{
  "_id": "6a185c99acfb0bcc41dbbc50",
  "Package": "SEMgraph",
  "Title": "Network Analysis and Causal Inference Through Structural\nEquation Modeling",
  "Version": "1.2.4",
  "Date": "2025-12-10",
  "Authors@R": "c(\nperson(\"Mario\", \"Grassi\", role = \"aut\", email=\"mario.grassi@unipv.it\"),\nperson(\"Fernando\", \"Palluzzi\", role = \"aut\", email=\"fernando.palluzzi@gmail.com\"),\nperson(\"Barbara\", \"Tarantino\", role = c(\"cre\"), email=\"barbara.tarantino01@universitadipavia.it\"))",
  "Description": "Estimate networks and causal relationships in complex\nsystems through Structural Equation Modeling. This package also\nincludes functions for importing, weight, manipulate, and fit\nbiological network models within the Structural Equation\nModeling framework as outlined in the Supplementary Material of\nGrassi M, Palluzzi F, Tarantino B (2022)\n<doi:10.1093/bioinformatics/btac567>.",
  "URL": "https://github.com/fernandoPalluzzi/SEMgraph",
  "VignetteBuilder": "knitr",
  "License": "GPL-3",
  "LazyData": "true",
  "Encoding": "UTF-8",
  "NeedsCompilation": "no",
  "RoxygenNote": "7.3.3",
  "Maintainer": "Barbara Tarantino\n<barbara.tarantino01@universitadipavia.it>",
  "Author": "Mario Grassi [aut], Fernando Palluzzi [aut], Barbara Tarantino\n[cre]",
  "Packaged": {
    "Date": "2026-05-28 14:51:04 UTC",
    "User": "root"
  },
  "Config/pak/sysreqs": "libglpk-dev libpng-dev libxml2-dev libssl-dev\nlibnode-dev zlib1g-dev",
  "Repository": "https://fernandopalluzzi.r-universe.dev",
  "Date/Publication": "2025-12-18 15:43:59 UTC",
  "RemoteUrl": "https://github.com/fernandopalluzzi/semgraph",
  "RemoteRef": "HEAD",
  "RemoteSha": "31eff1eab1f15e93d2e1bfcc869770424f75fb1a",
  "MD5sum": "b5982e5472547c9e7268052047a7ff1a",
  "_user": "fernandopalluzzi",
  "_type": "src",
  "_file": "SEMgraph_1.2.4.tar.gz",
  "_fileid": "2cd018f8ce78cbacb261166c4c4c670c48562885662985dea6a6328cd6ac49a1",
  "_filesize": 5608686,
  "_sha256": "2cd018f8ce78cbacb261166c4c4c670c48562885662985dea6a6328cd6ac49a1",
  "_created": "2026-05-28T14:51:04.000Z",
  "_published": "2026-05-28T15:17:45.211Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 78318628779,
      "time": 227,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7269248042"
    },
    {
      "job": 78318628716,
      "time": 178,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7269226892"
    },
    {
      "job": 78318628906,
      "time": 200,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7269774411"
    },
    {
      "job": 78318628656,
      "time": 160,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7269716700"
    },
    {
      "job": 78317119586,
      "time": 363,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7269122015"
    },
    {
      "job": 78318628748,
      "time": 170,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7269223289"
    },
    {
      "job": 78318628701,
      "time": 180,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7269229288"
    },
    {
      "job": 78318628771,
      "time": 234,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7269253329"
    },
    {
      "job": 78318628709,
      "time": 177,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7269227736"
    }
  ],
  "_buildurl": "https://github.com/r-universe/fernandopalluzzi/actions/runs/26581816708",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/fernandopalluzzi/semgraph",
  "_commit": {
    "id": "31eff1eab1f15e93d2e1bfcc869770424f75fb1a",
    "author": "grassiMario <93978837+grassiMario@users.noreply.github.com>",
    "committer": "GitHub <noreply@github.com>",
    "message": "Update DESCRIPTION",
    "time": 1766072639
  },
  "_maintainer": {
    "name": "Barbara Tarantino",
    "email": "barbara.tarantino01@universitadipavia.it",
    "login": "barbaratarantino",
    "linkedin": "in/barbara-t",
    "description": "",
    "uuid": 62012637
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "igraph",
