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<meta property="og:description" content="Lists model equations, initial parameter values, optimised parameters with some
uncertainty statistics, the chi2 error levels calculated according to FOCUS
guidance (2006) as defined therein, formation fractions, DT50 values and
optionally the data, consisting of observed, predicted and residual values." />
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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, initial parameter values, optimised parameters with some
uncertainty statistics, the chi2 error levels calculated according to FOCUS
guidance (2006) as defined therein, formation fractions, DT50 values 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'><a href='https://rdrr.io/r/base/summary.html'>summary</a></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'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>x</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Extremes.html'>max</a></span>(<span class='fl'>3</span>, <span class='fu'><a href='https://rdrr.io/r/base/options.html'>getOption</a></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 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>errparms </dt><dd><p>Error model parameters.</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'><a href='https://rdrr.io/r/base/summary.html'>summary</a></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: 0.9.49.6
#> R version used for fitting: 3.6.1
#> Date of fit: Wed Sep 18 17:54:50 2019
#> Date of summary: Wed Sep 18 17:54:50 2019
#>
#> Equations:
#> d_parent/dt = - k_parent_sink * parent
#>
#> Model predictions using solution type analytical
#>
#> Fitted using 131 model solutions performed in 0.27 s
#>
#> Error model: Constant variance
#>
#> Error model algorithm: OLS
#>
#> Starting values for parameters to be optimised:
#> value type
#> parent_0 101.240000 state
#> k_parent_sink 0.100000 deparm
#> sigma 5.265546 error
#>
#> 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
#> sigma 5.265546 0 Inf
#>
#> Fixed parameter values:
#> None
#>
#> Optimised, transformed parameters with symmetric confidence intervals:
#> Estimate Std. Error Lower Upper
#> parent_0 109.200 3.70400 99.630 118.700
#> log_k_parent_sink -3.291 0.09176 -3.527 -3.055
#> sigma 5.266 1.31600 1.882 8.649
#>
#> Parameter correlation:
#> parent_0 log_k_parent_sink sigma
#> parent_0 1.000e+00 5.428e-01 1.648e-07
#> log_k_parent_sink 5.428e-01 1.000e+00 2.513e-07
#> sigma 1.648e-07 2.513e-07 1.000e+00
#>
#> 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 29.47 4.218e-07 99.6300 118.70000
#> k_parent_sink 0.03722 10.90 5.650e-05 0.0294 0.04712
#> sigma 5.26600 4.00 5.162e-03 1.8820 8.64900
#>
#> FOCUS 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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<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>
<p>Johannes Ranke</p>
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