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diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index 73410181..65bc6326 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -8,11 +8,13 @@ <title>Summary method for class "mkinfit" — summary.mkinfit • mkin</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,16 +34,18 @@ -<meta property="og:title" content="Summary method for class "mkinfit" — summary.mkinfit" /> -<meta property="og:description" content="Lists model equations, initial parameter values, optimised parameters with some - uncertainty statistics, the chi2 error levels calculated according to FOCUS - guidance (2006) as defined therein, formation fractions, DT50 values and - optionally the data, consisting of observed, predicted and residual values." /> +<meta property="og:title" content="Summary method for class "mkinfit" — summary.mkinfit" /> +<meta property="og:description" content="Lists model equations, initial parameter values, optimised parameters with +some uncertainty statistics, the chi2 error levels calculated according to +FOCUS guidance (2006) as defined therein, formation fractions, DT50 values +and optionally the data, consisting of observed, predicted and residual +values." /> <meta name="twitter:card" content="summary" /> + <!-- mathjax --> <script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> @@ -112,7 +116,6 @@ <a href="../news/index.html">News</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -134,19 +137,21 @@ </div> <div class="ref-description"> - - <p>Lists model equations, initial parameter values, optimised parameters with some - uncertainty statistics, the chi2 error levels calculated according to FOCUS - guidance (2006) as defined therein, formation fractions, DT50 values and - optionally the data, consisting of observed, predicted and residual values.</p> - + <p>Lists model equations, initial parameter values, optimised parameters with +some uncertainty statistics, the chi2 error levels calculated according to +FOCUS guidance (2006) as defined therein, formation fractions, DT50 values +and optionally the data, consisting of observed, predicted and residual +values.</p> </div> <pre class="usage"><span class='co'># S3 method for mkinfit</span> -<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></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='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></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'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>x</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Extremes.html'>max</a></span>(<span class='fl'>3</span>, <span class='fu'><a href='https://rdrr.io/r/base/options.html'>getOption</a></span>(<span class='st'>"digits"</span>) - <span class='fl'>3</span>), <span class='no'>...</span>)</pre> - +<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>x</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Extremes.html'>max</a></span>(<span class='fl'>3</span>, <span class='fu'><a href='https://rdrr.io/r/base/options.html'>getOption</a></span>(<span class='st'>"digits"</span>) - + <span class='fl'>3</span>), <span class='no'>...</span>)</pre> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> @@ -155,91 +160,94 @@ <td><p>an object of class <code><a href='mkinfit.html'>mkinfit</a></code>.</p></td> </tr> <tr> - <th>x</th> - <td><p>an object of class <code>summary.mkinfit</code>.</p></td> - </tr> - <tr> <th>data</th> - <td><p>logical, indicating whether the data should be included in the summary.</p></td> + <td><p>logical, indicating whether the data should be included in the +summary.</p></td> </tr> <tr> <th>distimes</th> - <td><p>logical, indicating whether DT50 and DT90 values should be included.</p></td> + <td><p>logical, indicating whether DT50 and DT90 values should be +included.</p></td> </tr> <tr> <th>alpha</th> - <td><p>error level for confidence interval estimation from t distribution</p></td> - </tr> - <tr> - <th>digits</th> - <td><p>Number of digits to use for printing</p></td> + <td><p>error level for confidence interval estimation from t +distribution</p></td> </tr> <tr> <th>...</th> <td><p>optional arguments passed to methods like <code>print</code>.</p></td> </tr> + <tr> + <th>x</th> + <td><p>an object of class <code>summary.mkinfit</code>.</p></td> + </tr> + <tr> + <th>digits</th> + <td><p>Number of digits to use for printing</p></td> + </tr> </table> - + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> <p>The summary function returns a list with components, among others</p> <dt>version, Rversion</dt><dd><p>The mkin and R versions used</p></dd> - <dt>date.fit, date.summary</dt><dd><p>The dates where the fit and the summary were produced</p></dd> + <dt>date.fit, date.summary</dt><dd><p>The dates where the fit and the summary were + produced</p></dd> + <dt>diffs</dt><dd><p>The differential equations used in the model</p></dd> <dt>use_of_ff</dt><dd><p>Was maximum or minimum use made of formation fractions</p></dd> - <dt>residuals, residualVariance, sigma, modVariance, df</dt><dd><p>As in summary.modFit</p></dd> - <dt>cov.unscaled, cov.scaled, info, niter, stopmess, par</dt><dd><p>As in summary.modFit</p></dd> - <dt>bpar</dt><dd><p>Optimised and backtransformed parameters</p></dd> - <dt>diffs </dt><dd><p>The differential equations used in the model</p></dd> - <dt>data </dt><dd><p>The data (see Description above).</p></dd> - <dt>start </dt><dd><p>The starting values and bounds, if applicable, for optimised parameters.</p></dd> - <dt>fixed </dt><dd><p>The values of fixed parameters.</p></dd> - <dt>errmin </dt><dd><p>The chi2 error levels for each observed variable.</p></dd> - <dt>bparms.ode </dt><dd><p>All backtransformed ODE parameters, for use as starting parameters for - related models.</p></dd> - <dt>errparms </dt><dd><p>Error model parameters.</p></dd> - <dt>ff </dt><dd><p>The estimated formation fractions derived from the fitted model.</p></dd> - <dt>distimes </dt><dd><p>The DT50 and DT90 values for each observed variable.</p></dd> + <dt>bpar</dt><dd><p>Optimised and backtransformed + parameters</p></dd> + <dt>data</dt><dd><p>The data (see Description above).</p></dd> + <dt>start</dt><dd><p>The starting values and bounds, if applicable, for optimised + parameters.</p></dd> + <dt>fixed</dt><dd><p>The values of fixed parameters.</p></dd> + <dt>errmin </dt><dd><p>The chi2 error levels for + each observed variable.</p></dd> + <dt>bparms.ode</dt><dd><p>All backtransformed ODE + parameters, for use as starting parameters for related models.</p></dd> + <dt>errparms</dt><dd><p>Error model parameters.</p></dd> + <dt>ff</dt><dd><p>The estimated formation fractions derived from the fitted + model.</p></dd> + <dt>distimes</dt><dd><p>The DT50 and DT90 values for each observed variable.</p></dd> <dt>SFORB</dt><dd><p>If applicable, eigenvalues of SFORB components of the model.</p></dd> The print method is called for its side effect, i.e. printing the summary. - <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>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, + <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://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></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 used for fitting: 0.9.49.6 + <pre class="examples"><div class='input'> + <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></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 used for fitting: 0.9.49.6 #> R version used for fitting: 3.6.1 -#> Date of fit: Thu Sep 19 09:52:40 2019 -#> Date of summary: Thu Sep 19 09:52:40 2019 +#> Date of fit: Fri Oct 25 02:09:45 2019 +#> Date of summary: Fri Oct 25 02:09:45 2019 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent #> #> Model predictions using solution type analytical #> -#> Fitted using 131 model solutions performed in 0.27 s +#> Fitted using 131 model solutions performed in 0.274 s #> #> Error model: Constant variance #> #> Error model algorithm: OLS #> #> Starting values for parameters to be optimised: -#> value type -#> parent_0 101.240000 state -#> k_parent_sink 0.100000 deparm -#> sigma 5.265546 error +#> 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 -#> sigma 5.265546 0 Inf #> #> Fixed parameter values: #> None @@ -287,17 +295,15 @@ #> 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> +#> 118 parent 0.39 1.351 -0.9613</div><div class='input'> +</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#references">References</a></li> - <li><a href="#examples">Examples</a></li> </ul> |