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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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