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(>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>
</div>
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<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
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