- Removed
reshape2dependency; replaced with base R equivalents (tapply,as.data.frame.table). - Fixed
theme_ridges()partial argument match (center→center_axis_labels). - Fixed parallel log file leak in
null_model_parallelusingtempfile()andon.exit(). - Refactored
selectX()to eliminate duplicate verbose/non-verbose code paths. - Added
utils::globalVariables()declarations to suppress R CMD check NOTEs for ggplot2 aesthetics. - Dropped
SystemRequirements: C++14from DESCRIPTION. - Added GitHub community health files:
CONTRIBUTING.md,CODE_OF_CONDUCT.md, issue templates, PR template, and CI workflow. - Expanded test coverage with
test-gam_utils.R. - Repository migrated: development moved from personal branches to CSOgroup/SelectSim;
devbranch merged intomainfor initial public release. - Bumped version to 0.1.6 across all source files
- Updated citation (
inst/CITATION,README) to the published Nature Genetics article: Iyer A, Petrovic M, Sesia D, Nanni L, Mina M, Ciriello G (2026). Evolving patterns of co-mutations from tumor initiation to metastatic progression. Nature Genetics. DOI: 10.1038/s41588-026-02661-4
- Added a
NEWS.mdfile to track changes to the package. - Renamed the package to SelectSim by creating a new Git repository.
- Created the CSOgroup repository and moved the code there.
- Created the GitHub website.
- Added Mijan to the author list.
- Removed the C/C++ code dependency to avoid installation difficulties across systems.
- Moved to
Matrixpackage functions and removed theRcppfunctions and compiled code.
- Moved to
- Updated the website and vignette accordingly.
- Fixed bug of outlier functions and added C/C++ code back.
- More description in functions