From ead80514e4230e73ec0d0242503943c8fee07bc2 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Sat, 28 Jun 2014 09:06:08 +0200 Subject: Rename ChangeLog to NEWS, new entry style, Makefile update --- ChangeLog | 81 --------------------------------------------------- GNUmakefile | 2 +- NEWS | 96 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 3 files changed, 97 insertions(+), 82 deletions(-) delete mode 100644 ChangeLog create mode 100644 NEWS diff --git a/ChangeLog b/ChangeLog deleted file mode 100644 index 5b455706..00000000 --- a/ChangeLog +++ /dev/null @@ -1,81 +0,0 @@ -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 diff --git a/GNUmakefile b/GNUmakefile index b71e81c9..39143ec3 100644 --- a/GNUmakefile +++ b/GNUmakefile @@ -16,7 +16,7 @@ SDDIR ?= $(HOME)/svn/kinfit.r-forge/www/mkin_static #------------------------------------------------------------------------------ # These must be manually kept up to date #------------------------------------------------------------------------------ -pkgfiles = ChangeLog \ +pkgfiles = NEWS \ data/* \ DESCRIPTION \ inst/unitTests* \ diff --git a/NEWS b/NEWS new file mode 100644 index 00000000..cb3143a5 --- /dev/null +++ b/NEWS @@ -0,0 +1,96 @@ +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