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authorJohannes Ranke <jranke@uni-bremen.de>2016-09-10 05:21:52 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2016-09-10 05:55:25 +0200
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+ <div class="span8">
+ <h1>mkin</h1>
+
+<p><a href="http://cran.r-project.org/package=mkin"><img src="http://www.r-pkg.org/badges/version/mkin" alt=""/></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>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>
+
+<pre><code class="r">install.packages(&quot;mkin&quot;)
+</code></pre>
+
+<h2>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
+&#39;Credits and historical remarks&#39; 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 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 = &quot;obs&quot;</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&amp;root=kinfit&amp;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&amp;root=kinfit&amp;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>
+
+<h2>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 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>René Lehmann [ctb]</li>
+ <li>Eurofins Regulatory AG [cph]</li>
+ </ul>
+ </div>
+</div>
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