NEWS

---

inferCSN 1.2.3

• func:

  • Optimize check_parameters() for check input parameters.

• docs:

  • Updated documentation across multiple functions.

inferCSN 1.2.2

• func:

  • Removed network_sift() and weight_sift() functions.
  • Removed S4 method for data.frame.

• docs:

  • Updated documentation across multiple functions.

inferCSN 1.2.1

• func:

  • Fixed warning on Windows platform for better compatibility.

• docs:

  • Updated documentation across multiple functions.

inferCSN 1.2.0 (2025-10-16)

• func:

  • Removed srm related functions and files.
  • Removed RcppArmadillo dependency.
  • Removed Makevars files for simplified build process.
  • Reorganized package structure by moving and removing files.

• refactor:

  • Updated package template structure.
  • Cleaned up package dependencies and build configuration.

• docs:

  • Updated package logo.
  • Improved documentation formatting.

inferCSN 1.1.9

• func:

  • Enhanced logo printing functionality.

• docs:

  • Updated documentation across multiple functions.

inferCSN 1.1.8

• func:

  • Added inferCSN_logo() function for displaying package logo.
  • Added new parameters for log_message() function.
  • Modified .cores_detect() function for better CPU core detection.
  • Removed PKG_LIBS from Makevars and Makevars.win files.
  • Moved utility functions to thisutils package.

• refactor:

  • Updated pkgdown webpage theme.
  • Fixed warnings and errors in GCC compilation.
  • Optimized document structure.

• docs:

  • Added examples in README.
  • Updated package description.
  • Updated renv configuration files.

inferCSN 1.1.7 (2025-03-30)

• func:
  • Added sparse_cov_cor() function for sparse covariance and correlation computation.
  • Removed deprecated sparseCovCor function.
  • Updated documentation for sparse_cor() function.

inferCSN 1.1.6 (2025-03-27)

• func:

  • Fixed error in table_to_matrix() function.
  • Optimized performance for matrix operations.

• bugs:

  • Fixed error in pkgdown build process.

• docs:

  • Added example for calculate_accuracy() function.
  • Modified examples for plot_network_heatmap() function.
  • Updated badge display.
  • Updated ProjectId.

inferCSN 1.1.3

• func:

  • Added new network evaluation functions for assessing network quality.
  • Updated import records for better dependency management.

• docs:

  • Edited documentation for multiple functions.
  • Modified documentation for plot_network_heatmap() function.
  • Updated test-coverage.yaml file.
  • Renamed files for better organization.

• refactor:

  • Added check workflow for automated testing.
  • Modified import statements.

inferCSN 1.1.2

• func:

  • Renamed fit_sparse_regression() to fit_srm() for shorter function name.
  • Modified parameters for multiple functions.

• docs:

  • Updated package logo.
  • Updated badge display.

inferCSN 1.1.1

• func:
  • Renamed function fit_sparse_regression() to fit_srm().

inferCSN 1.1.0

• func:
  • Modified algorithm parameter to non-exported for internal use.

inferCSN 1.0.9

• func:

  • Added new utility functions including %s%, matrix_to_table(), pearson_correlation(), simulate_sparse_matrix(), plot_coefficients(), split_indices(), subsampling_fun(), and weight_sift().
  • Added new C++ functions including network_format(), prepare_calculate_metrics() for improved performance.
  • Added CITATION file for proper citation.
  • Renamed function from percent_samples to subsampling.
  • Imported native R pipe operator |> for better compatibility with R >= 4.1.0.

• refactor:

  • Renamed function %s% to %ss%.
  • Renamed functions to calculate_metrics().
  • Modified structure of sparse_regression() output.
  • Modified normalization method implementation.
  • Updated log_message() function.
  • Improved documentation across multiple functions.

• bugs:

  • Fixed multiple coding style issues.
  • Fixed error in various functions.
  • Fixed warning when package installation.
  • Fixed download badge display.

• docs:

  • Optimized function documentation.
  • Updated .gitignore.
  • Updated packages record information.

• deps:

  • Deleted suggests packages that are no longer needed.
  • Deleted useless packages from dependencies.

inferCSN 1.0.8 (2024-08-24)

• func:

  • Added log_message() function for consistent logging across package.
  • Added export of log_message() for user access.
  • Modified documentation for multiple functions.

• deps:

  • Added import of cli package for better message formatting.
  • Modified Imports section.
  • Removed exports for internal functions.

• docs:

  • Updated README.
  • Improved documentation consistency.

• refactor:

  • Coding style improvements.

inferCSN 1.0.7

• func:

  • Removed export of prepare_network_data() as internal function.
  • Modified documentation for multiple functions.

• bugs:

  • Fixed error for normalization() when setting method to softmax.

inferCSN 1.0.6

• func:

  • Added new visualization functions: plot_embedding() and plot_weight_distribution().
  • Added new parameters for plot_weight_distribution().
  • Added asMatrixParallel() for parallel matrix operations.
  • Added RcppParallel support for improved performance.
  • Added PKG_LIBS information in Makevars.
  • Added new function check_sparsity() for sparsity checking.
  • Added new global variables.
  • Renamed performance_evaluation functions.
  • Renamed files and functions for better organization.
  • Support for sparse matrix operations.
  • Updated R version requirement.
  • Reduced computation complexity for better performance.
  • Removed export of check_parameters().

• bugs:

  • Fixed error for .weight_sift().
  • Fixed error and improved coding style in plot_scatter().
  • Fixed document issues.

