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For the evaluation of pesticide degradation experiments, -detailed guidance and helpful tools have been developed as detailed in -'Credits and historical remarks' below.</p> - -<h2>Usage</h2> - -<p>For a start, have a look a the code examples provided for -<a href="http://kinfit.r-forge.r-project.org/mkin_static/plot.mkinfit.html"><code>plot.mkinfit</code></a> -and -<a href="http://kinfit.r-forge.r-project.org/mkin_static/plot.mmkin.html"><code>plot.mmkin</code></a>, and -at the package vignettes -<a href="http://kinfit.r-forge.r-project.org/mkin_static/vignettes/FOCUS_L.html"><code>FOCUS L</code></a> and -<a href="http://kinfit.r-forge.r-project.org/mkin_static/vignettes/FOCUS_D.html"><code>FOCUS D</code></a>.</p> - -<h2>Documentation</h2> - -<p>The <a href="http://kinfit.r-forge.r-project.org/mkin_static">HTML documentation</a> is -maintained at the R-Forge project site.</p> - -<h2>Features</h2> - -<ul> -<li>Highly flexible model specification using -<a href="http://kinfit.r-forge.r-project.org/mkin_static/mkinmod.html"><code>mkinmod</code></a>, -including equilibrium reactions and using the single first-order -reversible binding (SFORB) model, which will automatically create -two latent state variables for the observed variable.</li> -<li>As of version 0.9-39, fitting of several models to several datasets, optionally in -parallel, is supported, see for example -<a href="http://kinfit.r-forge.r-project.org/mkin_static/plot.mmkin.html"><code>plot.mmkin</code></a>.</li> -<li>Model solution (forward modelling) in the function -<a href="http://kinfit.r-forge.r-project.org/mkin_static/mkinpredict.html"><code>mkinpredict</code></a> -is performed either using the analytical solution for the case of -parent only degradation, an eigenvalue based solution if only simple -first-order (SFO) or SFORB kinetics are used in the model, or -using a numeric solver from the <code>deSolve</code> package (default is <code>lsoda</code>).</li> -<li>If a C compiler is installed, the kinetic models are compiled from automatically -generated C code, see<br/> -<a href="http://kinfit.r-forge.r-project.org/mkin_static/vignettes/compiled_models.html">vignette <code>compiled_models</code></a>. -The autogeneration of C code was -inspired by the <a href="https://github.com/karlines/ccSolve"><code>ccSolve</code></a> package. Thanks -to Karline Soetaert for her work on that.</li> -<li>By default, kinetic rate constants and kinetic formation fractions are -transformed internally using -<a href="http://kinfit.r-forge.r-project.org/mkin_static/transform_odeparms.html"><code>transform_odeparms</code></a> -so their estimators can more reasonably be expected to follow -a normal distribution. This has the side effect that no constraints -are needed in the optimisation. Thanks to RenĂ© Lehmann for the nice -cooperation on this, especially the isometric logration transformation -that is now used for the formation fractions.</li> -<li>A side effect of this is that when parameter estimates are backtransformed -to match the model definition, confidence intervals calculated from -standard errors are also backtransformed to the correct scale, and will -not include meaningless values like negative rate constants or -formation fractions adding up to more than 1, which can not occur in -a single experiment with a single defined radiolabel position.</li> -<li>The usual one-sided t-test for significant difference from zero is nevertheless -shown based on estimators for the untransformed parameters.</li> -<li>Summary and plotting functions. The <code>summary</code> of an <code>mkinfit</code> object is in -fact a full report that should give enough information to be able to -approximately reproduce the fit with other tools.</li> -<li>The chi-squared error level as defined in the FOCUS kinetics guidance -(see below) is calculated for each observed variable.</li> -<li>Iteratively reweighted least squares fitting is implemented in a similar way -as in KinGUII and CAKE (see below). Simply add the argument -<code>reweight = "obs"</code> to your call to <code>mkinfit</code> and a separate variance -componenent for each of the observed variables will be optimised -in a second stage after the primary optimisation algorithm has converged.