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diff --git a/docs/dev/reference/summary.mkinfit.html b/docs/dev/reference/summary.mkinfit.html deleted file mode 100644 index f627c2f6..00000000 --- a/docs/dev/reference/summary.mkinfit.html +++ /dev/null @@ -1,334 +0,0 @@ -<!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><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 method for class "mkinfit" — summary.mkinfit • mkin</title><!-- jquery --><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/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><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/5.12.1/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/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><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"><script src="../pkgdown.js"></script><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="robots" content="noindex"><!-- 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><!--[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 data-spy="scroll" data-target="#toc"> - 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Articles - - <span class="caret"></span> - </a> - <ul class="dropdown-menu" role="menu"><li> - <a href="../articles/mkin.html">Introduction to mkin</a> - </li> - <li class="divider"> - <li class="dropdown-header">Example evaluations with (generalised) nonlinear least squares</li> - <li> - <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a> - </li> - <li> - <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> - </li> - <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> - </li> - <li class="divider"> - <li class="dropdown-header">Example evaluations with hierarchical models (nonlinear mixed-effects models)</li> - <li> - <a href="../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a> - </li> - <li> - <a href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a> - 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</div> - - <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for mkinfit</span></span> -<span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">object</span>, data <span class="op">=</span> <span class="cn">TRUE</span>, distimes <span class="op">=</span> <span class="cn">TRUE</span>, alpha <span class="op">=</span> <span class="fl">0.05</span>, <span class="va">...</span><span class="op">)</span></span> -<span></span> -<span><span class="co"># S3 method for summary.mkinfit</span></span> -<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, digits <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="fl">3</span>, <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"digits"</span><span class="op">)</span> <span class="op">-</span> <span class="fl">3</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> - </div> - - <div id="arguments"> - <h2>Arguments</h2> - <dl><dt>object</dt> -<dd><p>an object of class <a href="mkinfit.html">mkinfit</a>.</p></dd> - - -<dt>data</dt> -<dd><p>logical, indicating whether the data should be included in the -summary.</p></dd> - - -<dt>distimes</dt> -<dd><p>logical, indicating whether DT50 and DT90 values should be -included.</p></dd> - - -<dt>alpha</dt> -<dd><p>error level for confidence interval estimation from t -distribution</p></dd> - - -<dt>...</dt> -<dd><p>optional arguments passed to methods like <code>print</code>.</p></dd> - - -<dt>x</dt> -<dd><p>an object of class <code>summary.mkinfit</code>.</p></dd> - - -<dt>digits</dt> -<dd><p>Number of digits to use for printing</p></dd> - -</dl></div> - <div id="value"> - <h2>Value</h2> - - -<p>The summary function returns a list with components, among others</p> -<dl><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 and fractional eigenvector component -g of SFORB systems in the model.</p></dd> - -</dl><p>The print method is called for its side effect, i.e. printing the summary.</p> - </div> - <div id="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://esdac.jrc.ec.europa.eu/projects/degradation-kinetics" class="external-link">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> - </div> - <div id="author"> - <h2>Author</h2> - <p>Johannes Ranke</p> - </div> - - <div id="ref-examples"> - <h2>Examples</h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> -<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">FOCUS_2006_A</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.2.3 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.3 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Sun Apr 16 08:34:39 2023 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Sun Apr 16 08:34:39 2023 </span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Equations:</span> -<span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - k_parent * parent</span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type analytical </span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted using 131 model solutions performed in 0.009 s</span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Error model: Constant variance </span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Error model algorithm: OLS </span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Starting values for parameters to be optimised:</span> -<span class="r-out co"><span class="r-pr">#></span> value type</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 101.24 state</span> -<span class="r-out co"><span class="r-pr">#></span> k_parent 0.10 deparm</span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Starting values for the transformed parameters actually optimised:</span> -<span class="r-out co"><span class="r-pr">#></span> value lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 101.240000 -Inf Inf</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_parent -2.302585 -Inf Inf</span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fixed parameter values:</span> -<span class="r-out co"><span class="r-pr">#></span> None</span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Results:</span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> AIC BIC logLik</span> -<span class="r-out co"><span class="r-pr">#></span> 55.28197 55.5203 -24.64099</span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Optimised, transformed parameters with symmetric confidence intervals:</span> -<span class="r-out co"><span class="r-pr">#></span> Estimate Std. Error Lower Upper</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 109.200 3.70400 99.630 118.700</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_parent -3.291 0.09176 -3.527 -3.055</span> -<span class="r-out co"><span class="r-pr">#></span> sigma 5.266 1.31600 1.882 8.649</span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Parameter correlation:</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 log_k_parent sigma</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 1.000e+00 5.428e-01 1.642e-07</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_parent 5.428e-01 1.000e+00 2.507e-07</span> -<span class="r-out co"><span class="r-pr">#></span> sigma 1.642e-07 2.507e-07 1.000e+00</span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Backtransformed parameters:</span> -<span class="r-out co"><span class="r-pr">#></span> Confidence intervals for internally transformed parameters are asymmetric.</span> -<span class="r-out co"><span class="r-pr">#></span> t-test (unrealistically) based on the assumption of normal distribution</span> -<span class="r-out co"><span class="r-pr">#></span> for estimators of untransformed parameters.</span> -<span class="r-out co"><span class="r-pr">#></span> Estimate t value Pr(>t) Lower Upper</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 109.20000 29.47 4.218e-07 99.6300 118.70000</span> -<span class="r-out co"><span class="r-pr">#></span> k_parent 0.03722 10.90 5.650e-05 0.0294 0.04712</span> -<span class="r-out co"><span class="r-pr">#></span> sigma 5.26600 4.00 5.162e-03 1.8820 8.64900</span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> FOCUS Chi2 error levels in percent:</span> -<span class="r-out co"><span class="r-pr">#></span> err.min n.optim df</span> -<span class="r-out co"><span class="r-pr">#></span> All data 8.385 2 6</span> -<span class="r-out co"><span class="r-pr">#></span> parent 8.385 2 6</span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Estimated disappearance times:</span> -<span class="r-out co"><span class="r-pr">#></span> DT50 DT90</span> -<span class="r-out co"><span class="r-pr">#></span> parent 18.62 61.87</span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Data:</span> -<span class="r-out co"><span class="r-pr">#></span> time variable observed predicted residual</span> -<span class="r-out co"><span class="r-pr">#></span> 0 parent 101.24 109.153 -7.9132</span> -<span class="r-out co"><span class="r-pr">#></span> 3 parent 99.27 97.622 1.6484</span> -<span class="r-out co"><span class="r-pr">#></span> 7 parent 90.11 84.119 5.9913</span> -<span class="r-out co"><span class="r-pr">#></span> 14 parent 72.19 64.826 7.3641</span> -<span class="r-out co"><span class="r-pr">#></span> 30 parent 29.71 35.738 -6.0283</span> -<span class="r-out co"><span class="r-pr">#></span> 62 parent 5.98 10.862 -4.8818</span> -<span class="r-out co"><span class="r-pr">#></span> 90 parent 1.54 3.831 -2.2911</span> -<span class="r-out co"><span class="r-pr">#></span> 118 parent 0.39 1.351 -0.9613</span> -<span class="r-in"><span></span></span> -</code></pre></div> - </div> - </div> - <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> - - - <footer><div class="copyright"> - <p></p><p>Developed by Johannes Ranke.</p> -</div> - -<div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> -</div> - - </footer></div> - - - - - - - </body></html> - |