{ "_id": "6a0f695cacfb0bcc41c5decd", "Package": "porridge", "Type": "Package", "Title": "Ridge-Type Penalized Estimation of a Potpourri of Models", "Version": "0.3.3", "Date": "2024-02-21", "Author": "Wessel N. van Wieringen [aut, cre]\n(), Mehran Aflakparast\n[ctb] (part of the R-code of the mixture functionality)", "Maintainer": "Wessel N. van Wieringen ", "Authors@R": "c(person(\"Wessel N.\", \"van Wieringen\", role = c(\"aut\", \"cre\"),\nemail=\"w.vanwieringen@vumc.nl\",\ncomment = c(ORCID = \"0000-0002-5100-9123\")),\nperson(\"Mehran\", \"Aflakparast\", role = \"ctb\",\ncomment=\"part of the R-code of the mixture functionality\"))", "Description": "The name of the package is derived from the French, 'pour'\nridge, and provides functionality for ridge-type estimation of\na potpourri of models. Currently, this estimation concerns that\nof various Gaussian graphical models from different study\ndesigns. Among others it considers the regular Gaussian\ngraphical model and a mixture of such models. The\nporridge-package implements the estimation of the former either\nfrom i) data with replicated observations by penalized\nloglikelihood maximization using the regular ridge penalty on\nthe parameters (van Wieringen, Chen, 2021) or ii) from\nnon-replicated data by means of either a ridge estimator with\nmultiple shrinkage targets (as presented in van Wieringen et\nal. 2020, ) or the generalized\nridge estimator that allows for both the inclusion of\nquantitative and qualitative prior information on the precision\nmatrix via element-wise penalization and shrinkage (van\nWieringen, 2019, ).\nAdditionally, the porridge-package facilitates the ridge\npenalized estimation of a mixture of Gaussian graphical models\n(Aflakparast et al., 2018). On another note, the package also\nincludes functionality for ridge-type estimation of the\ngeneralized linear model (as presented in van Wieringen,\nBinder, 2022, ).", "License": "GPL (>= 2)", "LazyLoad": "yes", "URL": "https://www.math.vu.nl/~wvanwie/", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-21 08:56:59 UTC", "User": "root" }, "Repository": "https://wvanwie.r-universe.dev", "Date/Publication": "2024-02-22 02:30:32 UTC", "RemoteUrl": "https://github.com/cran/porridge", "RemoteRef": "HEAD", "RemoteSha": "928649f5e7d4453cf7a0b4eeef0eb0906dd51f41", "MD5sum": "7f0dadb97089c9f58b8a18157b65b9ed", "_user": "wvanwie", "_type": "src", "_file": "porridge_0.3.3.tar.gz", "_fileid": "95081e5e223c105b52c4ca425b27ba241cd860c17ea0f4a8a72eab621d46ab0e", "_filesize": 363062, "_sha256": "95081e5e223c105b52c4ca425b27ba241cd860c17ea0f4a8a72eab621d46ab0e", "_created": "2026-05-21T08:56:59.000Z", "_published": "2026-05-21T20:21:48.600Z", "_distro": "noble", "_jobs": [ { "job": 77261059242, "time": 174, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "7131534904" }, { "job": 77261038251, "time": 197, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7131542697" }, { "job": 77261038295, "time": 183, "config": "linux-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7131537898" }, { "job": 77261038258, "time": 197, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7131542705" }, { "job": 77261038055, "time": 229, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7131531210" }, { "job": 77261038289, "time": 269, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "7131562300" }, { "job": 77261038282, "time": 218, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7131538903" }, { "job": 77261064010, "time": 497, "config": "macos-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7131633753" }, { "job": 77261057152, "time": 233, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7131472957" }, { "job": 