      "version": ">= 1.6.0",
      "role": "Depends"
    },
    {
      "package": "lavaan",
      "version": ">= 0.6-1",
      "role": "Depends"
    },
    {
      "package": "R",
      "version": ">= 4.0",
      "role": "Depends"
    },
    {
      "package": "aspect",
      "role": "Imports"
    },
    {
      "package": "boot",
      "role": "Imports"
    },
    {
      "package": "corpcor",
      "role": "Imports"
    },
    {
      "package": "dagitty",
      "role": "Imports"
    },
    {
      "package": "flip",
      "role": "Imports"
    },
    {
      "package": "gdata",
      "role": "Imports"
    },
    {
      "package": "ggm",
      "role": "Imports"
    },
    {
      "package": "glasso",
      "role": "Imports"
    },
    {
      "package": "glmnet",
      "role": "Imports"
    },
    {
      "package": "graph",
      "role": "Imports"
    },
    {
      "package": "mgcv",
      "role": "Imports"
    },
    {
      "package": "mvtnorm",
      "role": "Imports"
    },
    {
      "package": "pbapply",
      "role": "Imports"
    },
    {
      "package": "protoclust",
      "role": "Imports"
    },
    {
      "package": "RBGL",
      "role": "Imports"
    },
    {
      "package": "Rgraphviz",
      "role": "Imports"
    },
    {
      "package": "graphite",
      "role": "Imports"
    },
    {
      "package": "AnnotationDbi",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "org.Hs.eg.db",
      "role": "Suggests"
    }
  ],
  "_owner": "fernandopalluzzi",
  "_selfowned": true,
  "_usedby": 1,
  "_updates": [
    {
      "week": "2025-47",
      "n": 1
    },
    {
      "week": "2025-51",
      "n": 12
    }
  ],
  "_tags": [],
  "_stars": 24,
  "_contributors": [
    {
      "user": "fernandopalluzzi",
      "count": 425,
      "uuid": 51379764
    },
    {
      "user": "grassimario",
      "count": 13,
      "uuid": 93978837
    }
  ],
  "_userbio": {
    "uuid": 51379764,
    "type": "user",
    "name": "Fernando Palluzzi",
    "description": "Senior Data Scientist @ Novo Nordisk - Integrated Omics Group"
  },
  "_downloads": {
    "count": 292,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/SEMgraph"
  },
  "_devurl": "https://github.com/fernandopalluzzi/semgraph",
  "_searchresults": 29,
  "_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/readme.html",
    "extra/readme.md",
    "extra/SEMgraph.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/fernandopalluzzi/semgraph",
  "_realowner": "fernandopalluzzi",
  "_cranurl": true,
  "_releases": [
    {
      "version": "1.0.3",
      "date": "2021-07-08"
    },
    {
      "version": "1.0.4",
      "date": "2021-11-16"
    },
    {
      "version": "1.0.5",
      "date": "2022-01-04"
    },
    {
      "version": "1.1.0",
      "date": "2022-03-24"
    },
    {
      "version": "1.1.1",
      "date": "2022-04-11"
    },
    {
      "version": "1.1.2",
      "date": "2022-07-06"
    },
    {
      "version": "1.1.3",
      "date": "2022-10-12"
    },
    {
      "version": "1.2.0",
      "date": "2023-05-04"
    },
    {
      "version": "1.2.1",
      "date": "2024-02-06"
    },
    {
      "version": "1.2.2",
      "date": "2024-07-22"
    },
    {
      "version": "1.2.3",
      "date": "2025-01-29"
    },
    {
      "version": "1.2.4",
      "date": "2025-12-17"
    }
  ],
  "_exports": [
    "ancestors",
    "clusterGraph",
    "clusterScore",
    "colorGraph",
    "cplot",
    "dagitty2graph",
    "descendants",
    "extractClusters",
    "factor.analysis",
    "gplot",
    "graph2dag",
    "graph2dagitty",
    "graph2lavaan",
    "lavaan2graph",
    "loadPathways",
    "localCI.test",
    "mergeNodes",
    "modelSearch",
    "orientEdges",
    "pairwiseMatrix",
    "parameterEstimates",
    "parents",
    "pathFinder",
    "properties",
    "resizeGraph",
    "SEMace",
    "SEMbap",
    "SEMdag",
    "SEMdci",
    "SEMgsa",
    "SEMpath",
