mkin/NAMESPACE, branch nlmixr Fitting kinetic models to chemical degradation data (also on github) https://cgit.jrwb.de/mkin/atom?h=nlmixr 2021-09-27T18:10:01Z intervals() methods, more DFOP/tc variants 2021-09-27T18:10:01Z Johannes Ranke jranke@uni-bremen.de 2021-09-27T18:10:01Z urn:sha1:5c15ef747568b3a9a9c094b6aa546dc80e3aa87a Let backtransform_odeparms handle nlmixr formation fractions 2021-06-17T11:58:34Z Johannes Ranke jranke@uni-bremen.de 2021-06-17T11:58:34Z urn:sha1:05baf3bf92cba127fd2319b779db78be86170e5e Also adapt summary.nlmixr.mmkin to correctly handle the way formation fractions are translated to nlmixr Finished 'summary.nlmixr.mmkin', checks, docs 2021-06-11T09:14:45Z Johannes Ranke jranke@uni-bremen.de 2021-06-11T09:14:45Z urn:sha1:0c9b2f0e3c8ce65cb790c9e048476784cbbea070 Rudimentary support for setting up nlmixr models 2021-06-09T15:00:41Z Johannes Ranke jranke@uni-bremen.de 2021-06-09T14:53:31Z urn: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 saemix 2021-02-06T17:30:32Z Johannes Ranke jranke@uni-bremen.de 2021-02-06T17:30:32Z urn:sha1:48c463680b51fa767b4cd7bd62865f192d0354ac Also after the upgrade from buster to bullseye of my local system, some test results for saemix have changed. Prepare for v1.0.0 2021-02-03T17:18:19Z Johannes Ranke jranke@uni-bremen.de 2021-02-03T15:41:31Z urn: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 coverage 2020-12-08T21:08:38Z Johannes Ranke jranke@uni-bremen.de 2020-12-08T21:08:38Z urn:sha1:f606838c5310f365eea1c0d6421f5c3636a4dc79 Support storing mkinmod compiled code as CFunc objects 2020-11-24T00:46:57Z Johannes Ranke jranke@uni-bremen.de 2020-11-20T18:43:46Z urn: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_func 2020-11-20T18:42:33Z Johannes Ranke jranke@uni-bremen.de 2020-11-20T18:42:33Z urn:sha1:3ded5c1c45d9dbd64d3d40835e68e8cf47932346 mkindsg class to hold groups of datasets 2020-11-12T10:11:03Z Johannes Ranke jranke@uni-bremen.de 2020-11-12T10:04:45Z urn: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()