From d1c9bd912e6ca66eda0fcdc6cd6e877f23a473c4 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 30 Jun 2014 09:55:18 +0200 Subject: Format the NEWS file in markdown, add Makefile target --- NEWS | 96 -------------------------------------------------------------------- 1 file changed, 96 deletions(-) delete mode 100644 NEWS (limited to 'NEWS') diff --git a/NEWS b/NEWS deleted file mode 100644 index cb3143a5..00000000 --- a/NEWS +++ /dev/null @@ -1,96 +0,0 @@ -CHANGES in mkin 0.9-30 - - * The ChangeLog was renamed to NEWS and the style of its entries is - now adapted to that of a NEWS file. For a detailed list of changes to the - mkin source please consult the commit history on - http://github.com/jranke/mkin - - * The order of some of the information blocks in print.summary.mkinfit.R() - has been ordered in a more logical way - - * The vignette FOCUS_Z has been 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 - -2014-06-26 Johannes Ranke 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 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 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 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 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 for mkin (0.9-23) - - * Backtransform fixed ODE parameters for the summary - -2013-10-21 Johannes Ranke 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 -- cgit v1.2.1