</li> -<li>When a metabolite decline phase is not described well by SFO kinetics, -SFORB kinetics can be used for the metabolite.</li> -</ul> - -<h2>GUI</h2> - -<p>There is a graphical user interface that I consider useful for real work. Please -refer to its <a href="http://kinfit.r-forge.r-project.org/gmkin_static">documentation page</a> -for installation instructions and a manual.</p> - -<h2>News</h2> - -<p>Yes, there is a ChangeLog, for the latest <a href="http://cran.r-project.org/web/packages/mkin/news.html">CRAN release</a> -and one for the <a href="https://github.com/jranke/mkin/blob/master/NEWS.md">github master branch</a>.</p> - -<h2>Credits and historical remarks</h2> - -<p><code>mkin</code> would not be possible without the underlying software stack consisting -of R and the packages <a href="http://cran.r-project.org/package=deSolve">deSolve</a> -and <a href="http://cran.r-project.org/package=FME">FME</a>, to say the least.</p> - -<p>It could not have been written without me being introduced to regulatory fate -modelling of pesticides by Adrian Gurney during my time at Harlan Laboratories -Ltd (formerly RCC Ltd). <code>mkin</code> greatly profits from and largely follows -the work done by the -<a href="http://focus.jrc.ec.europa.eu/dk">FOCUS Degradation Kinetics Workgroup</a>, -as detailed in their guidance document from 2006, slightly updated in 2011 and -2014.</p> - -<p>Also, it was inspired by the first version of KinGUI developed by -BayerCropScience, which is based on the MatLab runtime environment.</p> - -<p>The companion package -<a href="http://kinfit.r-forge.r-project.org/kinfit_static/index.html">kinfit</a> (now deprecated) was -<a href="https://r-forge.r-project.org/scm/viewvc.php?view=rev&root=kinfit&revision=2">started in 2008</a> and -<a href="http://cran.r-project.org/src/contrib/Archive/kinfit/">first published</a> on -CRAN on 01 May 2010.</p> - -<p>The first <code>mkin</code> code was -<a href="https://r-forge.r-project.org/scm/viewvc.php?view=rev&root=kinfit&revision=8">published on 11 May 2010</a> and the -<a href="http://cran.r-project.org/src/contrib/Archive/mkin">first CRAN version</a> -on 18 May 2010.</p> - -<p>In 2011, Bayer Crop Science started to distribute an R based successor to KinGUI named -KinGUII whose R code is based on <code>mkin</code>, but which added, amongst other -refinements, a closed source graphical user interface (GUI), iteratively -reweighted least squares (IRLS) optimisation of the variance for each of the -observed variables, and Markov Chain Monte Carlo (MCMC) simulation -functionality, similar to what is available e.g. in the <code>FME</code> package.</p> + </header><div class="row"> + <div class="contents col-md-9"> + <div id="mkin" class="section level1"> +<div class="page-header"><h1 class="hasAnchor"><a href="#mkin" class="anchor"> </a>mkin</h1></div> + +<p>The R package <strong>mkin</strong> provides calculation routines for the analysis of chemical degradation data, including <b>m</b>ulticompartment <b>kin</b>etics as needed for modelling the formation and decline of transformation products, or if several compartments are involved.</p> +<div id="installation" class="section level2"> +<h2 class="hasAnchor"> +<a href="#installation" class="anchor"> </a>Installation</h2> +<p>You can install the latest released version from <a href="http://cran.r-project.org/package=mkin">CRAN</a> from within R:</p> +<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">install.packages</span>(<span class="st">"mkin"</span>)</code></pre></div> +</div> +<div id="background" class="section level2"> +<h2 class="hasAnchor"> +<a href="#background" class="anchor"> </a>Background</h2> +<p>In the regulatory evaluation of chemical substances like plant protection products (pesticides), biocides and other chemicals, degradation data play an important role. For the evaluation of pesticide degradation experiments, detailed guidance and helpful tools have been developed as detailed in ‘Credits and historical remarks’ below.