mkin/R/mkinpredict.R, branch v0.9-35 Fitting kinetic models to chemical degradation data (also on github) https://erac.jrwb.de/mkin/atom?h=v0.9-35 2014-07-14T17:07:54Z Nearly complete support for IORE, pending mkinerrmin 2014-07-14T17:07:54Z Johannes Ranke jranke@uni-bremen.de 2014-07-14T17:07:54Z urn:sha1:a69bf39427ff4f93eebdc8bceacb8174ff13c085 First working fits with IORE model 2014-07-12T06:32:08Z Johannes Ranke jranke@uni-bremen.de 2014-07-12T06:32:08Z urn:sha1:316f1360d1e12eefe491f86b0bbcd6dcf091c736 Format of gmkin workspace files, copyright, updates 2014-02-27T15:36:11Z Johannes Ranke jranke@uni-bremen.de 2014-02-27T15:36:11Z urn:sha1:6910e67398dbcb548dae179d361cb24404ad75a4 - Change the format of the workspace files of gmkin so they can be distributed in the mkin package - Add gmkin workspace datasets FOCUS_2006_gmkin and FOCUS_2006_Z_gmkin - Restrict the unit test with the Schaefer data to parent and primary metabolites as formation fraction and DT50 for A2 are higly correlated and passing the test is platform dependent. For example, the test fails in 1 out of 14 platforms on CRAN as of today - Add Eurofins Regulatory AG copyright notices - Import FME and deSolve instead of depending on them to have cleaner startup Make it possible to use different ode solvers 2013-12-04T09:25:14Z = = 2013-12-04T09:25:14Z urn:sha1:8b94131388071980e62c17190eb4229e89975a0c Complete the fix for fixing initial values for state variables 2013-11-04T09:16:12Z jranke jranke@edb9625f-4e0d-4859-8d74-9fd3b1da38cb 2013-11-04T09:16:12Z urn:sha1:108955dfe9f328605844b5bfa6ed10190cb739e3 git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@133 edb9625f-4e0d-4859-8d74-9fd3b1da38cb - Add rtol argument in order to increase the precision of deSolve based 2012-07-03T15:46:14Z jranke jranke@edb9625f-4e0d-4859-8d74-9fd3b1da38cb 2012-07-03T15:46:14Z urn:sha1:5b28712ad11470293e7ab6746718ab3edcfe966b predictions for complex models - Improve default values for atol and set rtol default to 1e-10 git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@49 edb9625f-4e0d-4859-8d74-9fd3b1da38cb - Transferred some testing code from test.R to unit tests for mkinpredict 2012-04-25T10:33:53Z jranke jranke@edb9625f-4e0d-4859-8d74-9fd3b1da38cb 2012-04-25T10:33:53Z urn:sha1:c4e8498ee688fff1e1b2df1a7a65f888cb0d9d84 - Fixed the output format of mkinpredict to be uniform across solution types git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@33 edb9625f-4e0d-4859-8d74-9fd3b1da38cb - Added the reference fit data for FOCUS 2006 datasets from the kinfit package 2012-04-24T17:33:56Z jranke jranke@edb9625f-4e0d-4859-8d74-9fd3b1da38cb 2012-04-24T17:33:56Z urn:sha1:081b5f25cc4ef779175307d9ce20672e0573b7c9 - Used these data in unit tests for parent only models - Fixed SFORB data and calculation of formation fractions along the way - Reintroduced the test for the Schaefer 2007 data - Got rid of the mkinmod unit tests - they are too hard to maintain and the mkinfit tests test the model definitions as well git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@32 edb9625f-4e0d-4859-8d74-9fd3b1da38cb - Fixed a couple of things 2012-04-23T23:08:19Z jranke jranke@edb9625f-4e0d-4859-8d74-9fd3b1da38cb 2012-04-23T23:08:19Z urn:sha1:ea197b16fe5c582dd2a72e81d25c1ebbd5d527b3 - Now the eigenvalue based solutions are nicely consistent with the deSolve solutions, if enough output times are specified (100, sometimes more are needed, see test.R) - Workaround for invilr not to produce NaN values so often - Still a lot to do (see TODO) git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@30 edb9625f-4e0d-4859-8d74-9fd3b1da38cb - Fitting and summaries now work with the new parameter transformations. 2012-04-10T21:50:22Z jranke jranke@edb9625f-4e0d-4859-8d74-9fd3b1da38cb 2012-04-10T21:50:22Z urn: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