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2013-11-06Update of the vignettesjranke5-6/+8
git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@140 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-11-06- New candidate for release containing the latest changes to the GUIjranke7-726/+102
- 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 CRANjranke2-3/+7
git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@138 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 - Remove an outdated comment from the test script.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
2013-11-04- Now the eigenvalue based solution for FOCUS 2006 D works flawlessly withjranke1-20/+2
default starting parameters - Took out a relatively long-lasting test that did not say much git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@136 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
2013-11-04Fixing parameters (initial state and differential equation parameters) nowjranke1-6/+12
also works in the experimental GUI git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@134 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_initialsjranke3-2/+9
git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@132 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-10-30Fits can now be saved in the project file in the experimental GUI, and ↵jranke1-15/+39
reloaded from it, together with the datasets and models. git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@131 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-10-30Improved fit management in the experimental GUIjranke1-47/+99
git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@130 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-10-30- Backtransform fixed ODE parameters for the summary (compare ChangeLog)jranke3-17/+8
- 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.Rjranke2-6/+130
- 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
2013-10-28Make the left pane in the new experimental GUI layout smaller and the study ↵jranke1-12/+9
data simpler as editing study details is not the purpose of the GUI git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@127 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-10-26Some improvements in ChangeLog formattingjranke1-4/+4
git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@126 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-10-25A new layout for the GUI and an update of the staticdocs, as I just jranke1-0/+445
uploaded 0.9-22 for publication on CRAN git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@125 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-10-22Commented out some of the mkinfit examples using \dontrun{} markup as they ↵jranke1-1/+3
run a bit long git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@124 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-10-21Some more progress towards the gcombobox selection of modelsjranke1-32/+50
git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@122 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-10-21- Half way through replacing gnotebooks for the fitsjranke1-57/+32
git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@121 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-10-21- Simplified implementation of mkinerrmin (see ChangeLog)jranke3-9/+20
- 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
2013-10-19Fix the example of transform_odeparms help that was broken by making the columnjranke1-1/+1
names of the data frames "start" and "transformed" in the mkinfit objects consistent. git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@119 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-10-17- Fix reweighting for the case of many metabolitesjranke2-3/+4
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)jranke5-32/+120
git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@117 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-10-16- One possibility to handle the parameters each with several named widgets, ↵jranke1-19/+22
a bit clumsy git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@116 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-10-16- More consistent output regarding optimised and fixed parameters (see ↵jranke4-53/+112
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
2013-10-14- set svn keyword for Id tag in simple.Rjranke1-3/+3
- set initial foldlevel for two files to 0 git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@114 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-10-14- Added the header to the GUI filejranke1-44/+76
- Code reformatting and some reorganisation git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@113 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-10-11Some more plotting experimentsjranke1-4/+27
git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@112 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-10-11Added a button...jranke1-20/+32
git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@111 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-10-11Some additions, fixes and formatting of the help files for mkinfit and ↵jranke2-65/+78
mkinpredict. git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@110 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-10-10- IRLS is implementedjranke6-26/+120
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 ChangeLogjranke4-16/+66
- 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 ↵jranke4-18/+141
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
2013-10-07- Added a list of models to select fromjranke2-14/+64
- Started the model editor - Added two session files used for testing git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@106 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-10-07It seems that study and dataset handling now works as desired.jranke1-20/+21
git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@105 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-10-05- There was not really a bug, only the page load takes long using FF on Linuxjranke2-28/+37
- Switching datasets now works fast and seems to be reliable - Moved the save changes button to a new line after the forms - Took out some ggroups that were not necessary any more - The study selector in the dataset editor is now renewed when the dataframe with the studies is edited git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@104 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-10-04Switching datasets is much quicker now, but somehow I introduced a bug that jranke1-47/+33
makes the Javascript engine throw an error.. And updating the study selector box in the dataset editor does not work at the moment. git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@103 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-10-04Start to change the dataset editor head from glayout to gformlayout, hoping ↵jranke1-23/+26
that this will make it possible to manipulate the gedit instances from within a function. git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@102 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-10-03Just a small bugfix, took me a while to find this, to have a working versionjranke1-1/+1
git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@101 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-10-02Saving, editing and reloading of datasets now works.jranke2-41/+125
New TODO item is handling the observed variables correctly, and generating an empty grid git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@100 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-10-01- Remove mkin GUI project files, as they can be a source of error during ↵jranke4-17/+24
development - Make the index to the dataset list ds a character, in order to be able to count the entries correctly after deleting an entry - Make the dataset switcher a handler only for the click event, as otherwise it was called by the assignment of the new data to the gtable widget git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@98 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-09-25- Fixed the NOTES listed by R CMD checkjranke4-17/+26
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
2013-09-14Started a TODO listjranke1-0/+1
git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@96 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-09-14Now the titles of the datasets can be edited. jranke1-37/+51
Saving and reloading datasets is not implemented yet git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@95 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-09-14- Selection of datasets for editing now worksjranke1-38/+48
- Button for saving dataset changes introduced git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@94 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-09-13A little more progressjranke1-1/+1
git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@93 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-09-13Add and update a study combobox in the dataset editorjranke1-19/+39
Various other small things git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@92 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-09-13Just resolved a small conflict caused by a local change before updatingjranke2-3/+3
git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@91 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-09-06Start a dataset editorjranke3-5/+81
git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@90 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
2013-09-05Clean up the GUI directory, the old stuff does not really help a lotjranke15-279/+58
git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@89 edb9625f-4e0d-4859-8d74-9fd3b1da38cb

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