{"id":32209727,"url":"https://github.com/cfwp/rags2ridges","last_synced_at":"2025-10-22T06:15:33.001Z","repository":{"id":25851673,"uuid":"29291369","full_name":"CFWP/rags2ridges","owner":"CFWP","description":"Get ridge or die trying - 2 cents","archived":false,"fork":false,"pushed_at":"2025-08-29T15:59:06.000Z","size":8652,"stargazers_count":8,"open_issues_count":21,"forks_count":2,"subscribers_count":6,"default_branch":"master","last_synced_at":"2025-09-08T14:19:37.620Z","etag":null,"topics":["c-plus-plus","cran","graphical-models","machine-learning","networkscience","r","statistics"],"latest_commit_sha":null,"homepage":"","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/CFWP.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2015-01-15T10:00:07.000Z","updated_at":"2025-08-29T15:37:34.000Z","dependencies_parsed_at":"2023-10-14T21:23:56.825Z","dependency_job_id":null,"html_url":"https://github.com/CFWP/rags2ridges","commit_stats":{"total_commits":745,"total_committers":7,"mean_commits":"106.42857142857143","dds":0.5033557046979866,"last_synced_commit":"04027a52492eee0e4aa3ac2e5e508c5c4c266c80"},"previous_names":[],"tags_count":15,"template":false,"template_full_name":null,"purl":"pkg:github/CFWP/rags2ridges","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CFWP%2Frags2ridges","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CFWP%2Frags2ridges/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CFWP%2Frags2ridges/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CFWP%2Frags2ridges/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/CFWP","download_url":"https://codeload.github.com/CFWP/rags2ridges/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CFWP%2Frags2ridges/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":280390747,"owners_count":26322780,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","status":"online","status_checked_at":"2025-10-22T02:00:06.515Z","response_time":63,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["c-plus-plus","cran","graphical-models","machine-learning","networkscience","r","statistics"],"created_at":"2025-10-22T06:15:30.391Z","updated_at":"2025-10-22T06:15:32.995Z","avatar_url":"https://github.com/CFWP.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"\n[![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)\n[![CRAN version](https://www.r-pkg.org/badges/version/rags2ridges)](https://cran.r-project.org/package=rags2ridges)\n[![CRAN RStudio mirror downloads](https://cranlogs.r-pkg.org/badges/rags2ridges)](https://cran.r-project.org/package=rags2ridges/index.html)\n[![Total CRAN downloads](https://cranlogs.r-pkg.org/badges/grand-total/rags2ridges)](https://www.r-pkg.org/pkg/rags2ridges)\n\n\u003cimg src=\"man/figures/RAGS.png\" alt=\"\" /\u003e\n\n**rags2ridges**\n---------------\n\nThe R-package **rags2ridges** performs L2-penalized estimation of precison (and covariance) matrices. \nThe package contains *proper* L2-penalized maximum-likelihood estimators for the precision matrix as well as supporting functions to employ these estimators in a (integrative or meta-analytic) graphical modeling setting. The package has a modular setup and features fast and efficient algorithms.\n\n\n## Installation\n\nThe released and tested version of **rags2ridges** is available at\n[CRAN](https://cran.r-project.org/package=rags2ridges) (Comprehensive R Archive Network). It can be easily be installed from within R by running\n\n```R\ninstall.packages(\"rags2ridges\")\n```\n\nIf you wish to install the latest version of **rags2ridges** directly from the master branch here at GitHub, run\n\n```R\n#install.packages(\"remotes\")  # Uncomment if not installed\nremotes::install_github(\"CFWP/rags2ridges\")\n```\n\nNote, that this version is in development and is different from the version at CRAN. As such, it may be unstable. Be sure that you have the\n[package development prerequisites](https://support.posit.co/hc/en-us/articles/200486498-Package-Development-Prerequisites) if you wish to install the package from the source.\n\nVisit [CRAN](https://cran.r-project.org/package=rags2ridges/news/news.html), [the documentation site](https://cfwp.github.io/rags2ridges/news/index.html), or run `news(package = \"rags2ridges\")` after installation to view the latest notable changes to **rags2ridges**. \n\nFor previous versions of **rags2ridges**, visit the [archive at CRAN.](https://cran.r-project.org/src/contrib/Archive/rags2ridges/)\n\n\n## Usage and getting started\n\nThe `vignette(\"rags2ridges\")` provides a light introduction to **rags2ridges** and details how to quickly get started.\n\n\n## References\n\nRelevant publications to **rags2ridges** include (ordered according to year):\n\n 1. Peeters, C.F.W., Bilgrau, A.E., \u0026 van Wieringen, W.N. (2022). \n    *\"rags2ridges: A One-Stop-l2-Shop for Graphical Modeling of High-Dimensional Precision Matrices\"*. \n    Journal of Statistical Software, vol. 102(4):1-32.\n    ([doi:10.18637/jss.v102.i04](https://doi.org/10.18637/jss.v102.i04)).\n 2. Peeters, C.F.W., van de Wiel, M.A., \u0026 van Wieringen, W.N. (2020)\n    *\"The Spectral Condition Number Plot for Regularization Parameter Evaluation\"*,\n    Computational Statistics, vol. 35:629-646\n    ([doi:10.1007/s00180-019-00912-z](https://doi.org/10.1007/s00180-019-00912-z)).\n 3. Bilgrau\\*, A.E., Peeters\\*, C.F.W., Eriksen, P.S., Boegsted, M., \u0026 van Wieringen, W.N. (2020).\n    *\"Targeted Fused Ridge Estimation of Inverse Covariance Matrices from Multiple High-Dimensional Data Classes\"*,\n    Journal of Machine Learning Research, vol. 21(26):1-52\n    ([PDF](https://www.jmlr.org/papers/volume21/15-509/15-509.pdf)).\n 4. van Wieringen, W.N. \u0026 Peeters, C.F.W. (2016).\n    *\"Ridge Estimation of Inverse Covariance Matrices from High-Dimensional Data\"*, \n    Computational Statistics \u0026 Data Analysis, vol. 103:284-303\n    ([doi:10.1016/j.csda.2016.05.012](https://doi.org/10.1016/j.csda.2016.05.012)).\n 5. van Wieringen, W.N. \u0026 Peeters, C.F.W. (2015).\n    *\"Application of a New Ridge Estimator of the Inverse Covariance Matrix\n    to the Reconstruction of Gene-Gene Interaction Networks\"*.\n    In: di Serio, C., Lio, P., Nonis, A., and Tagliaferri, R. (Eds.)\n    `Computational Intelligence Methods for Bioinformatics and Biostatistics'.\n    Lecture Notes in Computer Science, vol. 8623. Springer, pp. 170-179\n    ([doi:10.1007/978-3-319-24462-4_15](https://doi.org/10.1007/978-3-319-24462-4_15)).\n\nPlease cite the relevant publications if you use **rags2ridges**.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcfwp%2Frags2ridges","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcfwp%2Frags2ridges","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcfwp%2Frags2ridges/lists"}