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diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html new file mode 100644 index 00000000..e0cdfe23 --- /dev/null +++ b/docs/reference/summary.mkinfit.html @@ -0,0 +1,229 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>summary.mkinfit. mkin</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> + +<!-- Bootstrap --> +<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> + +<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> + +<!-- Font Awesome icons --> +<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> + + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../pkgdown.js"></script> + +<!-- mathjax --> +<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> + +<!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--> + </head> + + <body> + <div class="container"> + <header> + +<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="../index.html">mkin</a> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../index.html">Home</a> +</li> +<li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + <ul class="nav navbar-nav navbar-right"> + <li> + <a href="https://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + </header> + + <div class="page-header"> + <h1> +</h1> +</div> + +<div class="row"> + <div class="col-md-9"> + + <p>Lists model equations, the summary as returned by <code>summary.modFit</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> + + + <pre><span class='co'># S3 method for mkinfit</span> +<span class='fu'>summary</span>(<span class='no'>object</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>distimes</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='no'>...</span>) +<span class='co'># S3 method for summary.mkinfit</span> +<span class='fu'>print</span>(<span class='no'>x</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fu'>max</span>(<span class='fl'>3</span>, <span class='fu'>getOption</span>(<span class='st'>"digits"</span>) - <span class='fl'>3</span>), <span class='no'>...</span>)</pre> + + <h2>Arguments</h2> + <dl class="dl-horizontal"> + <dt>object</dt> + <dd> + an object of class <code>mkinfit</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>&#8230;</dt> + <dd> + optional arguments passed to methods like <code>print</code>. +</dd> + </dl> + + <div class="Value"> + <h2>Value</h2> + + <p>The summary function returns a list derived from + <code>summary.modFit</code>, with components, among others</p> + <p>The print method is called for its side effect, i.e. printing the summary.</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='fu'>summary</span>(<span class='fu'>mkinfit</span>(<span class='fu'>mkinmod</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>)), <span class='no'>FOCUS_2006_A</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#> mkin version: 0.9.44.9000 +#> R version: 3.3.1 +#> Date of fit: Thu Oct 6 09:18:07 2016 +#> Date of summary: Thu Oct 6 09:18:07 2016 +#> +#> Equations: +#> d_parent = - k_parent_sink * parent +#> +#> Model predictions using solution type analytical +#> +#> Fitted with method Port using 35 model solutions performed in 0.079 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="col-md-3"> + <h2>Author</h2> + + Johannes Ranke + + </div> +</div> + + <footer> + <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + </footer> + </div> + + </body> +</html> |