NEWS

---

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.

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 1.1.3

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 1.1.2

##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 1.1.1

##Improvement

• Updated MTLR_pred_model_f function to make it simple

Version update

• Bumped version from 1.1.0 to 1.1.1.

CPSM 1.1.0

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 1.0.0

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 0.99.7

• 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 0.99.6

• 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 0.99.5

• 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 0.99.4

• 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 0.99.3

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 0.99.2

• Fixed indentation issues in R source files.
• Removed redundant Maintainer field from the DESCRIPTION file.