Changes in version 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 DESCRIPTION file include required biocview terms

Version update

  - Bumped version from 1.1.1 to 1.1.2.

                        Changes in version 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.

                        Changes in version 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

                        Changes in version 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).

                       Changes in version 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

                       Changes in version 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

                       Changes in version 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

                       Changes in version 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.

                       Changes in version 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.

                       Changes in version 0.99.2                        

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