Rename ChangeLog to NEWS, new entry style, Makefile update

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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/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

-

-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