		 CHANGES in mkin VERSION 0.9-31

BUG FIXES

 - The internal renaming of optimised parameters in Version 0.9-30 led to
 errors in the determination of the degrees of freedom for the chi2 error
 level calulations in `mkinerrmin()` used by the summary function.

 - Initial values for formation fractions were not set in all cases

		 CHANGES in mkin VERSION 0.9-30

NEW FEATURES

 - It is now possible to use formation fractions in combination with turning
 off the sink in `mkinmod()`.

MAJOR CHANGES

 - The original and the transformed parameters now have different names
 (e.g. `k_parent` and `log_k_parent`. They also differ in how many they are
 when we have formation fractions but no pathway to sink.

 - The order of some of the information blocks in `print.summary.mkinfit.R()`
 has been ordered in a more logical way

MINOR CHANGES

 - The vignette FOCUS_Z has been simplified to use formation fractions with
 turning off the sink, and slightly amended to use the new versions of DT50
 values calculated since mkin 0.9-29.

 - All vignettes have been rebuilt so they reflect all changes

 - The ChangeLog was renamed to NEWS.md and the entries were converted to
 markdown syntax compatible with the `tools::news()` function built into R.

 - The test suite was overhauled. Tests of the DFOP and SFORB models with
 dataset FOCUS_2006_A were removed, as they were too much dependent on the
 optimisation algorithm and/or starting parameters, because the dataset is
 SFO (compare kinfit vignette).

 - Also, the Schaefer complex case can now be fitted using formation fractions,
 and with the 'Port' optimisation method we also fit A2 in the same way as
 published in the Piacenza paper.

 - Some more checks were introduced to `mkinfit()`, leading to warnings or
 stopping execution if unsupported combinations of methods and parameters
 are requested.

		 CHANGES in mkin VERSION 0.9-29

 - R/mkinresplot.R: Make it possible to specify `xlim` - R/geometric_mean.R,
 man/geometric_mean.Rd: Add geometric mean function - R/endpoints.R,
 man/endpoints.Rd: Calculate additional (pseudo)-DT50 values for FOMC, DFOP,
 HS and SFORB. Avoid calculation of formation fractions from rate constants
 when they are directly fitted

		 CHANGES in mkin VERSION 0.9-28

 - Do not backtransform confidence intervals for formation fractions if more
 than one compound is formed, as such parameters only define the pathways
 as a set - Add historical remarks and some background to the main package
 vignette - Correct 'isotropic' into 'isometric' for the ilr transformation

		 CHANGES in mkin VERSION 0.9-27

 - Fork the GUI into a separate package [gmkin](http://github.com/jranke/gmkin)
 - DESCRIPTION, NAMESPACE, TODO: Adapt and add copyright information -
 Remove files belonging to the GUI - Possibility to fit without parameter
 transformations, using bounds as implemented in FME - Add McCall 2,4,5-T
 dataset - Enable selection of observed variables in plotting - Add possibility
 to show residual plot in `plot.mkinfit` - R/mkinparplot.R, man/mkinparplot.Rd:
 plot parameters with confidence intervals

		 CHANGES in mkin VERSION 0.9-25

 - Change vignette format from Sweave to knitr - Split examples vignette to
 FOCUS_L and FOCUS_Z - Remove warning about constant formation fractions
 in mkinmod as it was based on a misconception - 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 clean startup -
 Add a starter function for the GUI: `gmkin()` - Change the format of the
 workspace files of gmkin so they can be distributed and documented in the
 package - Add gmkin workspace datasets FOCUS_2006_gmkin and FOCUS_2006_Z_gmkin

		 CHANGES in mkin VERSION 0.9-24

 - Bugfix re-enabling the fixing of any combination of initial values for
 state variables - Default values for kinetic rate constants are not all 0.1
 any more but are "salted" with a small increment to avoid numeric artefacts
 with the eigenvalue based solutions

		 CHANGES in mkin VERSION 0.9-23

 - Backtransform fixed ODE parameters for the summary

		 CHANGES in mkin VERSION 0.9-22

 - Get rid of the optimisation step in `mkinerrmin` - this was
 unnecessary. Thanks to KinGUII for the inspiration - actually this is
 equation 6-2 in FOCUS kinetics p. 91 that I had overlooked originally - Fix
 `plot.mkinfit` as it passed graphical arguments like main to the solver -
 Do not use `plot=TRUE` in `mkinfit()` example - The first successful fits
 in the not so simple GUI - Fix iteratively reweighted least squares for
 the case of many metabolites - Unify naming of initial values of state
 variables - Unify naming in dataframes of optimised and fixed parameters
 in the summary - Show the weighting method for residuals in the summary -
 Correct the output of the data in the case of manual weighting - Implement
 IRLS assuming different variances for observed variables - Do not use 0
 values at time zero for chi2 error level calculations. This is the way
 it is done in KinGUII and it makes sense. It does impact the chi2 error
 levels in the output. Generally they seem to be lower for metabolites now,
 presumably because the mean of the observed values is higher

For a detailed list of changes to the mkin source please consult the commit
history on http://github.com/jranke/mkin
