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2014-02-27Format of gmkin workspace files, copyright, updatesJohannes Ranke2-1/+3
- 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 Ranke3-20/+13
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=2-7/+11
2013-12-04Remove mkinmod warning based on a misconceptionJohannes Ranke1-13/+2
2013-11-18Add GUI start function, keep GUI here in mkinJohannes Ranke1-0/+11
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
2013-11-04Complete the fix for fixing initial values for state variablesjranke2-1/+9
git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@133 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
2013-10-21- Simplified implementation of mkinerrmin (see ChangeLog)jranke1-6/+9
- Improve ChangeLog and add comment to source code - Simple test of the new mkinerrmin implementation in test.R - Added some summaries for documenting the changes in mkinerrmin git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@120 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
2013-10-17- 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
2013-10-16- 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 implementedjranke2-16/+60
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 ChangeLogjranke2-16/+34
- 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
2013-10-08- Added the possibility to specify the observed variable in mkinmod in a ↵jranke1-3/+4
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
2013-06-18Pending check-in of stuff started at east one month ago:jranke2-2/+5
- 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 1.0jranke3-2/+27
- 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
2013-03-04Introduce the possibility to place the legend with mkin using arguments lpos ↵jranke1-2/+3
and inset git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@72 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-02-21Make the use of globalVariable() conditional on R Version >= 2.15.1,jranke5-5/+8
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 vignettejranke4-14/+17
- 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
2013-02-18- Some more work on the vignettejranke1-2/+1
- Don't plot a main title in mkinresplot git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@66 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-02-18More work on the examples vignettejranke1-8/+16
git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@65 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
2013-02-17- Added the examples vignette to the kinfit packagejranke6-5/+50
- 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 fixesjranke3-4/+4
- 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
2012-12-13Small formatting improvementsjranke1-5/+8
git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@59 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2012-11-26- Added an S3 plot method for mkinfit modelsjranke3-37/+48
- 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 basedjranke3-5/+7
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
2012-06-28- Formatting improvement of mkinmodjranke2-18/+19
- Small fix in mkinplot git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@45 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 ↵jranke3-94/+100
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
2012-05-16Fixed a bug in mkinmod that produced a erroneous coefficient matrix if more ↵jranke1-4/+7
than one SFORB submodel is used git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@38 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2012-05-07- Moved the call to mkinerrmin to summary.mkinfitjranke2-46/+71
- 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 testsjranke2-80/+17
- 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
2012-04-25- Transferred some testing code from test.R to unit tests for mkinpredictjranke1-4/+4
- 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
2012-04-24- Added the reference fit data for FOCUS 2006 datasets from the kinfit packagejranke2-6/+49
- 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 thingsjranke4-3/+20
- 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
2012-04-16Overhaul of mkinmod in order to make it possible to choose between different ↵jranke1-52/+108
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
2012-04-15- Fixed the SFORB coefficient matrix, at least for the case where parent is ↵jranke1-2/+9
SFORB - This version works but is slower and less stable than mkin 0.8-11 - mkinplot is not adapted to this version git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@25 edb9625f-4e0d-4859-8d74-9fd3b1da38cb

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