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diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index ec79c37d..84e65787 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -10,23 +10,27 @@ <!-- jquery --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" 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" /> +<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" 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> +<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script> + +<!-- bootstrap-toc --> +<link rel="stylesheet" href="../bootstrap-toc.css"> +<script src="../bootstrap-toc.js"></script> <!-- Font Awesome icons --> -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" /> -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" /> +<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" /> +<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" /> <!-- clipboard.js --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script> <!-- headroom.js --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> @@ -41,7 +45,6 @@ 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" /> @@ -59,7 +62,7 @@ values." /> </head> - <body> + <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> <header> <div class="navbar navbar-default navbar-fixed-top" role="navigation"> @@ -73,7 +76,7 @@ values." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.9</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.1</span> </span> </div> @@ -117,7 +120,12 @@ values." /> </li> </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin/"> + <span class="fab fa fab fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> @@ -132,7 +140,7 @@ values." /> <div class="col-md-9 contents"> <div class="page-header"> <h1>Summary method for class "mkinfit"</h1> - + <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/summary.mkinfit.R'><code>R/summary.mkinfit.R</code></a></small> <div class="hidden name"><code>summary.mkinfit.Rd</code></div> </div> @@ -190,96 +198,97 @@ distribution</p></td> <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>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>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. +<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>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, - 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> +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: 0.9.49.9 -#> R version used for fitting: 3.6.3 -#> Date of fit: Mon Mar 30 21:43:00 2020 -#> Date of summary: Mon Mar 30 21:43:00 2020 + <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: 0.9.50.1 +#> R version used for fitting: 4.0.0 +#> Date of fit: Tue May 12 08:07:03 2020 +#> Date of summary: Tue May 12 08:07:03 2020 #> #> Equations: -#> d_parent/dt = - k_parent_sink * parent +#> d_parent/dt = - k_parent * parent #> #> Model predictions using solution type analytical #> -#> Fitted using 131 model solutions performed in 0.306 s +#> Fitted using 131 model solutions performed in 0.026 s #> #> Error model: Constant variance #> #> Error model algorithm: OLS #> #> Starting values for parameters to be optimised: -#> value type -#> parent_0 101.24 state -#> k_parent_sink 0.10 deparm +#> value type +#> parent_0 101.24 state +#> k_parent 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 +#> value lower upper +#> parent_0 101.240000 -Inf Inf +#> log_k_parent -2.302585 -Inf Inf #> #> Fixed parameter values: #> None #> +#> Results: +#> +#> AIC BIC logLik +#> 55.28197 55.5203 -24.64099 +#> #> Optimised, transformed parameters with symmetric confidence intervals: -#> Estimate Std. Error Lower Upper -#> parent_0 109.200 3.70400 99.630 118.700 -#> log_k_parent_sink -3.291 0.09176 -3.527 -3.055 -#> sigma 5.266 1.31600 1.882 8.649 +#> Estimate Std. Error Lower Upper +#> parent_0 109.200 3.70400 99.630 118.700 +#> log_k_parent -3.291 0.09176 -3.527 -3.055 +#> sigma 5.266 1.31600 1.882 8.649 #> #> Parameter correlation: -#> parent_0 log_k_parent_sink sigma -#> parent_0 1.000e+00 5.428e-01 1.642e-07 -#> log_k_parent_sink 5.428e-01 1.000e+00 2.507e-07 -#> sigma 1.642e-07 2.507e-07 1.000e+00 +#> parent_0 log_k_parent sigma +#> parent_0 1.000e+00 5.428e-01 1.642e-07 +#> log_k_parent 5.428e-01 1.000e+00 2.507e-07 +#> sigma 1.642e-07 2.507e-07 1.000e+00 #> #> 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 29.47 4.218e-07 99.6300 118.70000 -#> k_parent_sink 0.03722 10.90 5.650e-05 0.0294 0.04712 -#> sigma 5.26600 4.00 5.162e-03 1.8820 8.64900 +#> Estimate t value Pr(>t) Lower Upper +#> parent_0 109.20000 29.47 4.218e-07 99.6300 118.70000 +#> k_parent 0.03722 10.90 5.650e-05 0.0294 0.04712 +#> sigma 5.26600 4.00 5.162e-03 1.8820 8.64900 #> #> FOCUS 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 @@ -296,17 +305,10 @@ distribution</p></td> #> 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> - - <h2>Author</h2> - <p>Johannes Ranke</p> + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> + <nav id="toc" data-toggle="toc" class="sticky-top"> + <h2 data-toc-skip>Contents</h2> + </nav> </div> </div> @@ -317,7 +319,7 @@ distribution</p></td> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> </div> </footer> |