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authorJohannes Ranke <jranke@uni-bremen.de>2013-11-12 01:20:20 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2013-11-12 01:20:20 +0100
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treec984f3c3d57aaac034d718e3d77f80c4e23427dc /README.md
parentb167b8950b92bc0f4eb7a1f8eda06916343c680e (diff)
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The R package **mkin** provides calculation routines for the analysis of chemical
degradation data, including **m**ulticompartment **kin**etics as needed for modelling
the formation and decline of transformation products.
+
+## Installation
+
+You can install the latest released version from
+[CRAN](http://cran.r-project.org/package=mkin) from within R:
+
+```s
+install.packages('mkin')
+```
+
+A development version is usually available from [R-Forge](http://r-forge.r-project.org/R/?group_id=615):
+
+```s
+install.packages('mkin', repos = 'http://r-forge.r-project.org')
+```
+
+If R-Forge is lacking behind or if you prefer, you can install directly from
+github using the `devtools` package:
+
+```s
+require(devtools)
+install_github("mkin", "jranke")
+```
+
+## Usage
+
+For a start, have a look at the examples provided in the
+[mkinfit Documentation](http://kinfit.r-forge.r-project.org/mkin_static/mkinfit.html)
+or the package vignettes referenced from the
+[mkin package documentation page](http://kinfit.r-forge.r-project.org/mkin_static/mkinfit.html)
+
+## Credits
+
+`mkin` would not be possible without the underlying software stack consisting
+of R and the packages [deSolve](http://cran.r-project.org/package=deSolve),
+[minpack.lm](http://cran.r-project.org/package=minpack.lm) and
+[FME](http://cran.r-project.org/package=FME), to say the least.
+
+Also, it was inspired by the first version of KinGUI developed by BayerCropScience, which is based
+on the MatLab runtime environment.
+
+Bayer has developed a successor named KinGUII which is based on mkin, but which added, amongst other
+refinements, a graphical user interface (GUI, which is not open source, 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
+`FME` package.
+
+Syngenta has sponsored the development of an mkin based GUI application called CAKE, which
+adds IRLS and MCMC, is more limited in the model formulation, but puts more weight on usability.
+CAKE is available for download from the [CAKE website](http://projects.tessella.com/cake), where
+you can also find a zip archive of the R scripts derived from mkin, published under the GPL
+license.
+
+Finally, I just noticed the github repositories
+[StudyKin](http://github.com/zhenglei-gao/StudyKin) and
+[KineticEval](http://github.com/zhenglei-gao/KineticEval), the latter of which appears to be
+actively developed.

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