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@pneuvial pneuvial released this 18 Oct 22:58
· 314 commits to master since this release
v0.5.2
9d215d4

Version 0.5.2 [2017-10-17]

  • Added citation to Alia Dehman's PhD thesis to DESCRIPTION.

Version 0.5.1 [2017-10-16]

  • Added citation to Alia Dehman's PhD thesis to DESCRIPTION.
  • 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  • Dropped outdated BALD test script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.*

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
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