{ "_id": "6a23d1ab530b9bc726be31b6", "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": "2026-06-06 07:48:17 UTC", "User": "root" }, "Repository": "https://cran.r-universe.dev", "Date/Publication": "2024-02-22 02:30:32 UTC", "RemoteUrl": "https://github.com/cran/porridge", "RemoteRef": "HEAD", "RemoteSha": "928649f5e7d4453cf7a0b4eeef0eb0906dd51f41", "MD5sum": "6df38f873261c05bd7f02084f9462c7c", "_user": "cran", "_type": "src", "_file": "porridge_0.3.3.tar.gz", "_fileid": "fca0ce7ca6eeb0bfe4f185a144061583a528acab394eab07b672b7c4cc4595e3", "_filesize": 363929, "_sha256": "fca0ce7ca6eeb0bfe4f185a144061583a528acab394eab07b672b7c4cc4595e3", "_created": "2026-06-06T07:48:17.000Z", "_published": "2026-06-06T07:52:11.943Z", "_distro": "noble", "_jobs": [ { "job": 79862180009, "time": 174, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "7452596784" }, { "job": 79862180010, "time": 168, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7452595408" }, { "job": 79862179986, "time": 171, "config": "linux-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7452596258" }, { "job": 79862179991, "time": 177, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7452596438" }, { "job": 79862006008, "time": 198, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7452574811" }, { "job": 79862179959, "time": 142, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7452592562" } ], "_buildurl": "https://github.com/r-universe/cran/actions/runs/27056565424", "_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": false, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 0, "_contributors": [ { "user": "wvanwie", "count": 12, "uuid": 16555533 } ], "_userbio": { "uuid": 6899542, "type": "organization", "name": "cran", "description": "Unofficial read-only mirror of all CRAN R packages" }, "_downloads": { "count": 199, "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": false, "_nocasepkg": "porridge", "_universes": [ "cran" ], "_indexurl": "https://wvanwie.r-universe.dev/porridge", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.3.3", "date": "2026-06-06T07:51:13.000Z", "distro": "noble", "arch": "aarch64", "commit": "928649f5e7d4453cf7a0b4eeef0eb0906dd51f41", "fileid": "dbb7ab54c2ba56acc6fd1937274b7f9277c385060fb2513a9475c91f96041578", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/27056565424" }, { "r": "4.7.0", "os": "linux", "version": "0.3.3", "date": "2026-06-06T07:50:58.000Z", "distro": "noble", "arch": "x86_64", "commit": "928649f5e7d4453cf7a0b4eeef0eb0906dd51f41", "fileid": "ac97d5687abecaa78ac1e2ea01bb6dbdbb49181296168589b767d2639e32dc28", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/27056565424" }, { "r": "4.6.0", "os": "linux", "version": "0.3.3", "date": "2026-06-06T07:51:03.000Z", "distro": "noble", "arch": "aarch64", "commit": "928649f5e7d4453cf7a0b4eeef0eb0906dd51f41", "fileid": "335486103682d742824b5ff1168cd30427cacd339ba160cfd81d5b88d9c77ebe", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/27056565424" }, { "r": "4.6.0", "os": "linux", "version": "0.3.3", "date": "2026-06-06T07:51:03.000Z", "distro": "noble", "arch": "x86_64", "commit": "928649f5e7d4453cf7a0b4eeef0eb0906dd51f41", "fileid": "f56dc1ad43654ec4ccd12a0e39102ce2b1bf2f67064def9247dc0cb0988c098a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/27056565424" }, { "r": "4.6.0", "os": "wasm", "version": "0.3.3", "date": "2026-06-06T07:51:06.000Z", "arch": "emscripten", "commit": "928649f5e7d4453cf7a0b4eeef0eb0906dd51f41", "fileid": "22bbc43ac662b47bb0d7d596080a1b84e6e64d882f0e2a019b9b1ebc076a6e05", "status": "success", "buildurl": "https://github.com/r-universe/cran/actions/runs/27056565424" } ] }