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2013-12-04Make it possible to use different ode solvers=1-3/+5
2013-11-13Squashed commit of the following:jranke1-0/+2
commit d8dbf2ad866fb9d34cd1100000b9c116219ecef6 Author: Johannes Ranke <jranke@uni-bremen.de> Date: Wed Nov 13 22:09:41 2013 +0100 Add possibility to control more mkinfit arguments from the GUI commit 8f1bae2142b37a0ff6b8989b2d1569686937f68e Author: Johannes Ranke <jranke@uni-bremen.de> Date: Wed Nov 13 20:30:11 2013 +0100 Add initial weighting choice to GUI commit c99b5c298713a7c14e8ab5604c68613d0b7af27a Author: Johannes Ranke <jranke@uni-bremen.de> Date: Wed Nov 13 16:25:31 2013 +0100 Update of TODO from git bash on Windows commit 8bf2a6f8f6bd752433f06b26b5da334e958f5166 Author: Johannes Ranke <jranke@uni-bremen.de> Date: Wed Nov 13 16:00:01 2013 +0100 Update of README using TortoiseGit git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@162 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-11-05- Use an increasing small numeric value instead of random numbers for ↵jranke1-1/+5
generating different default values for kinetic rate constants to increase transparency and reproducibility. This also works nicely. - Remove an outdated comment from the test script. git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@137 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-11-04Add small random numbers to default initial values for rate constants to avoidjranke1-2/+2
numerical artefacts occurring in eigenvalue based solutions. git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@135 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-11-04Bugfix for a recently introduced breakage of fixed_initialsjranke1-1/+4
git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@132 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-10-30- Backtransform fixed ODE parameters for the summary (compare ChangeLog)jranke1-2/+2
- Reformatted ChangeLog - Version bump as mkin 0.9-22 is on CRAN git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@129 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-10-29- Just one little formatting change in mkinfit.Rjranke1-1/+2
- Some very basic fitting now works in the experimental GUI with the new widget layout git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@128 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-10-17- Fix reweighting for the case of many metabolitesjranke1-1/+1
git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@118 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-10-16- More consistent output regarding optimised and fixed parameters (see ↵jranke1-4/+9
ChangeLog) - Switch from gcanvas to gsvg - Start setting up the fits in the GUI - add files for testing gWidgetsWWW2 functionality git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@115 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-10-10- IRLS is implementedjranke1-14/+58
git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@109 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-10-10- Added a ChangeLogjranke1-16/+33
- Do not use time zero values of 0 for chi2 error level calculations (see changelog) - Show weighting method in summary - Correct the output of the data in the case of manual weights - Some reformatting in mkinfit.R - GUI: First attempt at representing a fit in the GUI git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@108 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-06-18Pending check-in of stuff started at east one month ago:jranke1-0/+3
- avoid returning factors in the data frame in mkin_wide_to_long - stop returning useless results with eigenvalue based solutions when observed absolute values are all very small - better test case for schaefer97 data making use of stepwise fitting - but the solution obtained in one step is better... git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@83 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-04-14- Update the TODO list, setting some requirements for version 1.0jranke1-2/+12
- 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
2013-03-15Add the solution type used in the fit to the summaryjranke1-0/+4
git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@77 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-03-12Improve formatting of data in print.summary.mkinfit()jranke1-1/+1
git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@76 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-03-05- Calculate confidence intervals for parameters based on the t distributionjranke1-22/+37
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
2013-02-21Make the use of globalVariable() conditional on R Version >= 2.15.1,jranke1-1/+1
in order to make mkin build on such R versions again. git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@70 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-02-18- Completion of the multicompartment part of the mkin examples vignettejranke1-9/+13
- Fix to chi2 error level calculation by correctly returning backtransformed parameters as bparms.optim and bparms.fixed - Adaptations of unit tests, summary and plot functions git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@67 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-02-17- Added the examples vignette to the kinfit packagejranke1-1/+2
- Added calls to utils::globalVariables to make R CMD check pass cleanly without NOTES git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@62 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-02-16- Some maintenance fixesjranke1-1/+1
- 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
2013-02-05- Prevent wrong association of colors and linetypes in plots during mkinfit ↵jranke1-6/+7
operation - Make solid lines the default in such plots, as in plot.mkinfit git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@60 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2012-11-26- Added an S3 plot method for mkinfit modelsjranke1-1/+1
- 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 basedjranke1-3/+4
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() functionjranke1-12/+16
- 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
2012-06-18Put the calculation of dissipation times, formation fractions and SFORB ↵jranke1-93/+5
eigenvalues into a separate function Some testing of this functionality in test.R git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@40 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2012-05-07- Moved the call to mkinerrmin to summary.mkinfitjranke1-33/+12
- 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
2012-04-25- Some more unit testsjranke1-8/+7
- Some more other tests in test.R - Adaptation of mkinplot git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@36 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2012-04-24- Added the reference fit data for FOCUS 2006 datasets from the kinfit packagejranke1-5/+28
- 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 a couple of thingsjranke1-1/+5
- 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
2012-04-23- Some fixes to mkinfit, to account for the changes in mkinmodjranke1-18/+25
- 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
2012-04-16- Start of an adaptation of mkinfit, but it seems nothing is really neededjranke1-0/+6
- Tests suggest that mkinmod is still buggy git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@27 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2012-04-11Added subversion keyword substitution to R source files in order to get ↵jranke1-1/+1
correct Id tags git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@23 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2012-04-10- Fitting and summaries now work with the new parameter transformations.jranke1-40/+29
- 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 functionjranke1-184/+45
- 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.jranke1-43/+53
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.jranke1-70/+328
git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@17 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2010-05-31- Added a test based on the KinGUI paper "complex case"jranke1-3/+3
- 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
2010-05-20Various improvements, the most prominent being the addition of the jranke1-12/+24
test dataset from the original KinGUI Piacenza paper. git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@10 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2010-05-18Much more complete version that was just submitted to CRAN.jranke1-18/+222
git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@9 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2010-05-11Initial upload of the upcoming multicompartment version of kinfit.jranke1-0/+66
Some functionality is still missing (chi2), some may never be implemented (FOMC model), but in general it is much more powerful than kinfit, owing to the powerful FME package. git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@8 edb9625f-4e0d-4859-8d74-9fd3b1da38cb

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