Version 0.5.6 [2018-02-08]
- changed dependencies to bioconductor packages ‘HiTC’ and ‘snpStats’ into Suggest and conditionnaly used them
Version 0.5.5 [2018-01-30]
- simplified code (replaced many C functions by a unique R function using Matrix)
- adjClust now properly handles similarities with diagonal entries different from 1
- removed arguments that were not used (blMin and verbose)
- simplified Hi-C example
Version 0.5.4 [2018-01-12]
- More tests for modify and modifySparse
- BUG FIX in condnCheck
Version 0.5.3 [2017-12-04]
- ‘height’ is now defined as the value of the linkage criterion (as is done in ‘hclust’), rather than the total inertia of the clustering (as is done in ‘rioja’).
- Added several representations for the dendrogram corresponding to different choices for the height.
- Improved documentation and vignettes.
- Removed non-standard fields in the output of ‘adjclust’ (#13).
- Added tests for: equivalence with ‘hclust’, comparing sum of heights and pseudo inertia, plots, non-increasing heights, cutree (#14).
- Fixed #13 (man).
- Fixed #15 (Cutree with decreasing merges).
- Fixed #3 (Non-positive ‘gains’).
- Using BiocStyle::html_document2 as a temporary fix for vignette compilation errors.
Version 0.5.2 [2017-10-17]
- Added citation to Alia Dehman’s PhD thesis to DESCRIPTION.
Version 0.5.1 [2017-10-16]
- More informative ‘Description’ of the method in DESCRIPTION
- Updates to test scripts to pass R CMD check on all windows platforms
- Moved README-*.png files to man/figures
Version 0.5.0 [2017-10-13]
- Bump version number for CRAN submission
Version 0.4.2 [2017-10-05]
- Added ‘chac’ S3 class and corresponding ‘plot’ and ‘summary’ methods
- Documentation cleanups
- Removed objects “R2.100” and “Dprime.100” (can be obtained from the imported ‘snpStats’ package)
- In ‘snpClust’: argument ‘stat’ is now passed to the ‘snpStats::ld’ function through ‘…’
- Some code cleanups
- Improved handling of default value for ‘h’ in ‘adjclust’ for ‘dist’ objects
- Renamed ‘prevfit’ into the more explicit ‘res_adjclust_0.3.0’
- Dropped ‘simmatrix’ toy data set (now generated on the fly in tests)
Version 0.4.1 [2017-09-15]
- Cleanups in Hi-C and LD vignettes and corresponding tests
- Dropped outdated BALD test script
- Added test script for NA values in LD
- Renamed Hi-C data sets and updated corresponding documentation
- Added package website generated by pkgdown
Version 0.4.0 [2017-08-29]
- Implemented interface to handle standard and sparse matrices in adjClust
- Implemented interface to handle either kernel or dissimilarities
- Implemented wrapper for SNP and Hi-C data
- Documented the package and created vignettes for the different use cases
- Added scripts to increase package coverage and test the equivalence with rioja for the small dimensional case
- Cleaned up code to improve efficiency and removed unnecessary scripts and functions
Version 0.3.0 [2017-02-13]
- Removed ‘adjClustBand’: main entry points are now ‘HeapHop’ and ‘adjClustBand_heap’.
- Updated test scripts and LD vignette accordingly.
- Added Travis CI and Appveyor support.
Version 0.2.3 [2017-02-02]
- Updated LD vignette
- In adjClustBand, renamed flavor “Koskas” to “PseudoMatrix”
Version 0.2.2 [2016-12-01]
- Added dummy R/adjclust.R so that document() adds ‘importFrom Rcpp evalCpp’ to NAMESPACE
- “Fixed” warning at check due to .hpp file in src (this warning should not exist IMHO)
Version 0.2.1 [2016-11-09]
- Added minimal documentation
- Replaced “std::cout” by “Rcpp::Rcout”, and so on for “exit()” and “cerr”.
Version 0.2.0 [2016-06-24]
- Incorporated Michel’s implementation (R function ‘HeapHop’)
- ‘adjClustBand’ is now a wrapper to call either Alia’s or Michel’s implementation
Version 0.1.0 [2016-06-24]
- Created from BALD
- Added a test to check that we are reproducing the results of BALD::cWard