Changelog
Source:NEWS.md
Colossus 1.0.0
CRAN release: 2024-02-20
- Initial submission
- C++ code modified to not apply OpenMP code if OpenMP isn’t detected, to resolve MacOS installation failures
Colossus 1.0.1
CRAN release: 2024-02-26
- Configuration improved to detect compiler information
- Linux configuration depends on the system wide c++ default and the compiler used to compile R
- OpenMP support is not used if the c++ default or the R compiler is clang
Colossus 1.0.2
- utility checks updated to check that keep_constant is 0/1 values
- code will fail if keep_constant is not integer valued and 0/1, with explanation of why
Colossus 1.0.3
- configuration script libraries moved from Suggested: to Imports:
- configuration script functions moved to non-exported functions in Colossus, circumvents note about imported libraries not being used and may be later used to provide the user with a function that informs them of why OpenMP is/isn’t supported
Colossus 1.0.4
- utility checks updated to check term numbers and subterm types in R side
- code will fail if term numbers are not integers, term numbers are missing, or subterm types are
Colossus 1.1.0
CRAN release: 2024-04-03
- Default Makevars is now fully portable
- By default only windows uses OpenMP now
- The GitHub version will include instructions on activating configuration to use OpenMP on gcc Linux
Colossus 1.1.1
CRAN release: 2024-04-30
- ggplot2 no longer required, now optional
- additional testing added for coverage
- default Makevars added via bash script
Colossus 1.1.2
- Log-likelihood bound functionality added
- subject to usual convergence issues, manual search option
Colossus 1.1.3
CRAN release: 2024-09-06
- Cox regression now removes rows that end before first event and start after last event
- Cox regression now sets constant rows to be constant, helps with aliasing
- Tests now use sink() to avoid printing as much excessive output to console. Tests now consolidated further.
Colossus 1.1.4.1
CRAN release: 2024-09-20
- Cox plotting functions now return the tables used for plots (only last plot table returned)
- Plotting vignette updated to include more details and plots
- survival package listed as suggested for plotting vignette
Colossus 1.1.4.2
CRAN release: 2024-10-21
- R errors and warnings sent to stop() and warning(). C++ errors and warnings still controlled by verbosity argument
- ggsave defaults to width/height = 7
- Updates started to fix possible OpenMP issues with fedora 36 running clang 18
- Unable to have debug printing as an option and cover the c++ files with testing, but still have test output be readable. debug output removed.
Colossus 1.1.5
- Started adding simplifications to allow for faster iterations
- Added simplification for linear ERR model
- Started gradient descent code
- Started external rate comparison options
- Added person-count and person-time table generation code and vignette
Colossus 1.1.6
- MacOS testing with OpenMP finished. MacOS use with OpenMP officially checked.
- By default the only systems that is forced to use single thread is linux using clang. This can be turned off by setting the “R_COLOSSUS_NOT_CRAN” environment variable.
Colossus 1.1.7
- Gradient descent algorithms tested further and presented in vignette
- Multiple realization function tested further
Colossus 1.1.8
- CurveSolve functions converted to c++ functions
- Testing scaled back to take up less time
Colossus 1.1.9
- Cox based functions switched covariance matrix calculation from negative inverse of log-likelihood second derivative, to expected information matrix.
Colossus 1.1.10
- Cox based functions updated to improve speed
- Additional CurveSolve output provided to give final window width and final step
Colossus 1.2
CRAN release: 2025-02-13
- Both Cox and Poisson functions now all return the expected information matrix derived covariance
Colossus 1.3.0
CRAN release: 2025-06-05
- Multiple realization code updated to improve speed
- lingering debugging variables removed: fir and der_iden
Colossus 1.3.1
- Convergence check performed more often
- Checks the actual maximum step taken to compare to threshold
- Previous versions may have run more iterations than necessary to meet derivative and step size thresholds
Colossus 1.4.0
- Switch to formula inputs and model classes
- Removed unused functions, to simplify documentation
Colossus 1.4.1
- Formula input now allows more general applications of factor, ns(), bs(), I(var^n), interaction, etc.
Colossus 1.4.2
- Option added to normalize covariates, either scaled by the mean or maximum values.
- Gradient descent option now calculates standard error and covariance through second derivative after regression.
Colossus 1.4.3
CRAN release: 2025-10-30
- Logistic regression added
- Newton step calculation now checks the predicted change in score, and moves in opposite direction if the expected score is worse
Colossus 1.4.4
- Corrected factorization not being applied to factored columns
- Fixed event assignment reordering the data
- Multiplicative and Multiplicative-excess models are now distinct. The default is left as multiplicative-excess.
Colossus 1.4.5
CRAN release: 2025-12-07
- Updated geometric-mixture code to apply defaults of 0.5 theta and only excess terms
- Corrected normalization for intercept parameters
Colossus 1.4.6
CRAN release: 2025-12-16
- Fixed bug in second derivative risk calculations, wrong correction to multi-term risk values.
- Improved results printing. Basic regression results only print term number column when multiple terms used. Likelihood boundary results now print the limit and score when negative limit hit.
- ncores option used for Colossus calculations now also applied to data.table operations. Previous number reset after calculations, may need to be manually reset if the regression hits an error.