{ "_id": "6aaceffa3d719c1f84073486", "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": "2026-09-18 07:26:15 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", "_user": "wvanwie", "_type": "src", "_file": "porridge_0.3.3.tar.gz", "_fileid": "https://r2.ropensci.org/7bf50bf979ef8626b55c5add3f346b0f1f6ce742a7cc3e0c821ca760115ffeef", "_filesize": 367171, "_sha256": "7bf50bf979ef8626b55c5add3f346b0f1f6ce742a7cc3e0c821ca760115ffeef", "_expires": "2026-12-27T08:02:00.000Z", "_created": "2026-09-18T07:26:15.000Z", "_published": "2026-09-18T08:02:02.565Z", "_jobs": [ { "job": 105518483849, "time": 292, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "10536557728" }, { "job": 105518483875, "time": 195, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "10536437826" }, { "job": 105518483936, "time": 171, "config": "linux-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "10536582471" }, { "job": 105518483845, "time": 173, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "10536238212" }, { "job": 105518483870, "time": 115, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "10536853475" }, { "job": 105518483988, "time": 430, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "10536901369" }, { "job": 105518483969, "time": 161, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "10537562549" }, { "job": 105518483881, "time": 334, "config": "macos-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "10536388986" }, { "job": 105517534546, "time": 217, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "10536083089" }, { "job": 105518483793, "time": 154, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "10536746729" }, { "job": 105518483947, "time": 380, "config": "windows-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "10537035549" }, { "job": 105518484134, "time": 209, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "10537005311" }, { "job": 105518483956, "time": 168, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "10536123474" }, { "job": 105518483914, "time": 381, "config": "windows-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "10536358324" }, { "job": 105518484005, "time": 167, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "10536432831" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/wvanwie/actions/runs/35319145318", "_status": "success", "_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" }, "_distro": "resolute", "_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", "followers": 4 }, "_downloads": { "count": 282, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/porridge" }, "_searchresults": 2, "_topics": [ "openblas", "cpp" ], "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/porridge.html" ], "_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": "0.3.32+ds-5", "name": "openblas", "homepage": "https://www.openblas.net/", "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)" }, { "shlib": "libblas", "package": "libopenblas0-pthread", "source": "openblas", "version": "0.3.32+ds-5", "name": "openblas", "homepage": "https://www.openblas.net/", "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)" }, { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "16-20260322-1ubuntu1", "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": "2026-09-18T07:31:06.000Z", "distro": "resolute", "arch": "aarch64", "commit": "928649f5e7d4453cf7a0b4eeef0eb0906dd51f41", "fileid": "https://r2.ropensci.org/8db21ffa7db5e6ceadb419d59b34b7d0f9373ccfe8b23102b5a8d1a9ce28d701", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/wvanwie/actions/runs/35319145318" }, { "r": "4.7.0", "os": "linux", "version": "0.3.3", "date": "2026-09-18T07:29:17.000Z", "distro": "resolute", "arch": "x86_64", "commit": "928649f5e7d4453cf7a0b4eeef0eb0906dd51f41", "fileid": "https://r2.ropensci.org/3f45c238ac682d14bc8b89a8d00419d3884d7d33cd1b403deb3d4b50224123a5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/wvanwie/actions/runs/35319145318" }, { "r": "4.6.1", "os": "linux", "version": "0.3.3", "date": "2026-09-18T07:29:11.000Z", "distro": "resolute", "arch": "aarch64", "commit": "928649f