</p> +</div> +<div id="usage" class="section level2"> +<h2 class="hasAnchor"> +<a href="#usage" class="anchor"> </a>Usage</h2> +<p>For a start, have a look a the code examples provided for <a href="http://kinfit.r-forge.r-project.org/mkin_static/plot.mkinfit.html"><code>plot.mkinfit</code></a> and <a href="http://kinfit.r-forge.r-project.org/mkin_static/plot.mmkin.html"><code>plot.mmkin</code></a>, and at the package vignettes <a href="http://kinfit.r-forge.r-project.org/mkin_static/vignettes/FOCUS_L.html"><code>FOCUS L</code></a> and <a href="http://kinfit.r-forge.r-project.org/mkin_static/vignettes/FOCUS_D.html"><code>FOCUS D</code></a>.</p> +</div> +<div id="documentation" class="section level2"> +<h2 class="hasAnchor"> +<a href="#documentation" class="anchor"> </a>Documentation</h2> +<p>The <a href="http://kinfit.r-forge.r-project.org/mkin_static">HTML documentation</a> is maintained at the R-Forge project site.</p> +</div> +<div id="features" class="section level2"> +<h2 class="hasAnchor"> +<a href="#features" class="anchor"> </a>Features</h2> +<ul><li>Highly flexible model specification using <a href="http://kinfit.r-forge.r-project.org/mkin_static/mkinmod.html"><code>mkinmod</code></a>, including equilibrium reactions and using the single first-order reversible binding (SFORB) model, which will automatically create two latent state variables for the observed variable.</li> +<li>As of version 0.9-39, fitting of several models to several datasets, optionally in parallel, is supported, see for example <a href="http://kinfit.r-forge.r-project.org/mkin_static/plot.mmkin.html"><code>plot.mmkin</code></a>.</li> +<li>Model solution (forward modelling) in the function <a href="http://kinfit.r-forge.r-project.org/mkin_static/mkinpredict.html"><code>mkinpredict</code></a> is performed either using the analytical solution for the case of parent only degradation, an eigenvalue based solution if only simple first-order (SFO) or SFORB kinetics are used in the model, or using a numeric solver from the <code>deSolve</code> package (default is <code>lsoda</code>).</li> +<li>If a C compiler is installed, the kinetic models are compiled from automatically generated C code, see<br><a href="http://kinfit.r-forge.r-project.org/mkin_static/vignettes/compiled_models.html">vignette <code>compiled_models</code></a>. The autogeneration of C code was inspired by the <a href="https://github.com/karlines/ccSolve"><code>ccSolve</code></a> package. Thanks to Karline Soetaert for her work on that.</li> +<li>By default, kinetic rate constants and kinetic formation fractions are transformed internally using <a href="http://kinfit.r-forge.r-project.org/mkin_static/transform_odeparms.html"><code>transform_odeparms</code></a> so their estimators can more reasonably be expected to follow a normal distribution. This has the side effect that no constraints are needed in the optimisation. Thanks to René Lehmann for the nice cooperation on this, especially the isometric logration transformation that is now used for the formation fractions.</li> +<li>A side effect of this is that when parameter estimates are backtransformed to match the model definition, confidence intervals calculated from standard errors are also backtransformed to the correct scale, and will not include meaningless values like negative rate constants or formation fractions adding up to more than 1, which can not occur in a single experiment with a single defined radiolabel position.</li> +<li>The usual one-sided t-test for significant difference from zero is nevertheless shown based on estimators for the untransformed parameters.</li> +<li>Summary and plotting functions. The <code>summary</code> of an <code>mkinfit</code> object is in fact a full report that should give enough information to be able to approximately reproduce the fit with other tools.</li> +<li>The chi-squared error level as defined in the FOCUS kinetics guidance (see below) is calculated for each observed variable.</li> +<li>Iteratively reweighted least squares fitting is implemented in a similar way as in KinGUII and CAKE (see below). Simply add the argument <code>reweight = "obs"</code> to your call to <code>mkinfit</code> and a separate variance componenent for each of the observed variables will be optimised in a second stage after the primary optimisation algorithm has converged.