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<h1>Summary method for class "mkinfit"</h1>
<small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/summary.mkinfit.R'><code>R/summary.mkinfit.R</code></a></small>
<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='op'>(</span><span class='va'>object</span>, data <span class='op'>=</span> <span class='cn'>TRUE</span>, distimes <span class='op'>=</span> <span class='cn'>TRUE</span>, alpha <span class='op'>=</span> <span class='fl'>0.05</span>, <span class='va'>...</span><span class='op'>)</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='op'>(</span><span class='va'>x</span>, digits <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Extremes.html'>max</a></span><span class='op'>(</span><span class='fl'>3</span>, <span class='fu'><a href='https://rdrr.io/r/base/options.html'>getOption</a></span><span class='op'>(</span><span class='st'>"digits"</span><span class='op'>)</span> <span class='op'>-</span> <span class='fl'>3</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</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>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>...</th>
<td><p>optional arguments passed to methods like <code>print</code>.</p></td>
</tr>
<tr>
<th>x</th>
<td><p>an object of class <code>summary.mkinfit</code>.</p></td>
</tr>
<tr>
<th>digits</th>
<td><p>Number of digits to use for printing</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>diffs</dt><dd><p>The differential equations used in the model</p></dd>
<dt>use_of_ff</dt><dd><p>Was maximum or minimum use made of formation fractions</p></dd>
<dt>bpar</dt><dd><p>Optimised and backtransformed
parameters</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="author"><a class="anchor" href="#author"></a>Author</h2>
<p>Johannes Ranke</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='op'>(</span><span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span>, <span class='va'>FOCUS_2006_A</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span><span class='op'>)</span>
</div><div class='output co'>#> mkin version used for fitting: 1.0.0
#> R version used for fitting: 4.0.3
#> Date of fit: Wed Feb 3 17:32:02 2021
#> Date of summary: Wed Feb 3 17:32:02 2021
#>
#> Equations:
#> d_parent/dt = - k_parent * parent
#>
#> Model predictions using solution type analytical
#>
#> Fitted using 131 model solutions performed in 0.028 s
#>
#> Error model: Constant variance
#>
#> Error model algorithm: OLS
#>
#> Starting values for parameters to be optimised:
#> value type
#> parent_0 101.24 state
#> k_parent 0.10 deparm
#>
#> Starting values for the transformed parameters actually optimised:
#> value lower upper
#> parent_0 101.240000 -Inf Inf
#> log_k_parent -2.302585 -Inf Inf
#>
#> Fixed parameter values:
#> None
#>
#> Results:
#>
#> AIC BIC logLik
#> 55.28197 55.5203 -24.64099
#>
#> 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 -3.291 0.09176 -3.527 -3.055
#> sigma 5.266 1.31600 1.882 8.649
#>
#> Parameter correlation:
#> parent_0 log_k_parent sigma
#> parent_0 1.000e+00 5.428e-01 1.642e-07
#> log_k_parent 5.428e-01 1.000e+00 2.507e-07
#> sigma 1.642e-07 2.507e-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 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
#>
#> 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><div class='input'>
</div></pre>
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