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  <main id="main" class="col-md-9"><div class="page-header">
      <img src="" class="logo" alt=""><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="d-none name"><code>summary.mkinfit.Rd</code></div>
    </div>

    <div class="ref-description section level2">
    <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 class="section level2">
    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
    <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 class="section level2">
    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></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 class="section level2">
    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></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 class="section level2">
    <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></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 class="section level2">
    <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2>
    <p>Johannes Ranke</p>
    </div>

    <div class="section level2">
    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></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">#&gt;</span> mkin version used for fitting:    1.2.6 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> R version used for fitting:       4.3.2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Date of fit:     Thu Nov 16 04:19:39 2023 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Thu Nov 16 04:19:39 2023 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Equations:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> d_parent/dt = - k_parent * parent</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Model predictions using solution type analytical </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Fitted using 131 model solutions performed in 0.009 s</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Error model: Constant variance </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Error model algorithm: OLS </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Starting values for parameters to be optimised:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>           value   type</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0 101.24  state</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k_parent   0.10 deparm</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Starting values for the transformed parameters actually optimised:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>                   value lower upper</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0     101.240000  -Inf   Inf</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> log_k_parent  -2.302585  -Inf   Inf</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Fixed parameter values:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> None</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Results:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span>        AIC     BIC    logLik</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>   55.28197 55.5203 -24.64099</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Optimised, transformed parameters with symmetric confidence intervals:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>              Estimate Std. Error  Lower   Upper</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0      109.200    3.70400 99.630 118.700</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> log_k_parent   -3.291    0.09176 -3.527  -3.055</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> sigma           5.266    1.31600  1.882   8.649</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Parameter correlation:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>               parent_0 log_k_parent     sigma</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0     1.000e+00    5.428e-01 1.642e-07</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> log_k_parent 5.428e-01    1.000e+00 2.507e-07</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> sigma        1.642e-07    2.507e-07 1.000e+00</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Backtransformed parameters:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Confidence intervals for internally transformed parameters are asymmetric.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> t-test (unrealistically) based on the assumption of normal distribution</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> for estimators of untransformed parameters.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>           Estimate t value    Pr(&gt;t)   Lower     Upper</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0 109.20000   29.47 4.218e-07 99.6300 118.70000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k_parent   0.03722   10.90 5.650e-05  0.0294   0.04712</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> sigma      5.26600    4.00 5.162e-03  1.8820   8.64900</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> FOCUS Chi2 error levels in percent:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>          err.min n.optim df</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> All data   8.385       2  6</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> parent     8.385       2  6</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Estimated disappearance times:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>         DT50  DT90</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> parent 18.62 61.87</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Data:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  time variable observed predicted residual</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>     0   parent   101.24   109.153  -7.9132</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>     3   parent    99.27    97.622   1.6484</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>     7   parent    90.11    84.119   5.9913</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>    14   parent    72.19    64.826   7.3641</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>    30   parent    29.71    35.738  -6.0283</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>    62   parent     5.98    10.862  -4.8818</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>    90   parent     1.54     3.831  -2.2911</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>   118   parent     0.39     1.351  -0.9613</span>
<span class="r-in"><span></span></span>
</code></pre></div>
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