Package: PRIMsrc

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Date   : 2015-01-20
o RELEASE 0.1.0
- Initial release of the package to GitHub.
- Test build under R 3.0.2 
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Date   : 2015-01-22
o RELEASE 0.2.0
- Test build under R 3.1.2 and release update to GitHub.
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Date   : 2015-02-01
o RELEASE 0.3.0
- Minor updates in the manual, email and version number.
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Date   : 2015-02-27
o RELEASE 0.4.0
- Extension to high-dimensional p > n and p >> n cases by adding an internal variable selection procedure 
  using the Elasticnet-Regularized Cox Regression function of the 'glmnet' package.
- Removed (temporarily) interactive option in sbh() in case no variables are selected by glmnet(...).
- Added dependency to glmnet package for initial variable selection.
- Added synthetic dataset #5 and example with p > n.
- Added real dataset #2 and example with p >> n.
- Added new ouputs 'selected' and 'used' in main function sbh(...) for variables effectively selected and used for peeling. 
- Removed returned values of box vertices that were redudant with the returned rules.
- Changed return value of variable traces: now also returns the matrix of traces by replication.
- Corrected superfluous codes in the parallelization section, before clusterCall(...) in sbh(...).
- Corrected number of replications in sbh(...) in case of parallelization. 
- Corrected stepwise variable selection procedure in peel.box() to account for missing values.
- Corrected definition of the cross-validated box vertices (definition) in the case of "combined CV" technique.
- Corrected generation of random seed when none is provided. 
- Minor updates, bugs and code improvements in sbh(...) and peel.box(...) functions.
- Updated manual, version number.
- Test build under R 3.0.2 and release update to GitHub.
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Date   : 2015-03-04
o RELEASE 0.5.0
- Change of package name and GitHub repository name from PrimSRC to PRIMsrc.
- Added CRAN/GitHub subfolder doc for PDF documentation files (including manual and applied study abstract).
- Removed option for overlaying plots of multiple PRSP objects 
  in plot.boxtrace(...) and plot.boxtraj(...).
- Added argument "toplot" to choose which covariates should be plotted
  in plot.boxtrace(...) and plot.boxtraj(...).
- Corrected handling of empty PRSP object (failed peeling) in all plotting functions.
- Implementation of plotting device now internal to all plotting functions.
- Removed internal functions from the manual, updated manual, version number.
- Test build under R 3.0.2 and release update to GitHub.
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Date   : 2015-03-16
o RELEASE 0.5.3
- Added S3-class generic summary function.
- Added S3-class generic predict function.
- Made all plotting functions S3-class functions and renamed them as plot.xxx(...).
- Test build under R 3.0.2 and release update to GitHub.
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Date   : 2015-04-10
o RELEASE 0.5.5
- Removed argument 'discr' in the main function: no special rounding of discrete covariate 
  decision rules is done any longer.
- Made the internal variable selection procedure conditional on whether p <= n or not.
- Corrected treatment of missing values in case of replications for the variable traces.
- Corrected output of variable trace modal values.
- Corrected pre-selected variable output.
- Several minor bugs corrected.
- Test build under R 3.0.2 and release update to GitHub.
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Date   : 2015-06-19
o RELEASE 0.5.6
- Correction/extension of internal variable selection procedure by cross-validing 
  both parameters: alpha (mixing) as well as lambda (shrinkage) in the Elasticnet-Regularized 
  Cox Regression function of the 'glmnet' package. This allows to get true lasso-ridge penalty.
- Improved robustness in internal functions list2mat and list2array.
- Minor improvement in internal function cv.folds.
- Added vignettes
- Test build under R 3.0.2 and release update to GitHub.
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Date   : 2015-07-28
o RELEASE 0.5.7
- Compliance with new R CMD check, which now checks code usage via 'codetools'.
  Functions and packages from default packages other than base which are used in the package
  code are now imported via the package namespace file (NAMESPACE).
  Added new field 'Imports' in the package description file (DESCRIPTION) 
  to match the functions and packages newly imported via NAMESPACE.
- Added Cumulative Hazard Summary statistic (derived from the Nelson-Aalen estimator) 
  as new peeling criterion option in the PRSP algorithm.
- Removed S3-class generic method for all plot functions and renaming as plot_xxx.
- Removed real dataset #2 for reasons of size and redundancy with real dataset #1.
- Built and tested under R-devel (2015-07-20 r68705). 
- Initial release to CRAN and update to GitHub.
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