</li> +<li>When a metabolite decline phase is not described well by SFO kinetics, SFORB kinetics can be used for the metabolite.</li> +</ul></div> +<div id="gui" class="section level2"> +<h2 class="hasAnchor"> +<a href="#gui" class="anchor"> </a>GUI</h2> +<p>There is a graphical user interface that I consider useful for real work. Please refer to its <a href="http://kinfit.r-forge.r-project.org/gmkin_static">documentation page</a> for installation instructions and a manual.</p> +</div> +<div id="news" class="section level2"> +<h2 class="hasAnchor"> +<a href="#news" class="anchor"> </a>News</h2> +<p>Yes, there is a ChangeLog, for the latest <a href="http://cran.r-project.org/web/packages/mkin/news.html">CRAN release</a> and one for the <a href="https://github.com/jranke/mkin/blob/master/NEWS.md">github master branch</a>.</p> +</div> +<div id="credits-and-historical-remarks" class="section level2"> +<h2 class="hasAnchor"> +<a href="#credits-and-historical-remarks" class="anchor"> </a>Credits and historical remarks</h2> +<p><code>mkin</code> would not be possible without the underlying software stack consisting of R and the packages <a href="http://cran.r-project.org/package=deSolve">deSolve</a> and <a href="http://cran.r-project.org/package=FME">FME</a>, to say the least.</p> +<p>It could not have been written without me being introduced to regulatory fate modelling of pesticides by Adrian Gurney during my time at Harlan Laboratories Ltd (formerly RCC Ltd). <code>mkin</code> greatly profits from and largely follows the work done by the <a href="http://focus.jrc.ec.europa.eu/dk">FOCUS Degradation Kinetics Workgroup</a>, as detailed in their guidance document from 2006, slightly updated in 2011 and in 2014.</p> +<p>Also, it was inspired by the first version of KinGUI developed by BayerCropScience, which is based on the MatLab runtime environment.</p> +<p>The companion package <a href="http://kinfit.r-forge.r-project.org/kinfit_static/index.html">kinfit</a> (now deprecated) was <a href="https://r-forge.r-project.org/scm/viewvc.php?view=rev&root=kinfit&revision=2">started in 2008</a> and <a href="http://cran.r-project.org/src/contrib/Archive/kinfit/">first published</a> on CRAN on 01 May 2010.</p> +<p>The first <code>mkin</code> code was <a href="https://r-forge.r-project.org/scm/viewvc.php?view=rev&root=kinfit&revision=8">published on 11 May 2010</a> and the <a href="http://cran.r-project.org/src/contrib/Archive/mkin">first CRAN version</a> on 18 May 2010.</p> +<p>In 2011, Bayer Crop Science started to distribute an R based successor to KinGUI named KinGUII whose R code is based on <code>mkin</code>, but which added, amongst other refinements, a closed source graphical user interface (GUI), iteratively reweighted least squares (IRLS) optimisation of the variance for each of the observed variables, and Markov Chain Monte Carlo (MCMC) simulation functionality, similar to what is available e.g. in the <code>FME</code> package.</p> +<p>Somewhat in parallel, Syngenta has sponsored the development of an <code>mkin</code> and KinGUII based GUI application called CAKE, which also adds IRLS and MCMC, is more limited in the model formulation, but puts more weight on usability. CAKE is available for download from the <a href="http://projects.tessella.com/cake">CAKE website</a>, where you can also find a zip archive of the R scripts derived from <code>mkin</code>, published under the GPL license.</p> +<p>Finally, there is <a href="http://github.com/zhenglei-gao/KineticEval">KineticEval</a>, which contains a further development of the scripts used for KinGUII, so the different tools will hopefully be able to learn from each other in the future as well.