The hardware and bandwidth for this mirror is donated by dogado GmbH, the Webhosting and Full Service-Cloud Provider. Check out our Wordpress Tutorial.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]dogado.de.

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

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.