{ "_id": "6aae53163d719c1f8407b462", "Package": "ggm", "Title": "Graphical Markov Models with Mixed Graphs", "Version": "2.5.5", "Authors@R": "c(person(given = \"Giovanni M.\", family = \"Marchetti\", email = \"giovanni.marchetti@unifi.it\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"https://orcid.org/0000-0003-4413-9349\")), person(\"Mathias\", \"Drton\", email = \"mathias.drton@tum.de\", role = \"aut\", comment = c(ORCID = \"https://orcid.org/0000-0001-5614-3025\")), person(\"Kayvan\", \"Sadeghi\", email = \"k.sadeghi@ucl.ac.uk\", role = \"aut\", comment = c(ORCID = \"https://orcid.org/0000-0001-7314-744X\")))", "biocViews": "", "Description": "Provides functions for defining mixed graphs containing\nthree types of edges, directed, undirected and bi-directed,\nwith possibly multiple edges. These graphs are useful because\nthey capture fundamental independence structures in\nmultivariate distributions and in the induced distributions\nafter marginalization and conditioning. The package is\nespecially concerned with Gaussian graphical models for (i) ML\nestimation for directed acyclic graphs, undirected and\nbi-directed graphs and ancestral graph models (ii) testing\nseveral conditional independencies (iii) checking global\nidentification of DAG Gaussian models with one latent variable\n(iv) testing Markov equivalences and generating Markov\nequivalent graphs of specific types. Note: The Bioconductor\npackage 'graph' is now a suggested dependency and is only\nrequired when working with 'graphNEL' objects.", "License": "GPL-2", "Encoding": "UTF-8", "LazyData": "true", "NeedsCompilation": "no", "Config/roxygen2/version": "8.1.0", "Roxygen": "list(markdown = TRUE)", "Config/pak/sysreqs": "libglpk-dev libxml2-dev", "Repository": "https://stathin.r-universe.dev", "Date/Publication": "2026-08-20 16:31:30 UTC", "RemoteUrl": "https://github.com/stathin/ggm", "RemoteRef": "HEAD", "RemoteSha": "f402a4c3784f93c86a48245280d5e49c0650b43c", "Packaged": { "Date": "2026-09-19 09:13:21 UTC", "User": "root" }, "Author": "Giovanni M. Marchetti [aut, cre] (ORCID:\n),\nMathias Drton [aut] (ORCID: ),\nKayvan Sadeghi [aut] (ORCID: )", "Maintainer": "Giovanni M. Marchetti ", "_user": "stathin", "_type": "src", "_file": "ggm_2.5.5.tar.gz", "_fileid": "https://r2.ropensci.org/d9a0bd68c4641ceee38c46ac23644208d4ec543e24e1f4bc8281ef6a236fe7bd", "_filesize": 544764, "_sha256": "d9a0bd68c4641ceee38c46ac23644208d4ec543e24e1f4bc8281ef6a236fe7bd", "_expires": "2026-12-28T09:17:08.000Z", "_created": "2026-09-19T09:13:21.000Z", "_published": "2026-09-19T09:17:10.209Z", "_jobs": [ { "job": 105873779065, "time": 135, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "10581632546" }, { "job": 105873779108, "time": 142, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "10581287169" }, { "job": 105873779116, "time": 146, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "10582291952" }, { "job": 105873779083, "time": 173, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "10581847428" }, { "job": 105873425873, "time": 174, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "10582022071" }, { "job": 105873779047, "time": 109, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "10581927107" }, { "job": 105873779143, "time": 68, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "10581102457" }, { "job": 105873779087, "time": 88, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "10581312137" }, { "job": 105873779076, "time": 102, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "10581102488" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/stathin/actions/runs/35433969890", "_status": "success", "_upstream": "https://github.com/stathin/ggm", "_commit": { "id": "f402a4c3784f93c86a48245280d5e49c0650b43c", "author": "Stathin ", "committer": "Stathin ", "message": "changes in RepMarDAG\n", "time": 1787243490 }, "_maintainer": { "name": "Giovanni M. Marchetti", "email": "giovanni.marchetti@unifi.it", "login": "stathin", "description": "Prof. of Statistics at the University of Florence", "uuid": 5725965, "orcid": "0000-0003-4413-9349" }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.6.0", "role": "Depends" }, { "package": "methods", "role": "Depends" }, { "package": "igraph", "role": "Imports" }, { "package": "graph", "role": "Suggests" }, { "package": "dagitty", "role": "Suggests" }, { "package": "graphLayout", "role": "Suggests" }, { "package": "gRbase", "role": "Suggests" } ], "_owner": "stathin", "_selfowned": true, "_usedby": 27, "_updates": [ { "week": "2026-25", "n": 2 }, { "week": "2026-26", "n": 6 }, { "week": "2026-28", "n": 2 }, { "week": "2026-29", "n": 5 }, { "week": "2026-30", "n": 3 }, { "week": "2026-31", "n": 3 }, { "week": "2026-32", "n": 1 }, { "week": "2026-33", "n": 1 }, { "week": "2026-34", "n": 1 } ], "_tags": [], "_stars": 0, "_contributors": [ { "user": "stathin", "count": 24, "uuid": 5725965 } ], "_userbio": { "uuid": 5725965, "type": "user", "name": "Giovanni Maria Marchetti", "followers": 2, "description": "Prof. of Statistics at the University of Florence" }, "_downloads": { "count": 8162, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/ggm" }, "_mentions": 19, "_devurl": "https://github.com/stathin/ggm", "_searchresults": 386, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/ggm.html", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt" ], "_homeurl": "https://github.com/stathin/ggm", "_realowner": "stathin", "_cranurl": true, "_releases": [ { "version": "0.5", "date": "2003-09-12" }, { "version": "0.8", "date": "2003-11-13" }, { "version": "0.8-1", "date": "2003-11-15" }, { "version": "1.0", "date": "2005-05-31" }, { "version": "1.0.2", "date": "2006-02-09" }, { "version": "1.0.3", "date": "2010-01-06" }, { "version": "1.0.4", "date": "2010-02-15" }, { "version": "1.99", "date": "2011-11-23" }, { "version": "1.99-1", "date": "2011-12-11" }, { "version": "1.99-2", "date": "2012-01-12" }, { "version": "1.99-3", "date": "2012-06-14" }, { "version": "1.99-5", "date": "2012-06-19" }, { "version": "1.995-0", "date": "2012-08-24" }, { "version": "1.995-2", "date": "2012-09-14" }, { "version": "1.995-3", "date": "2012-10-05" }, { "version": "1.995-5", "date": "2014-01-15" }, { "version": "2.0", "date": "2014-03-21" }, { "version": "2.1", "date": "2014-05-19" }, { "version": "2.2", "date": "2014-12-04" }, { "version": "2.3", "date": "2015-01-21" }, { "version": "2.5", "date": "2020-02-16" }, { "version": "2.5.1", "date": "2024-01-25" }, { "version": "2.5.2", "date": "2025-07-25" }, { "version": "2.5.4", "date": "2026-08-04" } ], "_exports": [ "adjMatrix", "AG", "allEdges", "basiSet", "bd", "bfsearch", "binve", "blkdiag", "blodiag", "ch", "checkIdent", "cmpGraph", "conComp", "correlations", "cycleMatrix", "DAG", "DG", "diagv", "drawGraph", "dSep", "edgematrix", "essentialGraph", "findPath", "fitAncestralGraph", "fitConGraph", "fitCovGraph", "fitDag", "fitDagLatent", "fitmlogit", "fundCycles", "grMAT", "hypercube", "icf", "In", "inducedChainGraph", "inducedConGraph", "inducedCovGraph", "inducedDAG", "inducedRegGraph", "isAcyclic", "isADMG", "isAG", "isGident", "likGau", "MAG", "makeMG", "marg.param", "MarkEqMag", "MarkEqRcg", "mat.mlogit", "Max", "MRG", "msep", "MSG", "null", "pa", "parcor", "pcor", "pcor_test", "pcor.test", "plotGraph", "powerset", "rcorr", "RepMarBG", "RepMarDAG", "RepMarUG", "RG", "rnormDag", "rsphere", "SG", "shipley_test", "shipley.test", "swp", "topOrder", "topSort", "transClos", "triDec", "UG", "unmakeMG" ], "_datasets": [ { "name": "anger", "title": "Anger data", "object": "anger", "class": [ "matrix", "array" ], "fields": [ "X", "Y", "Z", "U" ], "rows": 4, "table": true, "tojson": true }, { "name": "derived", "title": "Data on blood pressure body mass and age", "object": "derived", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "glucose", "title": "Glucose control", "object": "glucose", "class": [ "data.frame" ], "fields": [ "Y", "X", "Z", "U", "V", "W", "A", "B" ], "rows": 68, "table": true, "tojson": true }, { "name": "marks", "title": "Mathematics marks", "object": "marks", "class": [ "data.frame" ], "fields": [ "mechanics", "vectors", "algebra", "analysis", "statistics" ], "rows": 88, "table": true, "tojson": true }, { "name": "stress", "title": "Stress data", "object": "stress", "class": [ "matrix", "array" ], "fields": [ "Y", "V", "X", "U" ], "rows": 4, "table": true, "tojson": true }, { "name": "surdata", "title": "A simulated data set", "object": "surdata", "class": [ "data.frame" ], "fields": [ "A", "B", "X", "Z" ], "rows": 600, "table": true, "tojson": true } ], "_help": [ { "page": "ggm-package", "title": "ggm: Graphical Markov Models with Mixed Graphs", "topics": [ "ggm-package", "ggm", "ggm_package" ] }, { "page": "adjMatrix", "title": "Adjacency matrix of a graph", "topics": [ "adjMatrix" ] }, { "page": "AG", "title": "Ancestral graph", "topics": [ "AG" ] }, { "page": "allEdges", "title": "All edges of a graph", "topics": [ "allEdges" ] }, { "page": "anger", "title": "Anger data", "topics": [ "anger" ] }, { "page": "basiSet", "title": "Shipley basis set of a DAG", "topics": [ "basiSet" ] }, { "page": "bfsearch", "title": "Breadth first search", "topics": [ "bfsearch" ] }, { "page": "binve", "title": "Inverts a marginal log-linear parametrization", "topics": [ "binve" ] }, { "page": "blkdiag", "title": "Block diagonal matrix", "topics": [ "blkdiag" ] }, { "page": "blodiag", "title": "Block diagonal matrix", "topics": [ "blodiag" ] }, { "page": "checkIdent", "title": "Identifiability of a model with one latent variable", "topics": [ "checkIdent" ] }, { "page": "cmpGraph", "title": "The complementary graph", "topics": [ "cmpGraph" ] }, { "page": "conComp", "title": "Connectivity components", "topics": [ "conComp" ] }, { "page": "correlations", "title": "Marginal and partial correlations", "topics": [ "correlations" ] }, { "page": "cycleMatrix", "title": "Fundamental cycles", "topics": [ "cycleMatrix" ] }, { "page": "DAG", "title": "Directed acyclic graphs (DAGs)", "topics": [ "DAG" ] }, { "page": "derived", "title": "Data on blood pressure body mass and age", "topics": [ "derived" ] }, { "page": "DG", "title": "Directed graphs", "topics": [ "DG" ] }, { "page": "diagv", "title": "Matrix product with a diagonal matrix", "topics": [ "diagv" ] }, { "page": "drawGraph", "title": "Drawing a graph with a simple point and click interface.", "topics": [ "drawGraph" ] }, { "page": "dSep", "title": "d-separation", "topics": [ "dSep" ] }, { "page": "edgematrix", "title": "Conversion of an adjacency matrix of a DAG into an edge matrix", "topics": [ "edgematrix" ] }, { "page": "essentialGraph", "title": "Essential graph", "topics": [ "essentialGraph" ] }, { "page": "findPath", "title": "Finding paths", "topics": [ "findPath" ] }, { "page": "fitAncestralGraph", "title": "Fitting of Gaussian Ancestral Graph Models", "topics": [ "fitAncestralGraph" ] }, { "page": "fitConGraph", "title": "Fitting a Gaussian concentration graph model", "topics": [ "fitConGraph" ] }, { "page": "fitCovGraph", "title": "Fitting of Gaussian covariance graph models", "topics": [ "fitCovGraph" ] }, { "page": "fitDag", "title": "Fitting of Gaussian DAG models", "topics": [ "fitDag" ] }, { "page": "fitDagLatent", "title": "Fitting Gaussian DAG models with one latent variable", "topics": [ "fitDagLatent" ] }, { "page": "fitmlogit", "title": "Multivariate logistic models", "topics": [ "fitmlogit" ] }, { "page": "fundCycles", "title": "Fundamental cycles", "topics": [ "fundCycles" ] }, { "page": "glucose", "title": "Glucose control", "topics": [ "glucose" ] }, { "page": "grMAT", "title": "Graph to adjacency matrix", "topics": [ "grMAT" ] }, { "page": "hypercube", "title": "Create a Boolean matrix from all combinations of binary variables", "topics": [ "hypercube" ] }, { "page": "In", "title": "Indicator matrix", "topics": [ "In" ] }, { "page": "induced-graphs", "title": "Graphs induced by marginalization or conditioning", "topics": [ "induced-graphs", "inducedChainGraph", "inducedConGraph", "inducedCovGraph", "inducedDAG", "inducedRegGraph" ] }, { "page": "isAcyclic", "title": "Graph queries", "topics": [ "isAcyclic" ] }, { "page": "isADMG", "title": "Acyclic directed mixed graphs", "topics": [ "isADMG" ] }, { "page": "isAG", "title": "Ancestral graph", "topics": [ "isAG" ] }, { "page": "isGident", "title": "G-identifiability of an UG", "topics": [ "isGident" ] }, { "page": "likGau", "title": "Deviance of a Gaussian graphical model", "topics": [ "likGau" ] }, { "page": "MAG", "title": "Maximal ancestral graph", "topics": [ "MAG" ] }, { "page": "makeMG", "title": "Mixed Graphs", "topics": [ "makeMG" ] }, { "page": "marg.param", "title": "Link function of the marginal log-linear parameterization", "topics": [ "marg.param" ] }, { "page": "MarkEqMag", "title": "Markov equivalence of maximal ancestral graphs", "topics": [ "MarkEqMag" ] }, { "page": "MarkEqRcg", "title": "Markov equivalence for regression chain graphs", "topics": [ "MarkEqRcg" ] }, { "page": "marks", "title": "Mathematics marks", "topics": [ "marks" ] }, { "page": "mat.mlogit", "title": "Multivariate logistic parameterization", "topics": [ "mat.mlogit" ] }, { "page": "Max", "title": "Maximization for graphs", "topics": [ "Max" ] }, { "page": "MRG", "title": "Maximal ribbonless graph", "topics": [ "MRG" ] }, { "page": "msep", "title": "The m-separation criterion", "topics": [ "msep" ] }, { "page": "MSG", "title": "Maximal summary graph", "topics": [ "MSG" ] }, { "page": "null", "title": "Null space of a matrix", "topics": [ "null" ] }, { "page": "parcor", "title": "Partial correlations", "topics": [ "parcor" ] }, { "page": "pcor", "title": "Partial correlation", "topics": [ "pcor" ] }, { "page": "pcor_test", "title": "Test for zero partial association", "topics": [ "pcor.test", "pcor_test" ] }, { "page": "plotGraph", "title": "Plot mixed graphs", "topics": [ "plotGraph" ] }, { "page": "powerset", "title": "Power set", "topics": [ "powerset" ] }, { "page": "rcorr", "title": "Random correlation matrix", "topics": [ "rcorr" ] }, { "page": "RepMarBG", "title": "Representational Markov equivalence to bidirected graphs.", "topics": [ "RepMarBG" ] }, { "page": "RepMarDAG", "title": "Representational Markov equivalence to directed acyclic graphs.", "topics": [ "RepMarDAG" ] }, { "page": "RepMarUG", "title": "Representational Markov equivalence to undirected graphs.", "topics": [ "RepMarUG" ] }, { "page": "RG", "title": "Ribbonless graph", "topics": [ "RG" ] }, { "page": "rnormDag", "title": "Random samples from a decomposable Gaussian model", "topics": [ "rnormDag" ] }, { "page": "rsphere", "title": "Random vectors on a sphere", "topics": [ "rsphere" ] }, { "page": "SG", "title": "Summary graph", "topics": [ "SG" ] }, { "page": "shipley_test", "title": "Test of all independencies implied by a given DAG", "topics": [ "shipley.test", "shipley_test" ] }, { "page": "simple-graph-operations", "title": "Simple