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diff --git a/docs/summary.mkinfit.html b/docs/summary.mkinfit.html new file mode 100644 index 00000000..574c5c07 --- /dev/null +++ b/docs/summary.mkinfit.html @@ -0,0 +1,259 @@ +<!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>. Styled with <a href="https://getbootstrap.com/2.0.4/">bootstrap</a>.</p> + </footer> + </div> + </body> +</html>
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