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2014-06-26  Johannes Ranke <jranke@uni-bremen.de> for mkin (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/mkinfit.R, man/mkinfit.Rd: Calculate additional (pseudo)-DT50
	  values for FOMC, DFOP, HS and SFORB

2014-05-20  Johannes Ranke <jranke@uni-bremen.de> for mkin (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

2014-05-09  Johannes Ranke <jranke@uni-bremen.de> for mkin (0.9-27)

	* Fork the GUI into a separate package 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

2014-02-27  Johannes Ranke <jranke@uni-bremen.de> for mkin (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

2013-11-06  Johannes Ranke <jranke@uni-bremen.de> for mkin (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

2013-10-30  Johannes Ranke <jranke@uni-bremen.de> for mkin (0.9-23)

	* Backtransform fixed ODE parameters for the summary

2013-10-21  Johannes Ranke <jranke@uni-bremen.de> for mkin (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

Changes performed in earlier versions are documented in the subversion log
files on R-Forge http://www.r-forge.r-project.org/scm/?group_id=615

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