mkin/NAMESPACE, branch v0.9-37Fitting kinetic models to chemical degradation data (also on github)https://cgit.jrwb.de/mkin/atom?h=v0.9-372015-06-20T01:59:56ZLow-level generation of compiled models2015-06-20T01:59:56ZJohannes Rankejranke@uni-bremen.de2015-06-19T23:06:24Zurn:sha1:062b9cc1d084e8bb5e552076fc48ade4b3050644
As it is unclear if and when ccSolve will be published on CRAN,
the generation, compilation and use of the C version of the
system of differential equations was developed for mkin, inspired and
guided by the code from the ccSolve package. Many thanks again to
Karline Soetaert for all of her work on this and other R packages.
Now all model types, including the Hockey-Stick model for the parent
compund and the IORE model for parent and/or metabolites can be compiled.
Add a vignette showing the performance of compiled models2015-04-17T22:06:38ZJohannes Rankejranke@uni-bremen.de2015-04-17T22:06:38Zurn:sha1:a26b44d15c11ebb41083fc2efab0cc91a027b55bCompile differential equation models with ccSolve package2015-04-14T17:50:57ZJohannes Rankejranke@uni-bremen.de2015-04-14T17:50:57Zurn:sha1:b21c601052f85e392e48d903b8903a1a392fe786
If the ccSolve package is available, and time is not in the right hand
side of the equations (i.e. if only SFO and SFORB models are used),
the differential equation model is compiled from auto-generated C code.
Currently, one test (FOCUS 2006 D SFO_SFO) fails
Avoid NOTES in R CMD check2015-02-21T05:56:35ZJohannes Rankejranke@uni-bremen.de2015-02-21T05:56:35Zurn:sha1:42739646dc36ff74d43b638fc2c4f5259496e2b9
- Export S3 methods
- Avoid using undeclared variable names
McCall 2,4,5-T dataset, lower bound for transform_rates=FALSE2014-04-25T16:43:51ZJohannes Rankejranke@uni-bremen.de2014-04-25T16:43:51Zurn:sha1:59e2c3b5ce470ace53b93ad5e6e7d9acbfe86f21- Fixed the NOTES listed by R CMD check2013-09-25T09:18:52Zjrankejranke@edb9625f-4e0d-4859-8d74-9fd3b1da38cb2013-09-25T09:18:52Zurn:sha1:5da266adcf184c7922fd595eda24599621f92565
Candidate for publication on CRAN
git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@97 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
- Testing of the new fitting process with transformed parameters shows that it is 2012-04-11T15:49:50Zjrankejranke@edb9625f-4e0d-4859-8d74-9fd3b1da38cb2012-04-11T15:49:50Zurn:sha1:5587e833e0898e687466129dbc14950ddd58f1e0
less stable than the way of fitting used in mkin 0.8. Presumably this is due
to the frequent presence of products of two parameters (formation fractions and kinetic
rate constants) in the differential equations.
- mkinmod documentation was adapted to the new version
- Introduce vim fold markers to the mkinmod source for convenience
git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@24 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
- Fitting and summaries now work with the new parameter transformations.2012-04-10T21:50:22Zjrankejranke@edb9625f-4e0d-4859-8d74-9fd3b1da38cb2012-04-10T21:50:22Zurn:sha1:c1144753adfa0809003085009ebd85f8af9beda8
- The SFORB models with metabolites is broken (see TODO)
- Moved the vignette to the location recommended since R 2.14
- Added the missing documentation
- Commented out the schaefer_complex_case test, as this version of
mkin is not able to fit a model without sink and therefore
mkin estimated parameters are quite different
git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@22 edb9625f-4e0d-4859-8d74-9fd3b1da38cb