Version 0.6.9 [2024-10-07]
- Bug fix on OMP option (#81)
Version 0.6.9 [2024-02-07]
- 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