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2014-07-17Optimisation choice (Marq, Port, SANN), maximum number of iterationsJohannes Ranke1-1/+1
2014-07-16Fix sorting in fit list, add NEWS fileJohannes Ranke1-2/+2
2014-07-03Improve statusbar message, update dateJohannes Ranke1-1/+1
2014-05-07Depend on an mkin version that is without GUI for sureJohannes Ranke1-1/+1
2014-05-07Fork the gmkin GUI from mkin. See ChangeLog for detailsJohannes Ranke1-21/+10
2014-05-02Update of the FOCUS Z vignette, release candidateJohannes Ranke1-1/+1
2014-04-28Fix version, write ChangeLogJohannes Ranke1-1/+1
2014-04-28Bump versionJohannes Ranke1-2/+2
2014-04-28Remove unused RSVGTipsDevice from suggested packagesJohannes Ranke1-1/+1
2014-04-25McCall 2,4,5-T dataset, lower bound for transform_rates=FALSEJohannes Ranke1-1/+1
2014-04-22Possibility to fit without parameter transformationJohannes Ranke1-2/+2
2014-03-24Source of gWidgetsWWW2 package to comply with CRAN policyJohannes Ranke1-1/+3
2014-03-20Add copyright information and bugreport URLJohannes Ranke1-3/+5
2014-02-27Format of gmkin workspace files, copyright, updatesJohannes Ranke1-2/+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 Ranke1-2/+2
Conflicts: DESCRIPTION R/mkinfit.R
2014-01-17- Use mkinmod$spec instead of mkinmod$map wherever possible, in order to ↵Johannes Ranke1-1/+1
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
2013-12-04Update ChangeLog and DESCRIPTIONJohannes Ranke1-2/+2
2013-11-18Add GUI start function, keep GUI here in mkinJohannes Ranke1-3/+5
2013-11-17Conflicts:jranke1-3/+4
README.md TODO git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@163 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-11-06Another version bump as 0.9.24 is on CRAN nowjranke1-1/+1
git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@142 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-11-06Version bump as I have just release 0.9.23 to CRANjranke1-1/+1
git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@141 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-11-06- New candidate for release containing the latest changes to the GUIjranke1-1/+1
- Checking and releasing myself as r-forge has a stuffed build pipeline git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@139 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-11-05- Update of changelog and description file for release to CRANjranke1-1/+1
git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@138 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-11-04Bugfix for a recently introduced breakage of fixed_initialsjranke1-1/+1
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
2013-10-21- Simplified implementation of mkinerrmin (see ChangeLog)jranke1-1/+1
- 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
2013-10-16- More consistent output regarding optimised and fixed parameters (see ↵jranke1-1/+1
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 implementedjranke1-2/+2
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/+2
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 checkjranke1-2/+2
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
2013-09-13Just resolved a small conflict caused by a local change before updatingjranke1-2/+2
git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@91 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-06-18Start of new versionjranke1-2/+2
git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@84 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-04-14- Update the TODO list, setting some requirements for version 1.0jranke1-3/+3
- 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
2013-03-15Forgot to update the date in the last commitjranke1-1/+1
git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@78 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-03-15Add the solution type used in the fit to the summaryjranke1-1/+1
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()jranke1-2/+2
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 distributionjranke1-2/+2
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/+2
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,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 vignettejranke1-1/+1
- 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
2013-02-18More work on the examples vignettejranke1-2/+2
git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@65 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-02-17- Added the examples vignette to the kinfit packagejranke1-2/+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 fixesjranke1-2/+2
- 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 ↵jranke1-2/+2
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 modelsjranke1-2/+2
- 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
2012-09-20Some updates of the mkin vignettejranke1-2/+2
Added the kinfit vignette file to the repository git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@57 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2012-07-03- Add rtol argument in order to increase the precision of deSolve basedjranke1-2/+2
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
2012-06-28Update DESCRIPTION files to bump versionsjranke1-2/+2
git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@47 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2012-06-25- Document endpoints() functionjranke1-3/+3
- 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
2012-05-16Update of the DESCRIPTION file to produce a new version, as an important ↵jranke1-2/+2
error was fixed. git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@39 edb9625f-4e0d-4859-8d74-9fd3b1da38cb

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