{
  "_id": "6a23b9b4530b9bc726bd883e",
  "Package": "GraphMRcML",
  "Type": "Package",
  "Title": "Causal Network Inference via Mendelian Randomization with cML\nand Network Deconvolution",
  "Version": "0.1.0",
  "Authors@R": "c(\nperson(\"Zhaotong\", \"Lin\", role = c(\"aut\", \"cre\"),\nemail = \"lin00374@umn.edu\"),\nperson(\"Haoran\", \"Xue\", role = \"aut\"),\nperson(\"Wei\", \"Pan\", role = \"aut\"))",
  "Description": "Combines Mendelian randomization (constrained maximum\nlikelihood, cML) and network deconvolution for inference of\ncausal networks from GWAS summary data, as described in Lin,\nXue, and Pan (2023) <doi:10.1371/journal.pgen.1010762>.",
  "License": "GPL (>= 3)",
  "URL": "https://github.com/ZhaotongL/GraphMRcML,\nhttps://mrcieu.r-universe.dev/GraphMRcML",
  "Encoding": "UTF-8",
  "Config/roxygen2/version": "8.0.0",
  "Config/pak/sysreqs": "libglpk-dev libxml2-dev",
  "Repository": "https://mrcieu.r-universe.dev",
  "Date/Publication": "2026-05-07 18:57:42 UTC",
  "RemoteUrl": "https://github.com/ZhaotongL/GraphMRcML",
  "RemoteRef": "refs/pull/2/head",
  "RemoteSha": "a0942082654a1efe87fdc01a47cf4f1966ac0c45",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-06 05:48:39 UTC",
    "User": "root"
  },
  "Author": "Zhaotong Lin [aut, cre],\nHaoran Xue [aut],\nWei Pan [aut]",
  "Maintainer": "Zhaotong Lin <lin00374@umn.edu>",
  "MD5sum": "b239dd4ca332a542175120b709561a2b",
  "_user": "mrcieu",
  "_type": "src",
  "_file": "GraphMRcML_0.1.0.tar.gz",
  "_fileid": "ad9ccd13594c9954bfaede59c27f42c78bd3619ef92e66cb7f464839d64f210c",
  "_filesize": 121206,
  "_sha256": "ad9ccd13594c9954bfaede59c27f42c78bd3619ef92e66cb7f464839d64f210c",
  "_created": "2026-06-06T05:48:39.000Z",
  "_published": "2026-06-06T06:09:56.949Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 79855224766,
      "time": 104,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7451694548"
    },
    {
      "job": 79855224770,
      "time": 1252,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7451839162"
    },
    {
      "job": 79855224755,
      "time": 109,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7451695087"
    },
    {
      "job": 79855224765,
      "time": 81,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7451691628"
    },
    {
      "job": 79855077072,
      "time": 148,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7451681109"
    },
    {
      "job": 79855224750,
      "time": 98,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7451693816"
    },
    {
      "job": 79855224786,
      "time": 70,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7451690297"
    },
    {
      "job": 79855224789,
      "time": 62,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7451689221"
    },
    {
      "job": 79855224799,
      "time": 68,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7451690067"
    }
  ],
  "_buildurl": "https://github.com/r-universe/mrcieu/actions/runs/27054137798",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/ZhaotongL/GraphMRcML",
  "_commit": {
    "id": "a0942082654a1efe87fdc01a47cf4f1966ac0c45",
    "author": "Tom Palmer <remlapmot@hotmail.com>",
    "committer": "Tom Palmer <remlapmot@hotmail.com>",
    "message": "Document\n",
    "time": 1778180262
  },
  "_maintainer": {
    "name": "Zhaotong Lin",
    "email": "lin00374@umn.edu",
    "login": "zhaotongl",
    "description": "",
    "uuid": 45536679
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "igraph",
      "role": "Imports"
    },
    {
      "package": "MASS",
      "role": "Imports"
    },
    {
      "package": "pbmcapply",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    }
  ],
  "_owner": "zhaotongl",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 1
    },
    {
      "week": "2025-45",
      "n": 1
    },
    {
      "week": "2026-19",
      "n": 14
    }
  ],
  "_tags": [],
  "_stars": 9,
  "_contributors": [
    {
      "user": "zhaotongl",
      "count": 15,
      "uuid": 45536679
    }
  ],
  "_userbio": {
    "uuid": 15654827,
    "type": "organization",
    "name": "MRC Integrative Epidemiology Unit"
  },
  "_downloads": {
    "count": 0,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/GraphMRcML"
  },
  "_devurl": "https://github.com/zhaotongl/graphmrcml",
  "_searchresults": 0,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/GraphMRcML.html",
    "manual.pdf"
  ],
  "_cranurl": false,
  "_exports": [
    "cML_estimate_O",
    "cML_estimate_random_O",
    "cML_SdTheta_O",
    "Generate_Perturb",
    "Graph_Estimate",
    "Graph_Perturb",
    "Graph_Screen",
    "loglik",
    "mr_cML_DP_O",
    "mr_cML_O",
    "plot_graph",
    "subset_Graph_d1"
  ],
  "_help": [
    {
      "page": "cML_estimate_O",
      "title": "Constrained maximum likelihood estimate (single start)",
