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diff --git a/docs/summary.mkinfit.html b/docs/summary.mkinfit.html deleted file mode 100644 index 574c5c07..00000000 --- a/docs/summary.mkinfit.html +++ /dev/null @@ -1,259 +0,0 @@ -<!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<title>summary.mkinfit. mkin 0.9.44.9000</title> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> -<meta name="author" content=" - Johannes Ranke -"> - -<link href="css/bootstrap.css" rel="stylesheet"> -<link href="css/bootstrap-responsive.css" rel="stylesheet"> -<link href="css/highlight.css" rel="stylesheet"> -<link href="css/staticdocs.css" rel="stylesheet"> - -<!--[if lt IE 9]> - <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script> -<![endif]--> - -<script type="text/x-mathjax-config"> - MathJax.Hub.Config({ - tex2jax: { - inlineMath: [ ['$','$'], ["\\(","\\)"] ], - processEscapes: true - } - }); -</script> -<script type="text/javascript" - src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"> -</script> - </head> - - <body> - <div class="navbar"> - <div class="navbar-inner"> - <div class="container"> - <a class="brand" href="index.html">mkin 0.9.44.9000</a> - <div class="nav"> - <ul class="nav"> - <li><a href="index.html">Home</a></li> - <li><a href="reference.html">Reference</a></li> - </ul> - </div> - </div> - </div> -</div> - - - <div class="container"> - <header> - - </header> - - <h1> - Summary method for class "mkinfit" -</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> <span class="argument">=</span> <span class="number">TRUE</span><span class="keyword">,</span> <span class="argument">distimes</span> <span class="argument">=</span> <span class="number">TRUE</span><span class="keyword">,</span> <span class="argument">alpha</span> <span class="argument">=</span> <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> <span class="argument">=</span> <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) “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'> <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(>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> - - <footer> - <p class="pull-right"><a href="#">Back to top</a></p> -<p>Built by <a href="https://github.com/hadley/staticdocs">staticdocs</a>. 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