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2014-07-02Support formation fractions without sink pathway, updatesJohannes Ranke1-50/+113
2014-07-01One more source code commentJohannes Ranke1-0/+2
2014-06-27Reorganize the summary in a more logical orderJohannes Ranke1-19/+19
2014-05-20Step back regarding confidence intervals of formation fractionsJohannes Ranke1-3/+15
- 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
2014-05-09Set upper and lower boundx for untransformed fractionsJohannes Ranke1-3/+16
2014-04-30Fix of bug introduced with t-testJohannes Ranke1-1/+1
2014-04-30Restore t-test (1- and 2-sided) for fitted parametersJohannes Ranke1-3/+6
2014-04-25McCall 2,4,5-T dataset, lower bound for transform_rates=FALSEJohannes Ranke1-2/+11
2014-04-22Possibility to fit without parameter transformationJohannes Ranke1-8/+26
2014-02-27Format of gmkin workspace files, copyright, updatesJohannes Ranke1-0/+1
- 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
2014-01-22Merge branch 'master' of https://github.com/jranke/mkinJohannes Ranke1-3/+5
Conflicts: DESCRIPTION R/mkinfit.R
2014-01-17- Use mkinmod$spec instead of mkinmod$map wherever possible, in order to ↵Johannes Ranke1-4/+4
make it possible to to modify mkinmod$map when the mapping of internal to observed variables should be changed. Note that such modifications will confuse plot.mkinfit and summary.mkinfit. Setting the class attribute to modFit makes summary.modFit useable in such a case
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

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