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2014-07-12First working fits with IORE modelJohannes Ranke5-8/+48
2014-07-07Coefficient matrix for formation fractions, no sink and one pathwayJohannes Ranke1-22/+26
2014-07-02Do not introduce formation fractions for singular pathwaysJohannes Ranke2-27/+29
- As a consequence, we do not need implicit formation fractions in mkinfit
2014-07-02Warning -> message, and only if initial parameter was not 1Johannes Ranke1-2/+4
2014-07-02Set implicit formation fraction to 1 even if set otherwise in parms.iniJohannes Ranke1-6/+8
2014-07-02Move handling of implicitly fixed formation fractions to mkinfitJohannes Ranke2-19/+11
2014-07-02Support formation fractions without sink pathway, updatesJohannes Ranke4-102/+215
2014-07-01One more source code commentJohannes Ranke1-0/+2
2014-07-01One more check, update source code commentJohannes Ranke1-2/+3
2014-06-27Reorder endpoints in R/endpoints.R, update vignettesJohannes Ranke1-2/+2
2014-06-27Reorganize the summary in a more logical orderJohannes Ranke1-19/+19
2014-06-26Avoid calculation of formation fractions if fittedJohannes Ranke1-3/+5
2014-06-26Fix naming of SFORB DT50_bx values, fix docsJohannes Ranke1-2/+2
2014-06-26Calculate additional DT50 values for non-SFO modelsJohannes Ranke1-2/+20
2014-06-26Add function for geometric meanJohannes Ranke1-0/+4
2014-06-26Start new version, add xlim to mkinresplotJohannes Ranke1-2/+3
2014-06-25Remove old ID tag, improve commentJohannes Ranke2-4/+3
2014-05-20Step back regarding confidence intervals of formation fractionsJohannes Ranke2-5/+17
- 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
2014-05-15Start new version number, Fix #5 (Inf values in mkinparplot)Johannes Ranke1-1/+2
2014-05-12Fix positioning of labels in mkinparplotJohannes Ranke1-1/+1
2014-05-09Set upper and lower boundx for untransformed fractionsJohannes Ranke1-3/+16
2014-05-07Fork the GUI into package gmkin. See ChangeLog for detailsJohannes Ranke1-11/+0
2014-05-05Get old parameters timely (before calling layout)Johannes Ranke1-2/+2
2014-05-05Fix .Rbuildignore, control font size in mkinparplotJohannes Ranke1-1/+2
2014-05-02Improve labelling in mkinparplotJohannes Ranke1-5/+9
2014-05-02Improve display of confidence intervalsJohannes Ranke1-4/+8
2014-05-02Add missing files for plotting confindence intervalsJohannes Ranke1-0/+53
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
2014-04-29Restore graphics parameters after plotting with residualsJohannes Ranke1-0/+2
2014-04-29Fix y label in optional residual plot of plot.mkinfitJohannes Ranke1-1/+1
2014-04-28Fix a bug recently introduced to the Hockey stick modelJohannes Ranke1-3/+3
2014-04-28Option to add residual plot to plot.mkinfitJohannes Ranke2-16/+41
2014-04-26Fix the default case for obs_vars in plot.mkinfit()Johannes Ranke1-11/+5
2014-04-26Enable selection of observed variables to plotJohannes Ranke1-11/+14
2014-04-25McCall 2,4,5-T dataset, lower bound for transform_rates=FALSEJohannes Ranke2-4/+13
2014-04-22Possibility to fit without parameter transformationJohannes Ranke2-24/+51
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

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