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This is useful for specifying state.ini in a subsequent call to mkinfit
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For details see NEWS.md
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Add IORE support to mkinerrmin
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- As a consequence, we do not need implicit formation fractions in
mkinfit
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- 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
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- 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
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Conflicts:
DESCRIPTION
R/mkinfit.R
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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
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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
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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
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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
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git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@132 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
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- 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
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- 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
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git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@118 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
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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
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git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@109 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
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- 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
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- 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
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- 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
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git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@77 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
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git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@76 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
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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
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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
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- 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
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- 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
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- 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
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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
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- 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
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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
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- 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
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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
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- 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
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- 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
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- 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
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- 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
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