77261037563, "time": 161, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7146316258" }, { "job": 77261038222, "time": 182, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7131537692" }, { "job": 77261038203, "time": 226, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7131553109" }, { "job": 77261064461, "time": 155, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7131528535" } ], "_buildurl": "https://github.com/r-universe/wvanwie/actions/runs/26215901807", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/cran/porridge", "_commit": { "id": "928649f5e7d4453cf7a0b4eeef0eb0906dd51f41", "author": "Wessel N. van Wieringen ", "committer": "cran-robot ", "message": "version 0.3.3\n", "time": 1708569032 }, "_maintainer": { "name": "Wessel N. van Wieringen", "email": "w.vanwieringen@vumc.nl", "login": "wvanwie", "description": "", "uuid": 16555533, "orcid": "0000-0002-5100-9123" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "RcppArmadillo", "role": "LinkingTo" }, { "package": "MASS", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "mvtnorm", "role": "Imports" }, { "package": "Rcpp", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "pracma", "role": "Imports" }, { "package": "rags2ridges", "role": "Suggests" } ], "_owner": "cran", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 0, "_contributors": [ { "user": "wvanwie", "count": 12, "uuid": 16555533 } ], "_userbio": { "uuid": 16555533, "type": "user", "name": "Wessel N. van Wieringen" }, "_downloads": { "count": 236, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/porridge" }, "_searchresults": 2, "_topics": [ "openblas", "cpp" ], "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/porridge.html", "manual.pdf" ], "_realowner": "wvanwie", "_cranurl": false, "_releases": [ { "version": "0.0.1", "date": "2019-11-01" }, { "version": "0.0.2", "date": "2019-11-13" }, { "version": "0.0.3", "date": "2019-12-05" }, { "version": "0.0.4", "date": "2019-12-16" }, { "version": "0.1.0", "date": "2020-05-18" }, { "version": "0.1.1", "date": "2021-01-11" }, { "version": "0.2.0", "date": "2021-02-09" }, { "version": "0.2.1", "date": "2021-04-19" }, { "version": "0.3.0", "date": "2022-01-08" }, { "version": "0.3.1", "date": "2022-05-20" }, { "version": "0.3.2", "date": "2023-10-15" }, { "version": "0.3.3", "date": "2024-02-21" } ], "_exports": [ "genRidgePenaltyMat", "makeFoldsGLMcv", "optPenaltyGGMmixture.kCVauto", "optPenaltyGLM.kCVauto", "optPenaltyGLMmultiT.kCVauto", "optPenaltyPgen.kCVauto.banded", "optPenaltyPgen.kCVauto.groups", "optPenaltyPmultiT.kCVauto", "optPenaltyPrep.kCVauto", "optPenaltyPrepEdiag.kCVauto", "ridgeGGMmixture", "ridgeGLM", "ridgeGLMdof", "ridgeGLMmultiT", "ridgePgen", "ridgePgen.kCV", "ridgePgen.kCV.banded", "ridgePgen.kCV.groups", "ridgePmultiT", "ridgePrep", "ridgePrepEdiag" ], "_help": [ { "page": "porridge-package", "title": "Ridge-Type Penalized Estimation of a Potpourri of Models.", "topics": [ "porridge-package", "porridge" ] }, { "page": "genRidgePenaltyMat", "title": "Penalty parameter matrix for generalized ridge regression.", "topics": [ "genRidgePenaltyMat" ] }, { "page": "makeFoldsGLMcv", "title": "Generate folds for cross-validation of generalized linear models.", "topics": [ "makeFoldsGLMcv" ] }, { "page": "optPenaltyGGMmixture.kCVauto", "title": "Automatic search for optimal penalty parameter (mixture of GGMs).", "topics": [ "optPenaltyGGMmixture.kCVauto" ] }, { "page": "optPenaltyGLM.kCVauto", "title": "Automatic search for optimal penalty parameters of the targeted ridge GLM estimator.", "topics": [ "optPenaltyGLM.kCVauto" ] }, { "page": "optPenaltyGLMmultiT.kCVauto", "title": "Automatic