mkin/R/mkinerrmin.R, branch v1.0.3Fitting kinetic models to chemical degradation data (also on github)https://erac.jrwb.de/mkin/atom?h=v1.0.32020-11-12T10:11:03Zmkindsg class to hold groups of datasets2020-11-12T10:11:03ZJohannes Rankejranke@uni-bremen.de2020-11-12T10:04:45Zurn:sha1:7b807680b66269ff911df137f56e26775d84e283
- D24_2014 dataset on aerobic soil degradation of 2,4-D from the EU
assessment as mkindsg object with metadata
- f_time_norm_focus() to do time-step normalisation using the FOCUS
method
- focus_soil_moisture data with default moisture contents at pF1,
pF 2 and pF 2.5 for USDA soil types from FOCUS GW guidance
- Dataset generation scripts in inst/dataset_generation
- Depend on R >= 2.15.1 in order to facilitate the use of
utils::globalVariables()
Fast analytical solutions for saemix, update.mmkin2020-11-05T23:03:29ZJohannes Rankejranke@uni-bremen.de2020-11-05T23:03:29Zurn:sha1:b5b446b718b15ccaae5b197e147fc1358f0f564e
Also, use logit transformation for g and for solitary formation
fractions, addressing #10.
Avoid the call to merge for analytical solutions2020-05-09T19:18:42ZJohannes Rankejranke@uni-bremen.de2020-05-09T19:18:42Zurn:sha1:efab37957381919c21d874906ce870f4941c760a
This increases performance up to a factor of five!
Use roxygen for functions and methods2019-10-25T00:03:54ZJohannes Rankejranke@uni-bremen.de2019-10-24T22:37:42Zurn:sha1:0a3eb0893cb4bd1b12f07a79069d1c7f5e991495Refactor mkinfit, infrastructure work2019-10-21T10:11:34ZJohannes Rankejranke@uni-bremen.de2019-10-21T10:11:34Zurn:sha1:7624a2b8398b4ad665a3b0b622488e1893a5ee7c
mkinfit objects now include an ll() function to calculate the
log-likelihood. Part of the code was refactored, hopefully making it
easier to read and maintain. IRLS is currently the default algorithm for
the error model "obs", for no particular reason. This may be subject
to change when I get around to investigate.
Slow tests are now in a separate subdirectory and will probably
only be run by my own Makefile target.
Formatting of test logs is improved.
Roundtripping error model parameters works with a precision of 10% when
we use lots of replicates in the synthetic data (see slow tests). This
is not new in this commit, but as I think it is reasonable this
closes #7.
Adapt tests, vignettes and examples2019-04-10T08:17:35ZJohannes Rankejranke@uni-bremen.de2019-04-10T08:17:35Zurn:sha1:194659fcaccdd1ee37851725b8c72e99daa3a8cf
- Write the NEWS
- Static documentation rebuilt by pkgdown
- Adapt mkinerrmin
- Fix (hopefully all) remaining problems in mkinfit
Remove trailing whitespace, clean headers2016-11-17T17:23:31ZJohannes Rankejranke@uni-bremen.de2016-11-17T17:14:32Zurn:sha1:f3f415520c89f9d8526bf6fadc862ebd44be220d
Also ignore test.R in the top level directory, as it is not meant to
be public
Low-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.
Merge branch 'master' into iore2014-11-12T12:44:17ZJohannes Rankejranke@uni-bremen.de2014-11-12T12:44:17Zurn:sha1:401570aa9e58c4a2f2e939f37f496453d97d3f33Bug fix and unit tests for mkinerrmin2014-08-25T08:39:40ZJohannes Rankejranke@uni-bremen.de2014-08-25T08:39:40Zurn:sha1:f30472ecd2afea6bd2153b8ad2bb2f663f3a2742
See NEWS.md for details