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Changelog

Source: NEWS.md

Version 0.6.9 [2024-10-07]

CRAN release: 2024-02-08

  • Bug fix on OMP option (#81)

Version 0.6.9 [2024-02-07]

CRAN release: 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

Version 0.6.8 [2024-01-10]

CRAN release: 2024-01-13

  • 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]

CRAN release: 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)

Version 0.6.6 [2022-09-13]

CRAN release: 2022-09-14

  • Minor updates in tests to comply with updates in Matrix 1.5.0

Version 0.6.5 [2022-08-18]

CRAN release: 2022-08-18

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

Version 0.6.4 [2022-03-30]

CRAN release: 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

Version 0.6.3 [2021-07-26]

CRAN release: 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]

CRAN release: 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).

Version 0.5.9 [2019-12-10]

CRAN release: 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]

CRAN release: 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]

CRAN release: 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]

CRAN release: 2017-10-18

  • 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