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Diffstat (limited to 'README.md')
| -rw-r--r-- | README.md | 29 |
1 files changed, 5 insertions, 24 deletions
@@ -12,22 +12,10 @@ if several compartments are involved. You can install the latest released version from [CRAN](http://cran.r-project.org/package=mkin) from within R: - ```r install.packages("mkin") ``` -If looking for the latest features, you can install directly from -[github](http://github.com/jranke/mkin), e.g. using the `devtools` package. -Using `quick = TRUE` skips docs, multiple-architecture builds, demos, and -vignettes, to make installation as fast and painless as possible. - - -```r -require(devtools) -install_github("jranke/mkin", quick = TRUE) -``` - ## Background In the regulatory evaluation of chemical substances like plant protection @@ -60,7 +48,7 @@ maintained at the R-Forge project site. two latent state variables for the observed variable. * As of version 0.9-39, fitting of several models to several datasets, optionally in parallel, is supported, see for example - [`plot.mmkin`](http://kinfit.r-forge.r-project.org/mkin_static/plot.mmkin.html) + [`plot.mmkin`](http://kinfit.r-forge.r-project.org/mkin_static/plot.mmkin.html). * Model solution (forward modelling) in the function [`mkinpredict`](http://kinfit.r-forge.r-project.org/mkin_static/mkinpredict.html) is performed either using the analytical solution for the case of @@ -73,10 +61,6 @@ maintained at the R-Forge project site. The autogeneration of C code was inspired by the [`ccSolve`](https://github.com/karlines/ccSolve) package. Thanks to Karline Soetaert for her work on that. -* Model optimisation with - [`mkinfit`](http://kinfit.r-forge.r-project.org/mkin_static/mkinfit.html) - internally using the `modFit` function from the `FME` package, - but using the Port routine `nlminb` per default. * By default, kinetic rate constants and kinetic formation fractions are transformed internally using [`transform_odeparms`](http://kinfit.r-forge.r-project.org/mkin_static/transform_odeparms.html) @@ -104,9 +88,7 @@ maintained at the R-Forge project site. componenent for each of the observed variables will be optimised in a second stage after the primary optimisation algorithm has converged. * When a metabolite decline phase is not described well by SFO kinetics, - either IORE kinetics (often producing failures of the integration algorithm) - or SFORB kinetics (working nicely) can be used for the metabolite, adding one - respectively two parameters to the system. + SFORB kinetics can be used for the metabolite. ## GUI @@ -122,9 +104,8 @@ and one for the [github master branch](https://github.com/jranke/mkin/blob/maste ## Credits and historical remarks `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. +of R and the packages [deSolve](http://cran.r-project.org/package=deSolve) +and [FME](http://cran.r-project.org/package=FME), to say the least. 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 @@ -138,7 +119,7 @@ Also, it was inspired by the first version of KinGUI developed by BayerCropScience, which is based on the MatLab runtime environment. The companion package -[kinfit](http://kinfit.r-forge.r-project.org/kinfit_static/index.html) was +[kinfit](http://kinfit.r-forge.r-project.org/kinfit_static/index.html) (now deprecated) was [started in 2008](https://r-forge.r-project.org/scm/viewvc.php?view=rev&root=kinfit&revision=2) and [first published](http://cran.r-project.org/src/contrib/Archive/kinfit/) on CRAN on 01 May 2010. |