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<title>summary.mkinfit. mkin 0.9-41</title>
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Johannes Ranke
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<h1>
Summary method for class "mkinfit"
</h1>
<div class="row">
<div class="span8">
<h2>Usage</h2>
<pre><div>"summary"(object, data = TRUE, distimes = TRUE, alpha = 0.05, ...)
"print"(x, digits = max(3, getOption("digits") - 3), ...)</div></pre>
<h2>Arguments</h2>
<dl>
<dt>object</dt>
<dd>
an object of class <code><a href='mkinfit.html'>mkinfit</a></code>.
</dd>
<dt>x</dt>
<dd>
an object of class <code>summary.mkinfit</code>.
</dd>
<dt>data</dt>
<dd>
logical, indicating whether the data should be included in the summary.
</dd>
<dt>distimes</dt>
<dd>
logical, indicating whether DT50 and DT90 values should be included.
</dd>
<dt>alpha</dt>
<dd>
error level for confidence interval estimation from t distribution
</dd>
<dt>digits</dt>
<dd>
Number of digits to use for printing
</dd>
<dt>...</dt>
<dd>
optional arguments passed to methods like <code>print</code>.
</dd>
</dl>
<div class="Description">
<h2>Description</h2>
<p>Lists model equations, the summary as returned by <code><a href='http://www.inside-r.org/packages/cran/FME/docs/modFit'>summary.modFit</a></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>
<div class="Value">
<h2>Value</h2>
<p><dl>
The summary function returns a list derived from
<code><a href='http://www.inside-r.org/packages/cran/FME/docs/modFit'>summary.modFit</a></code>, with components, among others
<dt>version, Rversion</dt><dd>The mkin and R versions used</dd></p>
<p><dt>date.fit, date.summary</dt><dd>The dates where the fit and the summary were produced</dd></p>
<p><dt>use_of_ff</dt><dd>Was maximum or minimum use made of formation fractions</dd></p>
<p><dt>residuals, residualVariance, sigma, modVariance, df</dt><dd>As in summary.modFit</dd></p>
<p><dt>cov.unscaled, cov.scaled, info, niter, stopmess, par</dt><dd>As in summary.modFit</dd></p>
<p><dt>bpar</dt><dd>Optimised and backtransformed parameters</dd></p>
<p><dt>diffs </dt><dd>The differential equations used in the model</dd></p>
<p><dt>data </dt><dd>The data (see Description above).</dd></p>
<p><dt>start </dt><dd>The starting values and bounds, if applicable, for optimised parameters.</dd></p>
<p><dt>fixed </dt><dd>The values of fixed parameters.</dd></p>
<p><dt>errmin </dt><dd>The chi2 error levels for each observed variable.</dd></p>
<p><dt>bparms.ode </dt><dd>All backtransformed ODE parameters, for use as starting parameters for
related models.</dd></p>
<p><dt>ff </dt><dd>The estimated formation fractions derived from the fitted model.</dd></p>
<p><dt>distimes </dt><dd>The DT50 and DT90 values for each observed variable.</dd></p>
<p><dt>SFORB</dt><dd>If applicable, eigenvalues of SFORB components of the model.</dd></p>
<p>The print method is called for its side effect, i.e. printing the summary.
</dl></p>
</div>
<div class="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://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p>
</div>
<h2 id="examples">Examples</h2>
<pre class="examples"><div class='input'> summary(mkinfit(mkinmod(parent = list(type = "SFO")), FOCUS_2006_A, quiet = TRUE))
</div>
<div class='output'>mkin version: 0.9.41
R version: 3.2.2
Date of fit: Mon Nov 9 09:06:13 2015
Date of summary: Mon Nov 9 09:06:13 2015
Equations:
d_parent = - k_parent_sink * parent
Model predictions using solution type analytical
Fitted with method Port using 35 model solutions performed in 0.1 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>
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<!-- <ul>
<li>summary.mkinfit</li><li>print.summary.mkinfit</li>
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<li> utilities </li>
</ul> -->
<h2>Author</h2>
Johannes Ranke
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