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Changelog

Source: NEWS.md

inferCSN 1.2.1

  • func:
    • Fixed warning on Windows platform for better compatibility.
  • docs:
    • Updated documentation across multiple functions.

inferCSN 1.2.0

CRAN release: 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

CRAN release: 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

CRAN release: 2025-03-27

  • func:
    • Fixed error in table_to_matrix() function.
    • Optimized performance for matrix operations.
  • bugs:
    • Fixed error in pkgdown build process.
  • docs:

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

CRAN release: 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

CRAN release: 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

CRAN release: 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

CRAN release: 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

CRAN release: 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

CRAN release: 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

CRAN release: 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

CRAN release: 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.