• docs:

  • Modified documentation for multiple functions.
  • Modified examples, parameters, and documentation.
  • Updated renv files.
  • Updated Makevars files.
  • Updated document for some parameters.

• refactor:

  • Coding style improvements.
  • Renamed functions and files.

inferCSN 1.0.5 (2024-06-26)

• func:

  • Added entropy to filter edges in network.
  • Added new function as_matrix() for matrix conversion.
  • Added new function plot_scatter() for scatter plot visualization.
  • Added new parameter for plot_scatter().
  • Added new function network_sift() for network filtering (renamed from previous version).
  • Added new functions: r_square(), plot_contrast_networks(), plot_dynamic_networks().
  • Added new function map_parallel() and parallelize_fun() for parallel processing.
  • Added .softmax() function.
  • Added new parameter heatmap_size_lock for network.heatmap().
  • Modified S4 method for inferCSN.
  • Removed dynamic.networks, contrast.networks functions (renamed/replaced).
  • Renamed net.format to network_format().
  • Renamed dynamic.networks to plot_static_networks().
  • Fixed errors and added new parameters for network_sift().
  • Deleted unnecessary functions.
  • Modified import functions and packages.
  • Using as_matrix() instead of as.matrix() for better performance.

• deps:

  • Removed progress package and added pbapply package.
  • Added new packages for enhanced functionality.
  • Updated imports.

• bugs:

  • Fixed error in check.parameters().
  • Fixed multiple errors.
  • Fixed warning.
  • Fixed note info.

• docs:

  • Updated badges.
  • Modified examples.
  • Updated _pkgdown.yml.
  • Modified examples and figure style.
  • Updated renv file.
  • Modified parameter description of functions.
  • Updated .gitignore.
  • Updated README.

• refactor:

  • Coding style improvements across multiple files.
  • Improved function organization.

inferCSN 1.0.3 (2024-04-17)

• func:

  • Added new function weight_filter() for filtering weights.
  • Added new parameters for network.heatmap().
  • Set crossweight example to \dontrun{} for CRAN compatibility.

• docs:

  • Updated NAMESPACE and import records.

inferCSN 1.0.2

• func:

  • Added new function normalization() for data normalization.
  • Added new function crossweight() for cross-weight analysis.
  • Added new function crossweight_params().
  • Added new function extract_net() (later deleted).
  • Added new example data example_meta_data.
  • Updated crossweight and related functions.
  • Updated example data.
  • Added new parameters for calculate.gene.rank().
  • Renamed function to filter_sort.matrix to handle CRAN warning.
  • Renamed multiple functions for consistency.
  • Deleted function extract_net().

• bugs:

  • Fixed error when sample.
  • Fixed multiple errors.
  • Fixed pkgdown error.

• docs:

  • Updated README.
  • Updated crossweight.Rd.
  • Updated _pkgdown.yml.
  • Updated NAMESPACE.
  • Updated renv.lock.
  • Modified examples.
  • Formatted progress information.

• refactor:

  • Fixed coding style issues.

inferCSN 1.0.1 (2024-03-15)

• func:

  • Added new function filter.sort.matrix() for efficient matrix filtering and sorting.
  • Optimized memory consumption for handling large datasets.
  • Modified function used to handle data.
  • Modified parameter k_folds.
  • Modified parameter regulators_num.
  • Renamed multiple functions for consistency: calculate.gene.rank(), sub.model.fit(), model.fit(), single.network().
  • Added examples for multiple functions including network.heatmap(), dynamic.networks().
  • Added new parameter for net.format().
  • Modified some functions for better performance.
  • Fixed error code.

• bugs:

  • Fixed multiple errors.

• docs:

  • Updated README with improved examples.
  • Updated _pkgdown.yml.
  • Updated .gitignore.
  • Updated cran_release.R.
  • Updated .Rbuildignore.
  • Modified parameter information.
  • Added test examples for table_to_matrix().
  • Updated logo.svg.

• refactor:

  • Removed test files.
  • Updated NAMESPACE.
  • Updated renv file.
  • Added examples throughout.

inferCSN 1.0.0 (2024-02-09)

• feat:

  • First major release of inferCSN package.
  • Core functionality for inferring cell-specific gene regulatory networks.
  • Sparse regression-based network inference algorithm.
  • Support for single-cell RNA-seq data.
  • Network visualization and analysis functions.
  • Performance evaluation metrics.

• docs:

  • Complete documentation for all exported functions.
  • Comprehensive README with usage examples.
  • Package website with pkgdown.

inferCSN 0.99.9 (2024-01-10)

• func:

  • Updated table_to_matrix.cpp for improved performance.
  • Updated version to 0.99.9 in preparation for CRAN submission.

• docs:

  • Updated cran_release.R.
  • Fixed example information.
  • Added new function and renamed files.

inferCSN 0.99.8 (2023-12-04)

• func:

  • Updated inferCSN() function with improvements.
  • Updated C++ functions for better performance.
  • Updated and formatted code across multiple files.
  • Updated example data.

• bugs:

  • Fixed pkgdown error.

• docs:

  • Fixed error and modified documentation.
  • Updated renv.lock.
  • Updated requirements.sh.

inferCSN 0.99.7 (2023-10-30)

• func:

  • Fixed error when compiling on CentOS system.
  • Updated requirements.sh.

• refactor:

  • Version update for CRAN submission preparation.

inferCSN 0.1.1

• func:

  • Initial package development.
  • Basic sparse regression implementation.
  • C++ integration for performance.

• docs:

  • Basic documentation structure.
  • Initial README.

inferCSN 0.1.0

• feat:
  • Initial version.