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authorJohannes Ranke <jranke@uni-bremen.de>2016-10-26 23:18:20 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2016-10-26 23:18:20 +0200
commit8f38147e145c66ebd27f5d9fcc6f00172c25872f (patch)
tree35123308ef781f6ad4b83b6d421d5e0e35d2e574 /docs/index.html
parentd106bebafe070cb803dd7205b1581b20eaf61cb5 (diff)
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+<!-- Generated by pkgdown: do not edit by hand --><html><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>Kinetic Evaluation of Chemical Degradation Data &bull; mkin</title><!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"><script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet"><script src="jquery.sticky-kit.min.js"></script><script src="pkgdown.js"></script><!-- mathjax --><script src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
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+ <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
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@@ -48,46 +15,54 @@
<a class="navbar-brand" href="index.html">mkin</a>
</div>
<div id="navbar" class="navbar-collapse collapse">
- <ul class="nav navbar-nav">
- <li>
+ <ul class="nav navbar-nav"><li>
<a href="index.html">Home</a>
</li>
<li>
<a href="reference/index.html">Reference</a>
</li>
- </ul>
- <ul class="nav navbar-nav navbar-right">
- <li>
+ </ul><ul class="nav navbar-nav navbar-right"><li>
<a href="https://github.com/jranke/mkin">
<span class="fa fa-github fa-lg"></span>
</a>
</li>
- </ul>
- </div><!--/.nav-collapse -->
+ </ul></div><!--/.nav-collapse -->
</div><!--/.container -->
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+
- </header>
+ </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>
- <div class="row">
- <div class="col-md-9">
-
-<h1 id="mkin">mkin</h1>
-<p><a href="http://cran.r-project.org/package=mkin"><img src="http://www.r-pkg.org/badges/version/mkin"></a></p>
<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>
-<h2 id="installation">Installation</h2>
+<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>
-<h2 id="background">Background</h2>
+</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 &lsquo;Credits and historical remarks&rsquo; below.</p>
-<h2 id="usage">Usage</h2>
+</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>
-<h2 id="documentation">Documentation</h2>
+</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>
-<h2 id="features">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>
+</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>
@@ -98,12 +73,20 @@
<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 id="gui">GUI</h2>
+</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>
-<h2 id="news">News</h2>
+</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>
-<h2 id="credits-and-historical-remarks">Credits and historical remarks</h2>
+</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>
@@ -112,16 +95,41 @@
<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.&nbsp;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>
-<h2 id="development">Development</h2>
+</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&hellip; 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>
+
+ <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&nbsp;holder</small></li>
+<li>Katrin Lindenberger<br><small class="roles">Contributor</small></li>
+<li>Ren&eacute; Lehmann<br><small class="roles">Contributor</small></li>
+<li>Eurofins Regulatory AG<br><small class="roles">Copyright&nbsp;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>
+
+
+ <footer><div class="copyright">
+ <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p>
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