Changes in version 1.2.3 - func: - Optimize check_parameters() for check input parameters. - docs: - Updated documentation across multiple functions. Changes in version 1.2.2 - func: - Removed network_sift() and weight_sift() functions. - Removed S4 method for data.frame. - docs: - Updated documentation across multiple functions. Changes in version 1.2.1 - func: - Fixed warning on Windows platform for better compatibility. - docs: - Updated documentation across multiple functions. Changes in version 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. Changes in version 1.1.9 - func: - Enhanced logo printing functionality. - docs: - Updated documentation across multiple functions. Changes in version 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. Changes in version 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. Changes in version 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. Changes in version 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. Changes in version 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. Changes in version 1.1.1 - func: - Renamed function fit_sparse_regression() to fit_srm(). Changes in version 1.1.0 - func: - Modified algorithm parameter to non-exported for internal use. Changes in version 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. Changes in version 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. Changes in version 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. Changes in version 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. Changes in version 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. Changes in version 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. Changes in version 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. Changes in version 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. Changes in version 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. Changes in version 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. Changes in version 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. Changes in version 0.99.7 (2023-10-30) - func: - Fixed error when compiling on CentOS system. - Updated requirements.sh. - refactor: - Version update for CRAN submission preparation. Changes in version 0.1.1 - func: - Initial package development. - Basic sparse regression implementation. - C++ integration for performance. - docs: - Basic documentation structure. - Initial README. Changes in version 0.1.0 - feat: - Initial version.