Changes in version 0.6.11 (2025-11-20) - Fix minor spelling errors - Update github test coverage workflow to v4 (#84) - Fix for upcoming "testthat" 3.3 release (#83) Changes in version 0.6.10 (2024-10-08) - Bug fix on OMP option (#81) Changes in version 0.6.9 (2024-02-08) - 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 Changes in version 0.6.8 (2024-01-13) - Fix CRAN error on useNames (deprecated NA) - Fix CRAN note on itemize (unnecessary use of itemize) - Limited OMP threads to 2 in examples, vignettes and tests - Updated citation of the package Changes in version 0.6.7 (2023-04-27) - 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) Changes in version 0.6.6 (2022-09-14) - Minor updates in tests to comply with updates in Matrix 1.5.0 Changes in version 0.6.5 (2022-08-18) - Code improvement: replaced class( ) != by equivalent expression using inherits( ) Changes in version 0.6.4 (2022-03-31) - Update URL in DESCRIPTION - Fixed bug in tests due to recent upgrade of Matrix - Slightly improved vignettes and references here and there Changes in version 0.6.3 (2021-07-26) - 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 Changes in version 0.6.2 - 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) Changes in version 0.5.99 (2020-06-18) - 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). Changes in version 0.5.9 (2019-12-10) - 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]. Changes in version 0.5.7 (2018-09-26) - 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 Changes in version 0.5.6 (2018-02-08) - changed dependencies to Bioconductor packages 'HiTC' and 'snpStats' into Suggest and conditionally used them Changes in version 0.5.5 - 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 Changes in version 0.5.4 - More tests for modify and modifySparse - BUG FIX in condnCheck Changes in version 0.5.3 - '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. Changes in version 0.5.2 (2017-10-18) - Added citation to Alia Dehman's PhD thesis to DESCRIPTION. Changes in version 0.5.1 - 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 Changes in version 0.5.0 - Bump version number for CRAN submission Changes in version 0.4.2 - 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) Changes in version 0.4.1 - 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 Changes in version 0.4.0 - 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 Changes in version 0.3.0 - Removed 'adjClustBand': main entry points are now 'HeapHop' and 'adjClustBand_heap'. - Updated test scripts and LD vignette accordingly. - Added Travis CI and AppVeyor support. Changes in 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 Changes in version 0.1.0 - Created from BALD - Added a test to check that we are reproducing the results of BALD::cWard