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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

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.
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