search for optimal penalty parameters of the targeted ridge GLM estimator.", "topics": [ "optPenaltyGLMmultiT.kCVauto" ] }, { "page": "optPenaltyPgen.kCVauto.banded", "title": "Automatic search for optimal penalty parameter (generalized ridge precision).", "topics": [ "optPenaltyPgen.kCVauto.banded" ] }, { "page": "optPenaltyPgen.kCVauto.groups", "title": "Automatic search for optimal penalty parameter (generalized ridge precision).", "topics": [ "optPenaltyPgen.kCVauto.groups" ] }, { "page": "optPenaltyPmultiT.kCVauto", "title": "Automatic search for optimal penalty parameter (ridge precision with multi-targets).", "topics": [ "optPenaltyPmultiT.kCVauto" ] }, { "page": "optPenaltyPrep.kCVauto", "title": "Automatic search for optimal penalty parameters (for precision estimation of data with replicates).", "topics": [ "optPenaltyPrep.kCVauto" ] }, { "page": "optPenaltyPrepEdiag.kCVauto", "title": "Automatic search for optimal penalty parameters (for precision estimation of data with replicates).", "topics": [ "optPenaltyPrepEdiag.kCVauto" ] }, { "page": "ridgeGGMmixture", "title": "Ridge penalized estimation of a mixture of GGMs.", "topics": [ "ridgeGGMmixture" ] }, { "page": "ridgeGLM", "title": "Ridge estimation of generalized linear models.", "topics": [ "ridgeGLM" ] }, { "page": "ridgeGLMdof", "title": "Degrees of freedom of the generalized ridge estimator.", "topics": [ "ridgeGLMdof" ] }, { "page": "ridgeGLMmultiT", "title": "Multi-targeted ridge estimation of generalized linear models.", "topics": [ "ridgeGLMmultiT" ] }, { "page": "ridgePgen", "title": "Ridge estimation of the inverse covariance matrix with element-wise penalization and shrinkage.", "topics": [ "ridgePgen" ] }, { "page": "ridgePgen.kCV", "title": "K-fold cross-validated loglikelihood of ridge precision estimator.", "topics": [ "ridgePgen.kCV" ] }, { "page": "ridgePgen.kCV.banded", "title": "K-fold cross-validated loglikelihood of ridge precision estimator for banded precisions.", "topics": [ "ridgePgen.kCV.banded" ] }, { "page": "ridgePgen.kCV.groups", "title": "K-fold cross-validated loglikelihood of ridge precision estimator with group-wise penalized variates.", "topics": [ "ridgePgen.kCV.groups" ] }, { "page": "ridgePmultiT", "title": "Ridge estimation of the inverse covariance matrix with multi-target shrinkage.", "topics": [ "ridgePmultiT" ] }, { "page": "ridgePrep", "title": "Ridge penalized estimation of the precision matrix from data with replicates.", "topics": [ "ridgePrep" ] }, { "page": "ridgePrepEdiag", "title": "Ridge penalized estimation of the precision matrix from data with replicates.", "topics": [ "ridgePrepEdiag" ] } ], "_rundeps": [ "lattice", "MASS", "Matrix", "mvtnorm", "pracma", "Rcpp", "RcppArmadillo" ], "_sysdeps": [ { "shlib": "liblapack", "package": "libopenblas0-pthread", "source": "openblas", "version": "0.3.26+ds-1ubuntu0.1", "name": "openblas", "homepage": "https://www.openblas.net/", "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)" }, { "shlib": "libblas", "package": "libopenblas0-pthread", "source": "openblas", "version": "0.3.26+ds-1ubuntu0.1", "name": "openblas", "homepage": "https://www.openblas.net/", "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)" }, { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_score": 1, "_indexed": true, "_nocasepkg": "porridge", "_universes": [ "wvanwie" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.3.3", "date": "2026-05-21T08:59:48.000Z", "distro": "noble", "arch": "aarch64", "commit": "928649f5e7d4453cf7a0b4eeef0eb0906dd51f41", "fileid": "eaf3bb48ce9a3b76dc09f7206cbcc4a6487d353c4f2999236ba0d2a8d1d3846b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/wvanwie/actions/runs/26215901807" }, { "r": "4.7.0", "os": "linux", "version": "0.3.3", "date": "2026-05-21T09:00:11.000Z", "distro": "noble", "arch": "x86_64", "commit": "928649f5e7d4453cf7a0b4eeef0eb0906dd51f41", "fileid": "22e10a423ef1e2e8a5b406b6fc3f05aa95bf495d78c99fabee64b4a7c483a3a1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/wvanwie/actions/runs/26215901807" }, { "r": "4.6.0", "os": "linux", "version": "0.3.3", "date": "2026-05-21T09:00:02.000Z", "distro": "noble", "arch": "aarch64", "commit": "928649f5e7d4453cf7a0b4eeef0eb0906dd51f41", "fileid": "2d6da11d890338ecb13577c52e441876fd9bd828132b842430fc8fc09a00cd18", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/wvanwie/actions/runs/26215901807" }, { "r": "4.6.0", "os": "linux", "version": "0.3.3", "date": "2026-05-21T09:00:08.000Z", "distro": "noble", "arch": "x86_64", "commit": "928649f5e7d4453cf7a0b4eeef0eb0906dd51f41", "fileid": "b0bf757be1767ec9d2db38f462c4fb4de0b602d0fffe5636285da1689ff2795b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/wvanwie/actions/runs/26215901807" }, { "r": "4.5.3", "os": "mac", "version": "0.3.3", "date": "2026-05-21T08:59:49.000Z", "arch": "aarch64", "commit": "928649f5e7d4453cf7a0b4eeef0eb0906dd51f41", "fileid": "be9756a7116491d060bd8ec722207ac3bed30198f7bdc21da92bc6bb47dc5a2b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/wvanwie/actions/runs/26215901807" }, { "r": "4.5.3", "os": "mac", "version": "0.3.3", "date": "2026-05-21T09:00:45.000Z", "arch": "x86_64", "commit": "928649f5e7d4453cf7a0b4eeef0eb0906dd51f41", "fileid": "76ac99ed4143ad5c853a2aba025621e2f584741f0aeb95ee683d4bd91fb2c320", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/wvanwie/actions/runs/26215901807" }, { "r": "4.6.0", "os": "mac", "version": "0.3.3", "date": "2026-05-21T08:59:44.000Z", "arch": "aarch64", "commit": "928649f5e7d4453cf7a0b4eeef0eb0906dd51f41", "fileid": "5c02833bf9cf1bf692f7891e97a58e83179bcc4f87c1cc724963ea1de3be51ad", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/wvanwie/actions/runs/26215901807" }, { "r": "4.6.0", "os": "mac", "version": "0.3.3", "date": "2026-05-21T09:02:48.000Z", "arch": "x86_64", "commit": "928649f5e7d4453cf7a0b4eeef0eb0906dd51f41", "fileid": "e2bdbd06a9356f2f23e01e749b55e0fea156da2dda67069c5d7712711f47fdef", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/wvanwie/actions/runs/26215901807" }, { "r": "4.6.0", "os": "wasm", "version": "0.3.3", "date": "2026-05-21T20:21:20.000Z", "arch": "emscripten", "commit": "928649f5e7d4453cf7a0b4eeef0eb0906dd51f41", "fileid": "0f5bfd1260a4eabcc74ba8d10cfdbe87599e628b2622c87483f6d5af4270431b", "status": "success", "buildurl": "https://github.com/r-universe/wvanwie/actions/runs/26215901807" }, { "r": "4.7.0", "os": "win", "version": "0.3.3", "date": "2026-05-21T08:58:51.000Z", "arch": "x86_64", "commit": "928649f5e7d4453cf7a0b4eeef0eb0906dd51f41", "fileid": "4c6ab4636f8fb49ae9b3ec38c4ed601a388933c7728a494edeef4d2982b9ce5e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/wvanwie/actions/runs/26215901807" }, { "r": "4.5.3", "os": "win", "version": "0.3.3", "date": "2026-05-21T08:59:57.000Z", "arch": "x86_64", "commit": "928649f5e7d4453cf7a0b4eeef0eb0906dd51f41", "fileid": "8e1be023d47b854d41d38c8388d4b8c6373e0531030522dd4b1009d8d9ecfff4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/wvanwie/actions/runs/26215901807" }, { "r": "4.6.0", "os": "win", "version": "0.3.3", "date": "2026-05-21T08:58:49.000Z", "arch": "x86_64", "commit": "928649f5e7d4453cf7a0b4eeef0eb0906dd51f41", "fileid": "9ca6c66f1e8de33b2d6a9a45e17ea4efd4b6a8942191b0bf9cadc9acba5f8ac3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/wvanwie/actions/runs/26215901807" } ] }