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<h1>Summary method for class "mkinfit"</h1>
<small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/summary.mkinfit.R" class="external-link"><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>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for mkinfit</span></span>
<span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">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>
<span></span>
<span><span class="co"># S3 method for summary.mkinfit</span></span>
<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">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" class="external-link">max</a></span><span class="op">(</span><span class="fl">3</span>, <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">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></span></code></pre></div>
</div>
<div id="arguments">
<h2>Arguments</h2>
<dl><dt>object</dt>
<dd><p>an object of class <a href="mkinfit.html">mkinfit</a>.</p></dd>
<dt>data</dt>
<dd><p>logical, indicating whether the data should be included in the
summary.</p></dd>
<dt>distimes</dt>
<dd><p>logical, indicating whether DT50 and DT90 values should be
included.</p></dd>
<dt>alpha</dt>
<dd><p>error level for confidence interval estimation from t
distribution</p></dd>
<dt>...</dt>
<dd><p>optional arguments passed to methods like <code>print</code>.</p></dd>
<dt>x</dt>
<dd><p>an object of class <code>summary.mkinfit</code>.</p></dd>
<dt>digits</dt>
<dd><p>Number of digits to use for printing</p></dd>
</dl></div>
<div id="value">
<h2>Value</h2>
<p>The summary function returns a list with components, among others</p>
<dl><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 and fractional eigenvector component
g of SFORB systems in the model.</p></dd>
</dl><p>The print method is called for its side effect, i.e. printing the summary.</p>
</div>
<div id="references">
<h2>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" class="external-link">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
</div>
<div id="author">
<h2>Author</h2>
<p>Johannes Ranke</p>
</div>
<div id="ref-examples">
<h2>Examples</h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</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></span></span>
<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.2.6 </span>
<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.3.1 </span>
<span class="r-out co"><span class="r-pr">#></span> Date of fit: Mon Oct 30 09:39:49 2023 </span>
<span class="r-out co"><span class="r-pr">#></span> Date of summary: Mon Oct 30 09:39:49 2023 </span>
<span class="r-out co"><span class="r-pr">#></span> </span>
<span class="r-out co"><span class="r-pr">#></span> Equations:</span>
<span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - k_parent * parent</span>
<span class="r-out co"><span class="r-pr">#></span> </span>
<span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type analytical </span>
<span class="r-out co"><span class="r-pr">#></span> </span>
<span class="r-out co"><span class="r-pr">#></span> Fitted using 131 model solutions performed in 0.02 s</span>
<span class="r-out co"><span class="r-pr">#></span> </span>
<span class="r-out co"><span class="r-pr">#></span> Error model: Constant variance </span>
<span class="r-out co"><span class="r-pr">#></span> </span>
<span class="r-out co"><span class="r-pr">#></span> Error model algorithm: OLS </span>
<span class="r-out co"><span class="r-pr">#></span> </span>
<span class="r-out co"><span class="r-pr">#></span> Starting values for parameters to be optimised:</span>
<span class="r-out co"><span class="r-pr">#></span> value type</span>
<span class="r-out co"><span class="r-pr">#></span> parent_0 101.24 state</span>
<span class="r-out co"><span class="r-pr">#></span> k_parent 0.10 deparm</span>
<span class="r-out co"><span class="r-pr">#></span> </span>
<span class="r-out co"><span class="r-pr">#></span> Starting values for the transformed parameters actually optimised:</span>
<span class="r-out co"><span class="r-pr">#></span> value lower upper</span>
<span class="r-out co"><span class="r-pr">#></span> parent_0 101.240000 -Inf Inf</span>
<span class="r-out co"><span class="r-pr">#></span> log_k_parent -2.302585 -Inf Inf</span>
