SelectSim 0.1.6

• Removed reshape2 dependency; 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_parallel using tempfile() and on.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++14 from 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; dev branch merged into main for 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

SelectSim 0.0.1.3

• Added a NEWS.md file 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.

SelectSim 0.0.1.4

• Added Mijan to the author list.
• Removed the C/C++ code dependency to avoid installation difficulties across systems.
  • Moved to Matrix package functions and removed the Rcpp functions and compiled code.
• Updated the website and vignette accordingly.

SelectSim 0.0.1.5

• Fixed bug of outlier functions and added C/C++ code back.
• More description in functions