# CPSM 0.99.2 (Unreleased)
- Fixed indentation issues in R source files.
- Removed redundant `Maintainer` field from the DESCRIPTION file.
# CPSM 0.99.3
## Updates
- Updated `DESCRIPTION` file to include `file LICENSE` in the `License` field.
- Removed indentation inconsistencies in all `R` scripts for better readability.
- Bumped the version from 0.99.2 to 0.99.3 as per Bioconductor guidelines.

## Fixes
- Addressed `BiocCheck` notes on coding practices.
# CPSM 0.99.4 (Unreleased)
- Removed indentation inconsistencies in all `R` scripts for better readability.
- Bumped the version from 0.99.3 to 0.99.4 as per Bioconductor guidelines.

# CPSM 0.99.5 (Unreleased)
- Updated the function previously dependent on the SurvMetrics package. The computation is now implemented using the survival and pec packages, removing the dependency on SurvMetrics.
- Resolved issues with the NAMESPACE file:
- Removed exportPattern("^[[:alpha:]]+") from the NAMESPACE file.
- Bumped the version from 0.99.4 to 0.99.5 as per Bioconductor guidelines

# CPSM 0.99.6 (Unreleased)
- Updated vigenette file "CPSM.Rmd" included YAML header of the vignette
- corrected input in MTLR_pred_model_f.R file
- updated .gitignore file
- Bumped the version from 0.99.5 to 0.99.6 as per Bioconductor guidelines

# CPSM 0.99.7 (Unreleased)
- Updated vigenette file "CPSM.Rmd", updated installation instruction as per Bioconductor guidelines
- updated data_process_f.R
- Updated DESCRIPTION  file to add author and version update
- Bumped the version from 0.99.6 to 0.99.7 as per Bioconductor guidelines

# CPSM 1.0.0 (Released)
## First Official release of the **CPSM** package on Bioconductor.
- Includes core functionality for:
- Data preprocessing, and data normalization
- Feature selection for survival modeling
- Model prediction and evaluation
- Visualization using survival cureves plots, mean-median barplot, nomograms.
## Documentation
- Initial vignette `CPSM.Rmd` added, detailing step-by-step usage of the package.
- Includes installation instructions, use-case workflows, and examples.
- Ensured compliance with Bioconductor submission guidelines.
- Bumped version from **0.99.7** (development) to **1.0.0** (release).

# CPSM 1.1.0 
## New Features
- **`predict_survival_risk_group_f()`**:
  - Added a new function to build Random Forest-based survival risk group classifiers using selected molecular features.
  - Automatically selects the best-performing model based on prediction accuracy across various `ntree` values (10 to 1000).
  - Outputs include predicted risk groups, prediction probabilities, misclassification summary, best model, and tree-wise performance matrix.
- **`km_overlay_plot_f()`**:
  - Introduced a new function to generate Kaplan-Meier survival plots overlayed with individual test sample survival curves.
  - Useful for visualizing predicted test sample risk in the context of population-level survival groups.
  - Includes annotated output with sample ID, predicted group, and probability.
## Updated data files, added new files
## Improvement
- Updated MTLR_pred_model_f function to compute MAE and improve the structure of function. 
## Documentation
- Updated Description file
- Updated vignette file `CPSM.Rmd`:
  - Included usage details and examples for new functions.
  - Enhanced step-by-step explanation of prediction and visualization workflows.
## Version update
- Bumped version from **1.0.0** to **1.1.0**

# CPSM 1.1.1
##Improvement
- Updated MTLR_pred_model_f function to make it simple
## Version update
- Bumped version from **1.1.0** to **1.1.1**.

# CPSM 1.1.2
##Improvement
- Updated MTLR_pred_model_f.R, Lasso_PI_scores_f.R, mean_median_surv_barplot_f.R, Nomogram_generate_f.R,surv_curve_plots_f.R script to remove undesired package
- Updated km_overlay_plot_f.R to improve figure 
- Updated DESCRIPTION file include required biocview terms
## Version update
- Bumped version from **1.1.1** to **1.1.2**.

# CPSM 1.1.3
## Updates
- Added CC0 license for processed data in the `/data` folder to comply with data-sharing requirements.
- Updated km_overlay_plot_f.R to improve figure
- Updated `DESCRIPTION` file:
  - Added contributors (`ctb`) to `Authors@R`.
  - Bumped version from 1.1.2 to 1.1.3.

# CPSM 1.3.0
## Updates
- Updated Lasso_PI_scores_f.R, MTLR_pred_model_f.R, Univariate_sig_features_f.R, km_overlay_plot_f.R, mean_median_surv_barplot_f.R, surv_curve_plots_f.R, predict_survival_risk_group_f.R  to provide customization for user  in cross-validation , Font-size and figure styling etc.
- Updated MTLR_pred_model_f.R to compute IBS (integrated brier score)
- Updated vignettes/CPSM.Rmd to provide improve description and workflow
- Updated tests/testthat files to incoprate updated changes
- Updated `DESCRIPTION` file:
  - Bumped version from 1.2.0 to 1.3.9.


# CPSM 1.3.1
## Updates
- Enhanced `Lasso_PI_scores_f.R` to compute the feature Stability Index and updated `Univariate_sig_features_f.R` to include the Proportional Hazards (PH) violation test for selected features.
- Updated `MTLR_pred_model_f.R` and `predict_survival_risk_group_f.R` to generate results for each cross-validation fold.
- Improved `train_test_normalization_f.R` by adding an additional filter to remove features with zero variance in at least 80% of training samples.
- Revised `vignettes/CPSM.Rmd` with improved descriptions and a clearer workflow.
- Updated `tests/testthat` files to reflect recent changes.
- Updated the `DESCRIPTION` file:
  - Version bumped from 1.3.0 to 1.3.1.