<span class="r-out co"><span class="r-pr">#></span> </span>
<span class="r-out co"><span class="r-pr">#></span> Fixed parameter values:</span>
<span class="r-out co"><span class="r-pr">#></span> None</span>
<span class="r-out co"><span class="r-pr">#></span> </span>
<span class="r-out co"><span class="r-pr">#></span> Results:</span>
<span class="r-out co"><span class="r-pr">#></span> </span>
<span class="r-out co"><span class="r-pr">#></span> AIC BIC logLik</span>
<span class="r-out co"><span class="r-pr">#></span> 55.28197 55.5203 -24.64099</span>
<span class="r-out co"><span class="r-pr">#></span> </span>
<span class="r-out co"><span class="r-pr">#></span> Optimised, transformed parameters with symmetric confidence intervals:</span>
<span class="r-out co"><span class="r-pr">#></span> Estimate Std. Error Lower Upper</span>
<span class="r-out co"><span class="r-pr">#></span> parent_0 109.200 3.70400 99.630 118.700</span>
<span class="r-out co"><span class="r-pr">#></span> log_k_parent -3.291 0.09176 -3.527 -3.055</span>
<span class="r-out co"><span class="r-pr">#></span> sigma 5.266 1.31600 1.882 8.649</span>
<span class="r-out co"><span class="r-pr">#></span> </span>
<span class="r-out co"><span class="r-pr">#></span> Parameter correlation:</span>
<span class="r-out co"><span class="r-pr">#></span> parent_0 log_k_parent sigma</span>
<span class="r-out co"><span class="r-pr">#></span> parent_0 1.000e+00 5.428e-01 1.642e-07</span>
<span class="r-out co"><span class="r-pr">#></span> log_k_parent 5.428e-01 1.000e+00 2.507e-07</span>
<span class="r-out co"><span class="r-pr">#></span> sigma 1.642e-07 2.507e-07 1.000e+00</span>
<span class="r-out co"><span class="r-pr">#></span> </span>
<span class="r-out co"><span class="r-pr">#></span> Backtransformed parameters:</span>
<span class="r-out co"><span class="r-pr">#></span> Confidence intervals for internally transformed parameters are asymmetric.</span>
<span class="r-out co"><span class="r-pr">#></span> t-test (unrealistically) based on the assumption of normal distribution</span>
<span class="r-out co"><span class="r-pr">#></span> for estimators of untransformed parameters.</span>
<span class="r-out co"><span class="r-pr">#></span> Estimate t value Pr(>t) Lower Upper</span>
<span class="r-out co"><span class="r-pr">#></span> parent_0 109.20000 29.47 4.218e-07 99.6300 118.70000</span>
<span class="r-out co"><span class="r-pr">#></span> k_parent 0.03722 10.90 5.650e-05 0.0294 0.04712</span>
<span class="r-out co"><span class="r-pr">#></span> sigma 5.26600 4.00 5.162e-03 1.8820 8.64900</span>
<span class="r-out co"><span class="r-pr">#></span> </span>
<span class="r-out co"><span class="r-pr">#></span> FOCUS Chi2 error levels in percent:</span>
<span class="r-out co"><span class="r-pr">#></span> err.min n.optim df</span>
<span class="r-out co"><span class="r-pr">#></span> All data 8.385 2 6</span>
<span class="r-out co"><span class="r-pr">#></span> parent 8.385 2 6</span>
<span class="r-out co"><span class="r-pr">#></span> </span>
<span class="r-out co"><span class="r-pr">#></span> Estimated disappearance times:</span>
<span class="r-out co"><span class="r-pr">#></span> DT50 DT90</span>
<span class="r-out co"><span class="r-pr">#></span> parent 18.62 61.87</span>
<span class="r-out co"><span class="r-pr">#></span> </span>
<span class="r-out co"><span class="r-pr">#></span> Data:</span>
<span class="r-out co"><span class="r-pr">#></span> time variable observed predicted residual</span>
<span class="r-out co"><span class="r-pr">#></span> 0 parent 101.24 109.153 -7.9132</span>
<span class="r-out co"><span class="r-pr">#></span> 3 parent 99.27 97.622 1.6484</span>
<span class="r-out co"><span class="r-pr">#></span> 7 parent 90.11 84.119 5.9913</span>
<span class="r-out co"><span class="r-pr">#></span> 14 parent 72.19 64.826 7.3641</span>
<span class="r-out co"><span class="r-pr">#></span> 30 parent 29.71 35.738 -6.0283</span>
<span class="r-out co"><span class="r-pr">#></span> 62 parent 5.98 10.862 -4.8818</span>
<span class="r-out co"><span class="r-pr">#></span> 90 parent 1.54 3.831 -2.2911</span>
<span class="r-out co"><span class="r-pr">#></span> 118 parent 0.39 1.351 -0.9613</span>
<span class="r-in"><span></span></span>
</code></pre></div>
</div>
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