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Diffstat (limited to 'NEWS')
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@@ -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 <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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