    "SEMrun",
    "SEMtree",
    "Shipley.test",
    "siblings",
    "transformData",
    "weightGraph"
  ],
  "_datasets": [
    {
      "name": "alsData",
      "title": "Amyotrophic Lateral Sclerosis (ALS) dataset",
      "object": "ALSdata",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "kegg",
      "title": "KEGG interactome",
      "object": "kegg",
      "class": [
        "igraph"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "kegg.pathways",
      "title": "KEGG pathways",
      "object": "kegg.pathways",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "sachs",
      "title": "Sachs multiparameter flow cytometry data and consensus model",
      "object": "sachs",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "alsData",
      "title": "Amyotrophic Lateral Sclerosis (ALS) dataset",
      "topics": [
        "alsData"
      ]
    },
    {
      "page": "ancestry",
      "title": "Node ancestry utilities",
      "topics": [
        "ancestors",
        "ancestry",
        "descendants",
        "parents",
        "siblings"
      ]
    },
    {
      "page": "clusterGraph",
      "title": "Topological graph clustering",
      "topics": [
        "clusterGraph"
      ]
    },
    {
      "page": "clusterScore",
      "title": "Module scoring",
      "topics": [
        "clusterScore"
      ]
    },
    {
      "page": "colorGraph",
      "title": "Vertex and edge graph coloring on the base of fitting",
      "topics": [
        "colorGraph"
      ]
    },
    {
      "page": "cplot",
      "title": "Subgraph mapping",
      "topics": [
        "cplot"
      ]
    },
    {
      "page": "dagitty2graph",
      "title": "Graph conversion from dagitty to igraph",
      "topics": [
        "dagitty2graph"
      ]
    },
    {
      "page": "extractClusters",
      "title": "Cluster extraction utility",
      "topics": [
        "extractClusters"
      ]
    },
    {
      "page": "factor.analysis",
      "title": "Factor analysis for high dimensional data",
      "topics": [
        "factor.analysis"
      ]
    },
    {
      "page": "gplot",
      "title": "Graph plotting with renderGraph",
      "topics": [
        "gplot"
      ]
    },
    {
      "page": "graph2dag",
      "title": "Convert directed graphs to directed acyclic graphs (DAGs)",
      "topics": [
        "graph2dag"
      ]
    },
    {
      "page": "graph2dagitty",
      "title": "Graph conversion from igraph to dagitty",
      "topics": [
        "graph2dagitty"
      ]
    },
    {
      "page": "graph2lavaan",
      "title": "Graph to lavaan model",
      "topics": [
        "graph2lavaan"
      ]
    },
    {
      "page": "kegg",
      "title": "KEGG interactome",
      "topics": [
        "kegg"
      ]
    },
    {
      "page": "kegg.pathways",
      "title": "KEGG pathways",
      "topics": [
        "kegg.pathways"
      ]
    },
    {
      "page": "lavaan2graph",
      "title": "lavaan model to graph",
      "topics": [
        "lavaan2graph"
      ]
    },
    {
      "page": "loadPathways",
      "title": "Import pathways and generate a reference network",
      "topics": [
        "loadPathways"
      ]
    },
    {
      "page": "localCI.test",
      "title": "Conditional Independence (CI) local tests of an acyclic graph",
      "topics": [
        "localCI.test"
      ]
    },
    {
      "page": "mergeNodes",
      "title": "Graph nodes merging by a membership attribute",
      "topics": [
        "mergeNodes"
      ]
    },
    {
      "page": "modelSearch",
      "title": "Optimal model search strategies",
      "topics": [
        "modelSearch"
      ]
    },
    {
      "page": "orientEdges",
      "title": "Assign edge orientation of an undirected graph",
      "topics": [
        "orientEdges"
      ]
    },
    {
      "page": "pairwiseMatrix",
      "title": "Pairwise plotting of multivariate data",
      "topics": [
        "pairwiseMatrix"
      ]
