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authorJohannes Ranke <jranke@uni-bremen.de>2016-10-06 09:40:35 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2016-10-06 09:40:35 +0200
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- <header>
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- </header>
-
- <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>
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-
-
- <h2>Author</h2>
-
- Johannes Ranke
-
-
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