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diff --git a/docs/dev/reference/summary.mkinfit.html b/docs/dev/reference/summary.mkinfit.html new file mode 100644 index 00000000..63a08d05 --- /dev/null +++ b/docs/dev/reference/summary.mkinfit.html @@ -0,0 +1,290 @@ +<!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, shrink-to-fit=no"><title>Summary method for class "mkinfit" — summary.mkinfit • mkin</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link 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+values."><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"></head><body> + <a href="#main" class="visually-hidden-focusable">Skip to contents</a> + + + <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="default" aria-label="Site navigation"><div class="container"> + + <a class="navbar-brand me-2" href="../index.html">mkin</a> + + <small class="nav-text text-info me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">1.2.10</small> + + + <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle 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pathway kinetics with residue data on cyantraniliprole</a></li> + <li><a class="dropdown-item" href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a></li> + <li><a class="dropdown-item" href="../articles/web_only/multistart.html">Short demo of the multistart method</a></li> + <li><hr class="dropdown-divider"></li> + <li><h6 class="dropdown-header" data-toc-skip>Performance</h6></li> + <li><a class="dropdown-item" href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a></li> + <li><a class="dropdown-item" href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a></li> + <li><a class="dropdown-item" href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a></li> + <li><hr class="dropdown-divider"></li> + <li><h6 class="dropdown-header" data-toc-skip>Miscellaneous</h6></li> + <li><a class="dropdown-item" 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<main id="main" class="col-md-9"><div class="page-header"> + + <h1>Summary method for class "mkinfit"</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/summary.mkinfit.R" class="external-link"><code>R/summary.mkinfit.R</code></a></small> + <div class="d-none name"><code>summary.mkinfit.Rd</code></div> + </div> + + <div class="ref-description section level2"> + <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> + + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for class '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 class '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 class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> + + +<dl><dt id="arg-object">object<a class="anchor" aria-label="anchor" href="#arg-object"></a></dt> +<dd><p>an object of class <a href="mkinfit.html">mkinfit</a>.</p></dd> + + +<dt id="arg-data">data<a class="anchor" aria-label="anchor" href="#arg-data"></a></dt> +<dd><p>logical, indicating whether the data should be included in the +summary.</p></dd> + + +<dt id="arg-distimes">distimes<a class="anchor" aria-label="anchor" href="#arg-distimes"></a></dt> +<dd><p>logical, indicating whether DT50 and DT90 values should be +included.</p></dd> + + +<dt id="arg-alpha">alpha<a class="anchor" aria-label="anchor" href="#arg-alpha"></a></dt> +<dd><p>error level for confidence interval estimation from t +distribution</p></dd> + + +<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt> +<dd><p>optional arguments passed to methods like <code>print</code>.</p></dd> + + +<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt> +<dd><p>an object of class <code>summary.mkinfit</code>.</p></dd> + + +<dt id="arg-digits">digits<a class="anchor" aria-label="anchor" href="#arg-digits"></a></dt> +<dd><p>Number of digits to use for printing</p></dd> + +</dl></div> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></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 class="section level2"> + <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></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 class="section level2"> + <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2> + <p>Johannes Ranke</p> + </div> + + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></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: 1.2.10 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.4.2 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Fri Feb 14 07:34:16 2025 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Fri Feb 14 07:34:16 2025 </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> + </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> + </nav></aside></div> + + + <footer><div class="pkgdown-footer-left"> + <p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown-footer-right"> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p> +</div> + + </footer></div> + + + + + + </body></html> + |