    },
    {
      "page": "parameterEstimates",
      "title": "Parameter Estimates of a fitted SEM",
      "topics": [
        "parameterEstimates"
      ]
    },
    {
      "page": "pathFinder",
      "title": "Perturbed path search utility",
      "topics": [
        "pathFinder"
      ]
    },
    {
      "page": "properties",
      "title": "Graph properties summary and graph decomposition",
      "topics": [
        "properties"
      ]
    },
    {
      "page": "resizeGraph",
      "title": "Interactome-assisted graph re-seizing",
      "topics": [
        "resizeGraph"
      ]
    },
    {
      "page": "sachs",
      "title": "Sachs multiparameter flow cytometry data and consensus model",
      "topics": [
        "sachs"
      ]
    },
    {
      "page": "SEMace",
      "title": "Compute the Average Causal Effect (ACE) for a given source-sink pair",
      "topics": [
        "SEMace"
      ]
    },
    {
      "page": "SEMbap",
      "title": "Bow-free covariance search and data de-correlation",
      "topics": [
        "SEMbap"
      ]
    },
    {
      "page": "SEMdag",
      "title": "Estimate a DAG from an input (or empty) graph",
      "topics": [
        "SEMdag"
      ]
    },
    {
      "page": "SEMdci",
      "title": "SEM-based differential network analysis",
      "topics": [
        "SEMdci"
      ]
    },
    {
      "page": "SEMgsa",
      "title": "SEM-based gene set analysis",
      "topics": [
        "SEMgsa"
      ]
    },
    {
      "page": "SEMpath",
      "title": "Search for directed or shortest paths between pairs of source-sink nodes",
      "topics": [
        "SEMpath"
      ]
    },
    {
      "page": "SEMrun",
      "title": "Fit a graph as a Structural Equation Model (SEM)",
      "topics": [
        "SEMrun"
      ]
    },
    {
      "page": "SEMtree",
      "title": "Tree-based structure learning methods",
      "topics": [
        "SEMtree"
      ]
    },
    {
      "page": "Shipley.test",
      "title": "Missing edge testing implied by a DAG with Shipley's basis-set",
      "topics": [
        "Shipley.test"
      ]
    },
    {
      "page": "summary.GGM",
      "title": "GGM model summary",
      "topics": [
        "summary.GGM"
      ]
    },
    {
      "page": "summary.RICF",
      "title": "RICF model summary",
      "topics": [
        "summary.RICF"
      ]
    },
    {
      "page": "transformData",
      "title": "Transform data methods",
      "topics": [
        "transformData"
      ]
    },
    {
      "page": "weightGraph",
      "title": "Graph weighting methods",
      "topics": [
        "weightGraph"
      ]
    }
  ],
  "_readme": "https://github.com/fernandopalluzzi/semgraph/raw/HEAD/README.md",
  "_rundeps": [
    "AnnotationDbi",
    "askpass",
    "aspect",
    "BH",
    "Biobase",
    "BiocGenerics",
    "BiocManager",
    "Biostrings",
    "bit",
    "bit64",
    "bitops",
    "blob",
    "boot",
    "cachem",
    "cherry",
    "class",
    "cli",
    "codetools",
    "corpcor",
    "cpp11",
    "crayon",
    "curl",
    "dagitty",
    "DBI",
    "dir.expiry",
    "e1071",
    "fastmap",
    "filelock",
    "flip",
    "foreach",
    "gdata",
    "generics",
    "ggm",
    "glasso",
    "glmnet",
    "glue",
    "graph",
    "graphite",
    "gtools",
    "hommel",
    "httr",
    "igraph",
    "IRanges",
    "iterators",
    "jsonlite",
    "KEGGREST",
    "lattice",
    "lavaan",
    "lifecycle",
    "lpSolve",
    "magrittr",
    "MASS",
    "Matrix",
    "memoise",
    "mgcv",
    "mime",
    "mnormt",
    "mvtnorm",
    "nlme",
    "numDeriv",
    "openssl",
    "pbapply",
    "pbivnorm",
    "pkgconfig",
    "plyr",
    "png",
    "protoclust",
    "proxy",
    "purrr",
    "quadprog",
    "R6",
    "rappdirs",
    "RBGL",
    "Rcpp",
    "RcppEigen",
    "Rgraphviz",
    "rlang",
    "RSQLite",
    "S4Vectors",
    "Seqinfo",
    "shape",
    "someMTP",
    "survival",
    "sys",
