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