Version 0.6.5 [2022-08-18]

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

Version 0.6.4 [2022-03-30]

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

‘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 ‘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)

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.

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)

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