mkin/NAMESPACE, branch v1.1.0Fitting kinetic models to chemical degradation data (also on github)https://cgit.jrwb.de/mkin/atom?h=v1.1.02022-03-07T13:55:21ZRemove nlmixr interface for release of mkin 1.1.02022-03-07T13:55:21ZJohannes Rankejranke@uni-bremen.de2022-03-07T11:03:40Zurn:sha1:7035cde3a53781721fe15a8893fdf328c789bdd2
I am postponing my attempts to get the nlmixr interface to CRAN, given
some problems with nlmixr using R-devel under Windows, see
https://github.com/nlmixrdevelopment/nlmixr/issues/596
and
https://github.com/r-hub/rhub/issues/512,
which is fixed by the removal of nlmixr from the testsuite.
For the tests to be more platform independent, the biphasic mixed
effects models test dataset was defined in a way that fitting
should be more robust (less ill-defined).
intervals() methods, more DFOP/tc variants2021-09-27T18:10:01ZJohannes Rankejranke@uni-bremen.de2021-09-27T18:10:01Zurn:sha1:5c15ef747568b3a9a9c094b6aa546dc80e3aa87aLet backtransform_odeparms handle nlmixr formation fractions2021-06-17T11:58:34ZJohannes Rankejranke@uni-bremen.de2021-06-17T11:58:34Zurn:sha1:05baf3bf92cba127fd2319b779db78be86170e5e
Also adapt summary.nlmixr.mmkin to correctly handle the way
formation fractions are translated to nlmixr
Finished 'summary.nlmixr.mmkin', checks, docs2021-06-11T09:14:45ZJohannes Rankejranke@uni-bremen.de2021-06-11T09:14:45Zurn:sha1:0c9b2f0e3c8ce65cb790c9e048476784cbbea070Rudimentary support for setting up nlmixr models2021-06-09T15:00:41ZJohannes Rankejranke@uni-bremen.de2021-06-09T14:53:31Zurn:sha1:c6eb6b2bb598002523c3d34d71b0e4a99671ccd6
- All degradation models are specified as ODE models. This appears to be
fast enough
- Error models are being translated to nlmixr as close to the mkin error
model as possible. When using the 'saem' backend, it appears not to be
possible to use the same error model for more than one observed variable
- No support yet for models with parallel formation of metabolites, where
the ilr transformation is used in mkin per default
- There is a bug in nlmixr which appears to be triggered if the data are
not balanced, see nlmixrdevelopment/nlmixr#530
- There is a print and a plot method, the summary method is not finished
Reintroduce interface to saemix2021-02-06T17:30:32ZJohannes Rankejranke@uni-bremen.de2021-02-06T17:30:32Zurn:sha1:48c463680b51fa767b4cd7bd62865f192d0354ac
Also after the upgrade from buster to bullseye of my local system, some
test results for saemix have changed.
Prepare for v1.0.02021-02-03T17:18:19ZJohannes Rankejranke@uni-bremen.de2021-02-03T15:41:31Zurn:sha1:f0ef23a7598e5d19648ae4edc2b74e0fba27a41c
- Improve authorship and copyright information
- Prepare pkgdown config
- Remove dependence on saemix as we need the development version which
is not ready for CRAN
- Temporarily remove saemix interface to check code coverage of the rest
mixed.mmkin and test coverage2020-12-08T21:08:38ZJohannes Rankejranke@uni-bremen.de2020-12-08T21:08:38Zurn:sha1:f606838c5310f365eea1c0d6421f5c3636a4dc79Support storing mkinmod compiled code as CFunc objects2020-11-24T00:46:57ZJohannes Rankejranke@uni-bremen.de2020-11-20T18:43:46Zurn:sha1:503441b0a958c1df50df0ee7cfc3bde4ea1b1865
With automatic reloading in mkinfit and mkinpredict in case the
DLL is not loaded and the original DLL path has been cleaned up.
Depends on jranke/inline@974bdea04fcedfafaab231e6f359c88270b56cb9
See inline#13
export create_deg_func2020-11-20T18:42:33ZJohannes Rankejranke@uni-bremen.de2020-11-20T18:42:33Zurn:sha1:3ded5c1c45d9dbd64d3d40835e68e8cf47932346