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Diffstat (limited to 'NEWS')
| -rw-r--r-- | NEWS | 96 |
1 files changed, 0 insertions, 96 deletions
@@ -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 <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
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