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2020-11-12mkindsg class to hold groups of datasetsJohannes Ranke1-1/+1
- D24_2014 dataset on aerobic soil degradation of 2,4-D from the EU assessment as mkindsg object with metadata - f_time_norm_focus() to do time-step normalisation using the FOCUS method - focus_soil_moisture data with default moisture contents at pF1, pF 2 and pF 2.5 for USDA soil types from FOCUS GW guidance - Dataset generation scripts in inst/dataset_generation - Depend on R >= 2.15.1 in order to facilitate the use of utils::globalVariables()
2020-05-11Avoid merge() and data.frame() in cost functionJohannes Ranke1-0/+1
also for deSolve and eigenvalue based solutions. This noticeably increases performance for these methods, see test.log and benchmark vignette.
2020-05-09Avoid the call to merge for analytical solutionsJohannes Ranke1-0/+1
This increases performance up to a factor of five!
2019-11-05Fix standardized residual plots in 'plot_res'Johannes Ranke1-3/+5
2019-11-04Scaled residual plotsJohannes Ranke1-9/+26
2019-10-25Use roxygen for functions and methodsJohannes Ranke1-19/+107
2019-10-21Improve some plotting routines, more testsJohannes Ranke1-22/+22
Static documentation rebuilt by pkgdown
2019-09-02Some changes to improve plots on beamer slidesJohannes Ranke1-4/+5
2019-05-08Add functionality to plot the error modelJohannes Ranke1-5/+14
by plotting squared residuals against predicted values, and showing the variance function used in the fitted error model. Rebuild docs
2017-09-06Use full fitted curve(s) for y axis scaling ...Johannes Ranke1-2/+1
... when using plot_sep() or plot.mkinfit(..., sep_obs = TRUE)
2017-09-06Fix scaling of residual plots ...Johannes Ranke1-2/+6
... in the case of separate plots for each observed variable as obtained with plot_sep() or plot.mkinfit(..., sep_obs = TRUE)
2016-12-07Use latex in plots when using tikzDeviceJohannes Ranke1-2/+9
2016-11-17Remove trailing whitespace, clean headersJohannes Ranke1-16/+16
Also ignore test.R in the top level directory, as it is not meant to be public
2016-09-10Plot using R model if compiled model is not availableJohannes Ranke1-2/+9
2016-06-28Convenience wrapper plot_sep, further vignette updatesJohannes Ranke1-0/+6
2016-06-27Show chi2 in plot.mkinfit, round with signifJohannes Ranke1-1/+18
2016-06-25Fix the plot margins for combined plotsJohannes Ranke1-0/+21
2016-06-25Now the old behaviour is restored for compatibility reasonsJohannes Ranke1-10/+17
When observed variables are not shown in separate plots, the residual plot is shown in the lower third of the total plotting area
2016-06-25Working state, but not backwards compatibleJohannes Ranke1-48/+88
In this commit, the separatation of plots for observed variables works. The formatting should be improved. However, in gmkin, plotting with show_residuals = TRUE is used, and the GUI expects that the residual plot is below the main plot. This behaviour should be restored.
2015-10-19Make plot.mkinfit work with models where full_name components are NULLJohannes Ranke1-0/+2
2015-10-16Full compound names in models that are shown in the plotJohannes Ranke1-2/+6
2014-08-29Avoid an unnecessary warningJohannes Ranke1-1/+1
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
2014-04-28Option to add residual plot to plot.mkinfitJohannes Ranke1-1/+27
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
2013-11-04Complete the fix for fixing initial values for state variablesjranke1-1/+4
git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@133 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
2013-03-04Introduce 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,jranke1-1/+2
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 vignettejranke1-3/+2
- 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- 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 packagejranke1-0/+23
- 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
2012-11-26- Added an S3 plot method for mkinfit modelsjranke1-0/+45
- 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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