    "V8",
    "vctrs",
    "XVector"
  ],
  "_vignettes": [
    {
      "source": "SEMgraph_tutorial.Rmd",
      "filename": "SEMgraph_tutorial.html",
      "title": "Get started",
      "author": "Fernando Paluzzi, Mario Grassi",
      "engine": "knitr::rmarkdown",
      "headings": [
        "1. Supplementary packages.",
        "2. Amyotrophic Lateral Sclerosis (ALS) data analysis.",
        "2.1. The ALS dataset.",
        "2.2. Model fitting.",
        "2.3. Total effect estimation as Average Causal Effect (ACE).",
        "2.4. Model estimation strategies.",
        "2.5. Communities and factor scores.",
        "3. Frontotemporal Dementia (FTD) data analysis.",
        "3.1. Gene Set Analysis (GSA).",
        "3.2. Network weighting and perturbed backbone extraction.",
        "3.3. Locating differentially connected genes.",
        "References"
      ],
      "created": "2025-12-15 16:02:12",
      "modified": "2025-12-16 14:34:24",
      "commits": 2
    }
  ],
  "_score": 6.319730494330225,
  "_indexed": true,
  "_nocasepkg": "semgraph",
  "_universes": [
    "fernandopalluzzi",
    "barbaratarantino"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.2.4",
      "date": "2026-05-28T14:55:23.000Z",
      "distro": "noble",
      "commit": "31eff1eab1f15e93d2e1bfcc869770424f75fb1a",
      "fileid": "03edd2c078ed23a525e4a662cf43b4302852a737a44c6d48a24ee13e05f4425b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/fernandopalluzzi/actions/runs/26581816708"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.2.4",
      "date": "2026-05-28T14:54:54.000Z",
      "distro": "noble",
      "commit": "31eff1eab1f15e93d2e1bfcc869770424f75fb1a",
      "fileid": "a71efc03423e4b0049d2970fb2a8a0969bab73c33d0a8eb96b7b8c94cac797ff",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/fernandopalluzzi/actions/runs/26581816708"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.2.4",
      "date": "2026-05-28T15:16:07.000Z",
      "commit": "31eff1eab1f15e93d2e1bfcc869770424f75fb1a",
      "fileid": "0cb18aeabc3d32a40ebc2d39eea0f113e5ff52efdf5fd009356620c36db1ef8c",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/fernandopalluzzi/actions/runs/26581816708"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.2.4",
      "date": "2026-05-28T15:13:56.000Z",
      "commit": "31eff1eab1f15e93d2e1bfcc869770424f75fb1a",
      "fileid": "56bab9f2efbf18ce60de261dd790d723f0afe4adff3d3066cd267fa8ca2af43d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/fernandopalluzzi/actions/runs/26581816708"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.2.4",
      "date": "2026-05-28T14:55:23.000Z",
      "commit": "31eff1eab1f15e93d2e1bfcc869770424f75fb1a",
      "fileid": "e797df40f2f10e8bb2df5a5a1b57edb82a113bc92f6cda7bcc35fed6ba9cb388",
      "status": "success",
      "buildurl": "https://github.com/r-universe/fernandopalluzzi/actions/runs/26581816708"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.2.4",
      "date": "2026-05-28T14:54:34.000Z",
      "commit": "31eff1eab1f15e93d2e1bfcc869770424f75fb1a",
      "fileid": "c50806397ffc6c5b314bb309e4435f0e2b9bad48eb5d98e91ff59da5d8475534",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/fernandopalluzzi/actions/runs/26581816708"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.2.4",
      "date": "2026-05-28T14:55:36.000Z",
      "commit": "31eff1eab1f15e93d2e1bfcc869770424f75fb1a",
      "fileid": "bb1444f84b56279294b2e01e46dcf352fd03814f6b93bcbacfbe2df490b7a9c2",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/fernandopalluzzi/actions/runs/26581816708"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.2.4",
      "date": "2026-05-28T14:54:25.000Z",
      "commit": "31eff1eab1f15e93d2e1bfcc869770424f75fb1a",
      "fileid": "1e3fc3e118d5a630e265045c06682850e12a974ff5153bc0d34e5cdf1c6bcc98",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/fernandopalluzzi/actions/runs/26581816708"
    }
  ]
}