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authorJohannes Ranke <jranke@uni-bremen.de>2016-09-10 05:21:52 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2016-09-10 05:55:25 +0200
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+
+ <h1>
+ Summary method for class &quot;mkinfit&quot;
+</h1>
+
+<div class="row">
+ <div class="span8">
+ <h2>Usage</h2>
+ <pre><span class="comment"># S3 method for mkinfit</span>
+<span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span><span class="keyword">(</span><span class="symbol">object</span><span class="keyword">,</span> <span class="argument">data</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="number">TRUE</span><span class="keyword">,</span> <span class="argument">distimes</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="number">TRUE</span><span class="keyword">,</span> <span class="argument">alpha</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="number">0.05</span><span class="keyword">,</span> <span class="symbol">...</span><span class="keyword">)</span>
+<span class="comment"># S3 method for summary.mkinfit</span>
+<span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/print'>print</a></span><span class="keyword">(</span><span class="symbol">x</span><span class="keyword">,</span> <span class="argument">digits</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/Extremes'>max</a></span><span class="keyword">(</span><span class="number">3</span><span class="keyword">,</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/options'>getOption</a></span><span class="keyword">(</span><span class="string">"digits"</span><span class="keyword">)</span> <span class="keyword">-</span> <span class="number">3</span><span class="keyword">)</span><span class="keyword">,</span> <span class="symbol">...</span><span class="keyword">)</span></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.rdocumentation.org/packages/FME/topics/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.rdocumentation.org/packages/FME/topics/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) &#147;Guidance Document on Estimating Persistence and
+ Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
+ Registration&#148; 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'> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span><span class="keyword">(</span><span class="functioncall"><a href='mkinfit.html'>mkinfit</a></span><span class="keyword">(</span><span class="functioncall"><a href='mkinmod.html'>mkinmod</a></span><span class="keyword">(</span><span class="argument">parent</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/list'>list</a></span><span class="keyword">(</span><span class="argument">type</span> <span class="argument">=</span> <span class="string">"SFO"</span><span class="keyword">)</span><span class="keyword">)</span><span class="keyword">,</span> <span class="symbol">FOCUS_2006_A</span><span class="keyword">,</span> <span class="argument">quiet</span> <span class="argument">=</span> <span class="number">TRUE</span><span class="keyword">)</span><span class="keyword">)</span></div>
+<div class='output'>mkin version: 0.9.44.9000
+R version: 3.3.1
+Date of fit: Sat Sep 10 05:53:12 2016
+Date of summary: Sat Sep 10 05:53:12 2016
+
+Equations:
+d_parent = - k_parent_sink * parent
+
+Model predictions using solution type analytical
+
+Fitted with method Port using 35 model solutions performed in 0.09 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(&gt;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>
+ </div>
+ <div class="span4 sidebar">
+ <!-- <ul>
+ <li>summary.mkinfit</li><li>print.summary.mkinfit</li>
+ </ul>
+ <ul>
+ <li> utilities </li>
+ </ul> -->
+
+
+
+ <h2>Author</h2>
+
+ Johannes Ranke
+
+
+ </div>
+</div>
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