Package: PRIMsrc

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Date   : 2015-01-20
o RELEASE 0.1.0
- Initial release to GitHub.
- Built and tested under R 3.1.2 and release update to GitHub.
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Date   : 2015-01-22
o RELEASE 0.2.0
- Built and tested 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.
- Built and tested under R 3.1.2 and release update to GitHub.
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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 internal peel.box(...) functions.
- Updated manual, version number.
- Built and tested under R 3.1.2 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.
- Built and tested under R 3.1.2 and release update to GitHub.
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Date   : 2015-03-16
o RELEASE 0.5.3
- Added S3-generic 'summary' function.
- Added S3-generic 'predict' function.
- Built and tested under R 3.1.2 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.
- Built and tested under R 3.1.2 and release update to GitHub.
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Date   : 2015-06-19
o RELEASE 0.5.6
- Correction/extension of internal variable pre-selection procedure by cross-validing 
  both parameters alpha (mixing) and lambda (shrinkage) of the 'glmnet' package. 
  This allows to get true lasso-ridge shrinkage estimates.
- Improved robustness in internal functions list2mat and list2array.
- Minor improvement in internal function cv.folds.
- Added vignettes
- Built and tested 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.
- Built and tested under R-devel (2015-07-20 r68705). 
- Initial release to CRAN and update to GitHub.
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Date   : 2015-08-28
o RELEASE 0.5.8
- Removed pre-selection of variables (covariates) by regular Cox-regression
  and made the remaining Elastic-Net pre-selection of variables optional by
  passing an additional argument in the main function sbh().
- Main function sbh() now returns the parameters used for configuring the parallelization.
- Replaced real dataset #2 of breast cancer data with lung cancer data for reason of size.
- Added S3-generic 'print' function and updated S3-generic 'summary' function.
- Created a new internal subroutine cv.presel() for (optional) variable pre-selection.
- Changed main argument of plot functions from `x` to `object`.
- Minor corrections in the manual.
- Built and tested under R-devel (2015-08-02 r68804) and release update to GitHub.
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Date   : 2015-09-07
o RELEASE 0.5.9
- Replaced plotting function plot_scatter(...) by S3-generic `plot` function.
- Corrected all plotting functions for the case of a NULL graphical device.
- Cross-validated estimates of box endpoint quantities of interest now contains 
  sample size for all peeling steps.
- Minor updates and corrections in the outputs of S3-generic functions.
- Minor updates and corrections in the documentation file and manual.
- Built and tested under R-devel (2015-08-02 r68804) and release update to GitHub.
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Date   : 2015-09-15
o RELEASE 0.6.0
- The matrix of original dataset is now returned by the main function sbh() 
  and not the submatrix of pre-selected covariates only.
- Corrected bugs in the output of main function sbh(): 
  . the returned vectors of `pre-selected` and `used` covariates are now in reference 
    to the original index of variables.
  . the value of traces and rules are now matched accordingly.
  . plot_boxtraj() and plot_boxtrace() are now corrected accordingly.  
- The value of `object$cvfit$cv.trace` of the `PRSP` object that is returned 
  by the main function sbh() now only contains the vector of the modal trace values 
  of covariate usage at each step.
- Updated S3-generic 'summary' and 'print' functions.
- Minor updates and corrections in the documentation file and manual.
- Built and tested under R-devel (2015-09-14 r69384) and release update to GitHub.
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Date   : 2015-10-11
o RELEASE 0.6.2
- Rename example datasets #4 and #5 into #1b and #4, respectively, 
  for consistency with companion article.
- Added argument `decimals` to main function sbh() to output results in
  user-specified significant decimals.
- Added examples for all S3-generic functions.
- Corrected output of decision rules in S3-generic `print` function in case `vs=TRUE`. 
- Renamed results 'varsign`, `selected` and `used` to 'CV.sign`, `CV.selected` and `CV.used` and
  moved them to `cvfit` field of return `PRSP` object.
- Minor improvement in output plot axes names of plot_boxtrace() function.  
- Updates of corresponding modifications in the documentation file and manual.
- Built and tested under R-devel (2015-09-14 r69384) and release update to GitHub.
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Date   : 2015-11-16
o RELEASE 0.6.3
- Changed random splitting in the cross-validation step to random stratified splitting 
  with/by conservation of events.
- Changed default values of metaparameters `alpha` to 0.05 (instead of 0.10) 
                                            `minn` to 5    (instead of 10).
- Modified computation of replicated cross-validated maximal peeling length in order to avoid 
  getting below the minimal box support threshold (i.e. the greater of `beta*n` or `minn`) 
  that could occur when combining results from the cross-validation loops and replicates. 
- Corrected behaviors in case `n` is less than `minn` and `n` is equal to `minn`.
- Corrected minor errors in list2array() and list2mat() internal functions.
- Corrected minor errors in plot() and predict() S3-generic functions.
- Updates in the manual file, including added explanation about the outputs of 
  averaged covariate traces, box membership indicators and box decision rules.  
- Updates in the CITATION file.  
- Built and tested under R-devel (2015-11-04 r69597) and release update to GitHub.
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