      "topics": [
        "cML_estimate_O"
      ]
    },
    {
      "page": "cML_estimate_random_O",
      "title": "Constrained MLE with random restarts",
      "topics": [
        "cML_estimate_random_O"
      ]
    },
    {
      "page": "cML_SdTheta_O",
      "title": "Standard error of the cML causal-effect estimate",
      "topics": [
        "cML_SdTheta_O"
      ]
    },
    {
      "page": "Generate_Perturb",
      "title": "Generate one LD-aware perturbed copy of the GWAS estimates",
      "topics": [
        "Generate_Perturb"
      ]
    },
    {
      "page": "Graph_Estimate",
      "title": "Estimate the pairwise causal-effect graph",
      "topics": [
        "Graph_Estimate"
      ]
    },
    {
      "page": "Graph_Perturb",
      "title": "GraphMRcML with data perturbation",
      "topics": [
        "Graph_Perturb"
      ]
    },
    {
      "page": "Graph_Screen",
      "title": "Screen instruments and prepare LD-aware perturbation matrices",
      "topics": [
        "Graph_Screen"
      ]
    },
    {
      "page": "loglik",
      "title": "Profile log-likelihood for the cML model",
      "topics": [
        "loglik"
      ]
    },
    {
      "page": "mr_cML_DP_O",
      "title": "MR-cML with data perturbation",
      "topics": [
        "mr_cML_DP_O"
      ]
    },
    {
      "page": "mr_cML_O",
      "title": "Mendelian randomization via cML with BIC selection",
      "topics": [
        "mr_cML_O"
      ]
    },
    {
      "page": "plot_graph",
      "title": "Build an igraph object for a GraphMRcML summary graph",
      "topics": [
        "plot_graph"
      ]
    },
    {
      "page": "subset_Graph_d1",
      "title": "Summarise GraphMRcML perturbation results for a subset of traits",
      "topics": [
        "subset_Graph_d1"
      ]
    }
  ],
  "_rundeps": [
    "cli",
    "cpp11",
    "dplyr",
    "generics",
    "glue",
    "igraph",
    "lattice",
    "lifecycle",
    "magrittr",
    "MASS",
    "Matrix",
    "pbmcapply",
    "pillar",
    "pkgconfig",
    "R6",
    "rlang",
    "tibble",
    "tidyselect",
    "utf8",
    "vctrs",
    "withr"
  ],
  "_score": 2.4313637641589874,
  "_indexed": true,
  "_nocasepkg": "graphmrcml",
  "_universes": [
    "mrcieu",
    "zhaotongl"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.1.0",
      "date": "2026-06-06T05:50:28.000Z",
      "distro": "noble",
      "commit": "a0942082654a1efe87fdc01a47cf4f1966ac0c45",
      "fileid": "febf665879dfed5275448e8ae4860528fe008b13adccf3c125597601b7f5f809",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/27054137798"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.1.0",
      "date": "2026-06-06T06:09:36.000Z",
      "distro": "noble",
      "commit": "a0942082654a1efe87fdc01a47cf4f1966ac0c45",
      "fileid": "db615953e11f4c32dd0ca55821fc1256e08db5e9dcbe9c4f53d5247013f12307",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/27054137798"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.1.0",
      "date": "2026-06-06T05:50:31.000Z",
      "commit": "a0942082654a1efe87fdc01a47cf4f1966ac0c45",
      "fileid": "706211e31bbfb855051b296ab6c4edf7e46880fdc905a967e8fb8663f1adac0c",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/27054137798"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.1.0",
      "date": "2026-06-06T05:50:04.000Z",
      "commit": "a0942082654a1efe87fdc01a47cf4f1966ac0c45",
      "fileid": "72daa86920d60d3f5bc4faf7928d49e49f1c29ab53e954a273107575157ba784",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/27054137798"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.1.0",
      "date": "2026-06-06T05:50:30.000Z",
      "commit": "a0942082654a1efe87fdc01a47cf4f1966ac0c45",
      "fileid": "e436f50abcce83ffeae5b2fded7487dfda743d6f3a1b84427766d73614177193",
      "status": "success",
      "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/27054137798"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.1.0",
      "date": "2026-06-06T05:49:49.000Z",
      "commit": "a0942082654a1efe87fdc01a47cf4f1966ac0c45",
      "fileid": "d2ad2c7d91b22bade0c9c2e5e0956787a9e56fcf9e4c7c30a3a2acb81a541a94",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/27054137798"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.1.0",
      "date": "2026-06-06T05:49:40.000Z",
      "commit": "a0942082654a1efe87fdc01a47cf4f1966ac0c45",
      "fileid": "2ba352aee662d036d070030a4ac762cf57666698c92313a4b79bfab8ba359d04",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/27054137798"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "0.1.0",
      "date": "2026-06-06T05:49:47.000Z",
      "commit": "a0942082654a1efe87fdc01a47cf4f1966ac0c45",
      "fileid": "efab2813a82d5ae151b2ed5deb8e7a4b2b5da66df5b2ef73d3326478e6532789",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/27054137798"
    }
  ]
}