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Showing content from http://cran.rstudio.com/web/packages/rJava/../matchingMarkets/../ggplot2/../adjclust/news/news.html below:

NEWS

• Bug fix on OMP option (#81)

• Properly handled OMP threads in C++ code (now default to 1 but with an option to increase this value)
• Reintroduced tests and examples
• Removed WCSS function that was not exported or documented
• Fixed a problem in S3class for a non exported function

• Fix CRAN error on useNames (deprecated NA)
• Fix CRAN note on itemize (unecessary use of itemize)
• Limited OMP threads to 2 in examples, vignettes and tests
• Updated citation of the package

• Fix #60 (increase test coverage)
• Fix #61 (NAMESPACE error in ‘SnpClust.matrix’)
• Fix #45 (update ‘calls’ for ’adjclust.*’ methods)
• Fix #49 (calls to ‘library’ in tests)
• Fix #55 (pkgdown action)
• Fix #40 (moved plotSim to a ggplot2 version)
• Fix #30 (improved plotSim, k and correct have been added as new arguments)
• Fix #62 (citation file corrected)
• Fix #68 (CRAN note)

• Minor updates in tests to comply with updates in Matrix 1.5.0

• Code improvement: replaced class( ) != by equivalent expression using inherits( )

• Update URL in DESCRIPTION
• Fixed bug in tests due to recent upgrade of Matrix
• Slightly improved vignettes and references here and there

• Fix issues for CRAN submission: RcppArmadillo moved to LinkingTo, version number
• Cleanup: move res_adjclust_0.3.0.rda from data/ to inst/extdata/
• Cleanup: remove useless data entries from pkgdown index, and add missing ones
• Update docs (using pkgdown)
• Move site to dedicated branch (release with pkgdown::deploy_to_branch())
• Add inst/CITATION and add Randriamihamison et al 2020

• Increase in speed by code optimization and by using RcppArmadillo (update by Gabriel Hoffman), at least for linux machines (uses OpenMP)
• reduces memory usage (update by Gabriel Hoffman)
• option to disable expensive checking code (strictCheck = TRUE by default, update by Gabriel Hoffman)

• Updated citation in DESCRIPTION and man files (almob paper) and added a CITATION file.
• removed exportation of S3 classes.
• changed cutree into a simple function ‘cutree_chac’ rather than a method (because stats::cutree is not a method).

• Clarified types of inputs handled by adjclust (‘S3 methods’).
• Shortened some examples.
• Rewrote plotSim to avoid CRAN error on devel (chose to use ‘S3 methods’ now).
• Fixed a similar problem in helpers.
• Clarified code and comments.
• Fixed Issue #35 (probably due to a change in the upstream snpStats package).
• Added a test on plotSim.
• Changed test on NA in snpStats package (probably due to a change in the upstream snpStats package) and fixed Issue #43.
• Minor updates to tests.
• The package passes R CMD check with [0;0;0].

• Example Hi-C data now 10x smaller (subset of the original one). The package is smaller and tests are faster.
• implemented a model selection approach based on slope heuristic or on the broken stick heuristic to select a relevant number of clusters
• fixed minor problems in some method definition for class ‘chac’
• proposed a log-transformation of data in the wrapper ‘hicClust’
• implemented a heatmap with possible highlighting of the constrained clustering
• implemented an option to display number of the merge on the dendrogram

• changed dependencies to Bioconductor packages ‘HiTC’ and ‘snpStats’ into Suggest and conditionally used them

• 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

• More tests for modify and modifySparse
• BUG FIX in condnCheck

• ‘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.

• 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

• Bump version number for CRAN submission

• 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)

• 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

• 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

• Removed ‘adjClustBand’: main entry points are now ‘HeapHop’ and ‘adjClustBand_heap’.
• Updated test scripts and LD vignette accordingly.
• Added Travis CI and AppVeyor support.

• Updated LD vignette
• In adjClustBand, renamed flavor “Koskas” to “PseudoMatrix”

• 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)

• Added minimal documentation
• Replaced “std::cout” by “Rcpp::Rcout”, and so on for “exit()” and “cerr”.

• Incorporated Michel’s implementation (R function ‘HeapHop’)
• ‘adjClustBand’ is now a wrapper to call either Alia’s or Michel’s implementation

• Created from BALD
• Added a test to check that we are reproducing the results of BALD::cWard

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