Changelog • HTRfit

CHANGES IN HTRfit VERSION 2.1.1

Improved Documentation: Clearer and more comprehensive information on HTRfit functionalities and usage.
Additional Metrics: Added RMSE for enhanced model evaluation.
Additional plot: Violin plot to measure proximity between actual and estimate for random effects.
Improved Flexibility: Ability to combine various genes behavior with combine_mock()
User experience: More informative messages.
R 4.4.0 Compatible: Fully supports the latest R version.

Improved Documentation: Clearer and more comprehensive information on HTRfit functionalities and usage.
Additional Metrics: Added PR curve, precision, recall, accuracy, and R2 for enhanced model evaluation.
Reduced Dependencies: Streamlined installation by removing the need for plotROC.

R files reorganization, log file enhancement and versioning
R files have been restructured to enhance clarity.
The log file location has been relocated to the R temporary directory.
A bug that was causing issues with writing the ‘group’ information in log files during model update has been fixed.
Fix NOTE “no visible binding for global variable” linked to ggplot2
Fix bug with packageVersion(“HTRfit”)

The metrics_plot function has been updated to display histograms instead of density plots.
The identity plot’s point shape has been modified, enhancing the visual clarity of comparisons between HTRfit and DESeq2 results.
Similar to the identity plot, the dispersion plot also benefits from improved point shape, contributing to a more effective visual analysis.
Add xlab/ylab to ROC plot
The vignette section now includes a new topic, “About mixed model evaluation”.

End of core development, Ready for beta testing
The functions, tests, and vignettes are fully functional and operational!
To do: 1) conducting installation tests , 2) seeking out beta testers for further evaluation.