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2014-07-14Merge bugfix release 0.9-31 from 'master' into ioreJohannes Ranke1-1/+1
2014-07-12First working fits with IORE modelJohannes Ranke3-3/+38
2014-07-11It is B. Mikolasch, not M. Mikolasch...Johannes Ranke1-1/+1
2014-07-02Support formation fractions without sink pathway, updatesJohannes Ranke3-16/+52
2014-06-26Fix naming of SFORB DT50_bx values, fix docsJohannes Ranke1-1/+1
2014-06-26Calculate additional DT50 values for non-SFO modelsJohannes Ranke1-5/+1
2014-06-26Add function for geometric meanJohannes Ranke1-0/+23
2014-06-26Start new version, add xlim to mkinresplotJohannes Ranke1-0/+4
2014-05-20Step back regarding confidence intervals of formation fractionsJohannes Ranke1-3/+3
- Don't give confidence intervals for formation fractions that belong to a set, only for single formation fractions - Update the vignette with history and background - Correct 'isotropic' into 'isometric' in the ilr documentation, the README and the comments in transform_odeparms - Candidate for release to CRAN
2014-05-07Fork the GUI into package gmkin. See ChangeLog for detailsJohannes Ranke3-77/+0
2014-05-02Add missing files for plotting confindence intervalsJohannes Ranke1-0/+35
2014-04-29Reformat McCall data to have one Rd file per objectJohannes Ranke2-35/+42
2014-04-28Adapt the documentation for the HS modelJohannes Ranke1-1/+2
2014-04-28Option to add residual plot to plot.mkinfitJohannes Ranke2-6/+19
2014-04-26Fix the default case for obs_vars in plot.mkinfit()Johannes Ranke1-2/+3
2014-04-26Enable selection of observed variables to plotJohannes Ranke1-11/+17
2014-04-25McCall 2,4,5-T dataset, lower bound for transform_rates=FALSEJohannes Ranke2-0/+36
2014-04-22Possibility to fit without parameter transformationJohannes Ranke2-9/+44
2014-02-27Format of gmkin workspace files, copyright, updatesJohannes Ranke2-0/+55
- 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
2013-12-04Make it possible to use different ode solvers=2-6/+17
2013-12-04Make clear in help file that gmkin is experimentalJohannes Ranke1-0/+3
2013-11-18Add GUI start function, keep GUI here in mkinJohannes Ranke1-0/+19
2013-10-22Commented out some of the mkinfit examples using \dontrun{} markup as they ↵jranke1-1/+3
run a bit long git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@124 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-10-19Fix the example of transform_odeparms help that was broken by making the columnjranke1-1/+1
names of the data frames "start" and "transformed" in the mkinfit objects consistent. git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@119 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-10-17- See ChangeLog entry for today (2 small bugfixes and lots of GUI progress)jranke1-1/+1
git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@117 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-10-11Some additions, fixes and formatting of the help files for mkinfit and ↵jranke2-65/+78
mkinpredict. git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@110 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-10-10- IRLS is implementedjranke1-8/+56
git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@109 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-10-08- Added the possibility to specify the observed variable in mkinmod in a ↵jranke1-2/+5
checklist - Added the spec list the the mkinmod objects - It seems that the GUI model editor is fully functional - Version bump due to the changes in the mkinmod function arguments, thought they are backward compatible git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@107 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-09-25- Fixed the NOTES listed by R CMD checkjranke1-11/+22
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
2013-04-14- Update the TODO list, setting some requirements for version 1.0jranke1-0/+42
- Check that initial values specified using parms.ini are actually needed for the model, stop otherwise - List all formation fractions in the same place in the summary, also if they were fitted in the model - Include an FOMC model coupled to two metabolites in the unit tests - Some updates needed because of the above - Update of static documentation including the vignettes - Update of the mkin vignettes in the vignettes directory git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@82 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-03-05- Calculate confidence intervals for parameters based on the t distributionjranke1-4/+16
Thanks to the CAKE developers at Tessella for the call to qt() - Calculate asymetric confidence intervals for backtransformed parameters - Overhaul and recompile vignettes git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@74 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-03-04Small updates of two mkin help filesjranke2-2/+2
git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@73 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-03-04Introduce the possibility to place the legend with mkin using arguments lpos ↵jranke1-1/+7
and inset git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@72 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-02-18- Fix the line types in plot.mkinfit again.jranke1-1/+2
git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@64 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-02-16- Some maintenance fixesjranke4-5/+6
- Start of the examples vignette git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@61 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2012-11-26- Added an S3 plot method for mkinfit modelsjranke2-31/+73
- Fixed a bug in the mkinfit summary method which crashed on missing covariance matrices git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@58 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2012-07-03- Add rtol argument in order to increase the precision of deSolve basedjranke2-15/+24
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
2012-06-25- Document endpoints() functionjranke3-2/+35
- Fix unit tests that were broken by introduction of the endpoints function - Small documentation fixes - Format output of backtransformed parameters - Integrate snippet for making static documentation using staticdocs by Hadley Wickham git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@41 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2012-05-07- Moved the call to mkinerrmin to summary.mkinfitjranke2-14/+13
- The argument to mkinerrmin is now an object of class mkinfit - Fixed the allocation of parameters to observed variables in mkinerrmin git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@37 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2012-04-24- Added the reference fit data for FOCUS 2006 datasets from the kinfit packagejranke5-2/+159
- 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
2012-04-23- Fixed the example in the mkinmod documentationjranke1-5/+11
- Fixed the vignette - Did not fix the unit tests for mkinmod yet git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@31 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2012-04-23- Some fixes to mkinfit, to account for the changes in mkinmodjranke1-6/+17
- See TODO for what remains to be done (not complete) git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@29 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2012-04-16Overhaul of mkinmod in order to make it possible to choose between different ↵jranke1-1/+11
model specifications - a variant with minimal use of formation fractions, and a variant with formation fractions everywhere. git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@26 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2012-04-11- Testing of the new fitting process with transformed parameters shows that ↵jranke1-12/+9
it is 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
2012-04-10- Fitting and summaries now work with the new parameter transformations.jranke4-16/+117
- 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
2012-04-03- Separated model prediction out into a separate functionjranke1-4/+2
- Created separate functions for parameter transformations (not documented yet) - Fitting of analytical models works - SFO_SFO model works, complex models do not at the moment - summary.mkinfit not operational at the moment git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@21 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2012-03-27Start of the transition to fitting transformed parameters.jranke4-54/+64
Many things are broken now (see TODO list) git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@20 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2012-03-15Update kinfit and mkin to the latest version published on BerliOS.jranke14-23/+344
git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@17 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2010-06-03- Add the documentation of the KinGUI test data resultsjranke1-1/+4
- Fix the corresponding test based on these results git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@12 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2010-05-31- Added a test based on the KinGUI paper "complex case"jranke1-1/+6
- Fix the DT50 calculation for the SFORB model - Added a bit more of a description git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@11 edb9625f-4e0d-4859-8d74-9fd3b1da38cb

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