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
Version 0.6.8 [2024-01-10]
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
Version 0.6.7 [2023-04-24]
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)
Version 0.6.6 [2022-09-13]
Minor updates in tests to comply with updates in Matrix 1.5.0
Version 0.6.5 [2022-08-18]
Code improvement: replaced class( ) != by equivalent expression using inherits( )
Version 0.6.4 [2022-03-30]
Update URL in DESCRIPTION
Fixed bug in tests due to recent upgrade of Matrix
Slightly improved vignettes and references here and there
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
Version 0.6.2 [2021-07-22]
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)
Version 0.5.99 [2020-06-08]
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).
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].
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
Version 0.5.6 [2018-02-08]
changed dependencies to Bioconductor packages 'HiTC' and 'snpStats' into
Suggest and conditionally 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.*
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