graph operations", "topics": [ "bd", "ch", "pa", "simple-graph-operations" ] }, { "page": "stress", "title": "Stress data", "topics": [ "stress" ] }, { "page": "surdata", "title": "A simulated data set", "topics": [ "surdata" ] }, { "page": "swp", "title": "Sweep operator", "topics": [ "swp" ] }, { "page": "topological-sort", "title": "Topological sort", "topics": [ "topological-sort", "topOrder", "topSort" ] }, { "page": "transClos", "title": "Transitive closure of a graph", "topics": [ "transClos" ] }, { "page": "triDec", "title": "Triangular decomposition of a covariance matrix", "topics": [ "triDec" ] }, { "page": "UG", "title": "Defining an undirected graph (UG)", "topics": [ "UG" ] }, { "page": "unmakeMG", "title": "Loopless mixed graphs components", "topics": [ "unmakeMG" ] } ], "_rundeps": [ "cli", "cpp11", "glue", "igraph", "lattice", "lifecycle", "magrittr", "Matrix", "pkgconfig", "rlang", "vctrs" ], "_score": 8.361111423426982, "_indexed": true, "_nocasepkg": "ggm", "_universes": [ "stathin" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.5.5", "date": "2026-09-19T09:15:31.000Z", "distro": "resolute", "commit": "f402a4c3784f93c86a48245280d5e49c0650b43c", "fileid": "https://r2.ropensci.org/695cadd8b7bba6e074eb0c2d3d294865058ef12d6c70db6c31b3e9b53b63573f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/stathin/actions/runs/35433969890" }, { "r": "4.6.1", "os": "linux", "version": "2.5.5", "date": "2026-09-19T09:15:39.000Z", "distro": "resolute", "commit": "f402a4c3784f93c86a48245280d5e49c0650b43c", "fileid": "https://r2.ropensci.org/c39038122b866fe79415353b853174fef9a6be0f272315fa0b4d2efdccca62b3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/stathin/actions/runs/35433969890" }, { "r": "4.5.3", "os": "mac", "version": "2.5.5", "date": "2026-09-19T09:15:38.000Z", "commit": "f402a4c3784f93c86a48245280d5e49c0650b43c", "fileid": "https://r2.ropensci.org/38455340a7f35a46042a2d6297dfc912bece3fb9d13497857c830565228af83b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/stathin/actions/runs/35433969890" }, { "r": "4.6.1", "os": "mac", "version": "2.5.5", "date": "2026-09-19T09:15:57.000Z", "commit": "f402a4c3784f93c86a48245280d5e49c0650b43c", "fileid": "https://r2.ropensci.org/4b4ac03d480799fbdcef42a94a2ef50702533b65b88bfaac4c3f6734257c0347", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/stathin/actions/runs/35433969890" }, { "r": "4.6.0", "os": "wasm", "version": "2.5.5", "date": "2026-09-19T09:15:30.000Z", "commit": "f402a4c3784f93c86a48245280d5e49c0650b43c", "fileid": "https://r2.ropensci.org/d15f1dad214406fdcf789b2efb9fbae7291ebfaf9bd13ca9cd0718f370bbd406", "status": "success", "buildurl": "https://github.com/r-universe/stathin/actions/runs/35433969890" }, { "r": "4.7.0", "os": "win", "version": "2.5.5", "date": "2026-09-19T09:14:23.000Z", "commit": "f402a4c3784f93c86a48245280d5e49c0650b43c", "fileid": "https://r2.ropensci.org/f09fa2cf44ad5ea5c532eb81b383c565e8176f6828a2835681b0af50e4a27271", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/stathin/actions/runs/35433969890" }, { "r": "4.5.3", "os": "win", "version": "2.5.5", "date": "2026-09-19T09:14:40.000Z", "commit": "f402a4c3784f93c86a48245280d5e49c0650b43c", "fileid": "https://r2.ropensci.org/9ff39b34430cbaabe022b6f11b4dda3dbb92cca4fe23f34fb49fe8df3afe5a03", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/stathin/actions/runs/35433969890" }, { "r": "4.6.1", "os": "win", "version": "2.5.5", "date": "2026-09-19T09:14:50.000Z", "commit": "f402a4c3784f93c86a48245280d5e49c0650b43c", "fileid": "https://r2.ropensci.org/98bb62a38237a448daa09063d48f2e2c336b49e615ecda9c97e6ae2c558a3600", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/stathin/actions/runs/35433969890" } ] }