</p> +</div> +<div id="development" class="section level2"> +<h2 class="hasAnchor"> +<a href="#development" class="anchor"> </a>Development</h2> +<p>Contributions are welcome! Your <a href="https://help.github.com/articles/fork-a-repo">mkin fork</a> is just a mouse click away… The master branch on github should always be in good shape, I implement new features in separate branches now. If you prefer subversion, project members for the <a href="http://r-forge.r-project.org/R/?group_id=615">r-forge project</a> are welcome as well. Generally, the source code of the latest CRAN version should be available there. You can also browse the source code at <a href="http://cgit.jrwb.de/mkin">cgit.jrwb.de/mkin</a>.</p> +</div> +</div> + </div> -<p>Somewhat in parallel, Syngenta has sponsored the development of an <code>mkin</code> and -KinGUII based GUI application called CAKE, which also adds IRLS and MCMC, is -more limited in the model formulation, but puts more weight on usability. -CAKE is available for download from the <a href="http://projects.tessella.com/cake">CAKE -website</a>, where you can also -find a zip archive of the R scripts derived from <code>mkin</code>, published under the GPL -license.</p> + <div class="col-md-3" id="sidebar"> + <h2>Links</h2><ul class="list-unstyled"><li>Download from CRAN at <a href="https://cran.r-project.org/package=mkin">https://cran.r-project.org/package=mkin</a></li> +<li>Browse source code at <a href="http://kinfit.r-forge.r-project.org/mkin_static%0A%20%20%20%20%20http://github.com/jranke/mkin">http://kinfit.r-forge.r-project.org/mkin_static + http://github.com/jranke/mkin</a></li> +<li>Report a bug at <a href="http://github.com/jranke/mkin/issues">http://github.com/jranke/mkin/issues</a></li> +</ul><h2>Authors</h2><ul class="list-unstyled"><li>Johannes Ranke<br><small class="roles">Author, maintainer, copyright holder</small></li> +<li>Katrin Lindenberger<br><small class="roles">Contributor</small></li> +<li>René Lehmann<br><small class="roles">Contributor</small></li> +<li>Eurofins Regulatory AG<br><small class="roles">Copyright holder</small></li> +</ul><h2>License</h2> +<p>GPL</p> + + <html><body><h2>Dev status</h2><ul class="list-unstyled"><li><a href="http://cran.r-project.org/package=mkin"> + <img src="http://www.r-pkg.org/badges/version/mkin"></a></li> +</ul></body></html></div> +</div> -<p>Finally, there is -<a href="http://github.com/zhenglei-gao/KineticEval">KineticEval</a>, which contains -a further development of the scripts used for KinGUII, so the different tools -will hopefully be able to learn from each other in the future as well.</p> -<h2>Development</h2> + <footer><div class="copyright"> + <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p> +</div> -<p>Contributions are welcome! Your -<a href="https://help.github.com/articles/fork-a-repo">mkin fork</a> is just a mouse click -away… The master branch on github should always be in good shape, I implement -new features in separate branches now. If you prefer subversion, project -members for the -<a href="http://r-forge.r-project.org/R/?group_id=615">r-forge project</a> are welcome as well. -Generally, the source code of the latest CRAN version should be available there. -You can also browse the source code at <a href="http://cgit.jrwb.de/mkin">cgit.jrwb.de/mkin</a>.</p> +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> - </div> + </footer></div> - <div class="span3 offset1 sidebar"> - <h2>Vignettes</h2> - <ul> - <li><a href="vignettes/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a></li> - <li><a href="vignettes/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a></li> - <li><a href="vignettes/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a></li> - <li><a href="vignettes/mkin.html">mkin - Kinetic evaluation of chemical degradation data</a></li> - <li><a href="vignettes/FOCUS_Z.pdf">Example evaluation of FOCUS dataset Z</a></li> - </ul> - <h2>Authors</h2> - <ul> - <li><a href='mailto:jranke@uni-bremen.de'>Johannes Ranke</a> [aut, cre, cph]</li> - <li>Katrin Lindenberger [ctb]</li> - <li>RenĂ© Lehmann [ctb]</li> - <li>Eurofins Regulatory AG [cph]</li> - </ul> - </div> -</div> - - <footer> - <p class="pull-right"><a href="#">Back to top</a></p> -<p>Built by <a href="https://github.com/hadley/staticdocs">staticdocs</a>. Styled with <a href="https://getbootstrap.com/2.0.4/">bootstrap</a>.</p> - </footer> - </div> - </body> -</html>
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