NEWS

SelectSim 0.1.6 (2026-07-21)

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

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.