5e7d4453cf7a0b4eeef0eb0906dd51f41", "fileid": "https://r2.ropensci.org/aded87874390767f235e2b7f58ce73f3b08f306a95d6af18dd6a1c9a78c7253d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/wvanwie/actions/runs/35319145318" }, { "r": "4.6.1", "os": "linux", "version": "0.3.3", "date": "2026-09-18T07:29:06.000Z", "distro": "resolute", "arch": "x86_64", "commit": "928649f5e7d4453cf7a0b4eeef0eb0906dd51f41", "fileid": "https://r2.ropensci.org/4a26b59ae864b7b93393dec0de4c199a48d719bae67245b9b55dd8797e996c68", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/wvanwie/actions/runs/35319145318" }, { "r": "4.5.3", "os": "mac", "version": "0.3.3", "date": "2026-09-18T07:57:19.000Z", "arch": "aarch64", "commit": "928649f5e7d4453cf7a0b4eeef0eb0906dd51f41", "fileid": "https://r2.ropensci.org/913171a1ff3dba78a4684c516d9d6438ff246b510772e7bd3e122617d9ebaee5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/wvanwie/actions/runs/35319145318" }, { "r": "4.5.3", "os": "mac", "version": "0.3.3", "date": "2026-09-18T07:37:45.000Z", "arch": "x86_64", "commit": "928649f5e7d4453cf7a0b4eeef0eb0906dd51f41", "fileid": "https://r2.ropensci.org/24880d1e6940f4c72ef72972f0d35cc4035821e349c7d035f6e5d38ceb1431b0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/wvanwie/actions/runs/35319145318" }, { "r": "4.6.1", "os": "mac", "version": "0.3.3", "date": "2026-09-18T08:00:55.000Z", "arch": "aarch64", "commit": "928649f5e7d4453cf7a0b4eeef0eb0906dd51f41", "fileid": "https://r2.ropensci.org/19eab4081c45eb53e67495e2d17dd859bbf725d1a90742cfc1a7bf2dd683abcb", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/wvanwie/actions/runs/35319145318" }, { "r": "4.6.1", "os": "mac", "version": "0.3.3", "date": "2026-09-18T07:35:33.000Z", "arch": "x86_64", "commit": "928649f5e7d4453cf7a0b4eeef0eb0906dd51f41", "fileid": "https://r2.ropensci.org/e961e38216f1c422d2f0be8f954ae91a2eb55eac87068e66834fe48cad674b01", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/wvanwie/actions/runs/35319145318" }, { "r": "4.6.0", "os": "wasm", "version": "0.3.3", "date": "2026-09-18T07:29:20.000Z", "arch": "emscripten", "commit": "928649f5e7d4453cf7a0b4eeef0eb0906dd51f41", "fileid": "https://r2.ropensci.org/70dad2c91a1f380fec2e2e1832fc4c946545e6972b25e537785758fc0894645c", "status": "success", "buildurl": "https://github.com/r-universe/wvanwie/actions/runs/35319145318" }, { "r": "4.7.0", "os": "win", "version": "0.3.3", "date": "2026-09-18T07:31:50.000Z", "arch": "aarch64", "commit": "928649f5e7d4453cf7a0b4eeef0eb0906dd51f41", "fileid": "https://r2.ropensci.org/f5130d93a6dddc05cf5052b4c0163223ea17f8181844760e73f796212dba2dbf", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/wvanwie/actions/runs/35319145318" }, { "r": "4.7.0", "os": "win", "version": "0.3.3", "date": "2026-09-18T07:28:15.000Z", "arch": "x86_64", "commit": "928649f5e7d4453cf7a0b4eeef0eb0906dd51f41", "fileid": "https://r2.ropensci.org/deea3adbfa49c724d4244ec2df1b81f65faf0e0d5e4704078ac3549bf3e149e0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/wvanwie/actions/runs/35319145318" }, { "r": "4.5.3", "os": "win", "version": "0.3.3", "date": "2026-09-18T07:28:51.000Z", "arch": "x86_64", "commit": "928649f5e7d4453cf7a0b4eeef0eb0906dd51f41", "fileid": "https://r2.ropensci.org/6eddaa1977aadb118ac2dd1ace966e646efeccaf757e1468ee431b7a416f2505", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/wvanwie/actions/runs/35319145318" }, { "r": "4.6.1", "os": "win", "version": "0.3.3", "date": "2026-09-18T07:31:45.000Z", "arch": "aarch64", "commit": "928649f5e7d4453cf7a0b4eeef0eb0906dd51f41", "fileid": "https://r2.ropensci.org/1380c4e86fef88f65635b59c850ed95c2897a2800ff608e59f36ecb5442dec38", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/wvanwie/actions/runs/35319145318" }, { "r": "4.6.1", "os": "win", "version": "0.3.3", "date": "2026-09-18T07:28:12.000Z", "arch": "x86_64", "commit": "928649f5e7d4453cf7a0b4eeef0eb0906dd51f41", "fileid": "https://r2.ropensci.org/edbc2b41a976190131de036b9fb01dbeff1332e2ff7fd9de88637cec25eecd66", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/wvanwie/actions/runs/35319145318" } ] }