{ "_id": "6ac204a4773a0037682c0972", "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) .", "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": "2026-10-04 07:36:16 UTC", "User": "root" }, "Author": "Zhaotong Lin [aut, cre],\nHaoran Xue [aut],\nWei Pan [aut]", "Maintainer": "Zhaotong Lin ", "_user": "mrcieu", "_type": "src", "_file": "GraphMRcML_0.1.0.tar.gz", "_fileid": "https://r2.ropensci.org/f0562bedf51719445b0ec177fa6c75ab530c5a6f1657fae0472bf155b33115c7", "_filesize": 122959, "_sha256": "f0562bedf51719445b0ec177fa6c75ab530c5a6f1657fae0472bf155b33115c7", "_expires": "2027-01-12T07:47:46.000Z", "_created": "2026-10-04T07:36:16.000Z", "_published": "2026-10-04T07:47:48.275Z", "_jobs": [ { "job": 111388833201, "time": 99, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11296749114" }, { "job": 111388833282, "time": 149, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11296854104" }, { "job": 111388833223, "time": 194, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "11297049092" }, { "job": 111388833212, "time": 217, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11297810205" }, { "job": 111388443821, "time": 147, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11297103308" }, { "job": 111388833216, "time": 89, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11296564649" }, { "job": 111388833229, "time": 77, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11296274792" }, { "job": 111388833262, "time": 57, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "11296883992" }, { "job": 111388833307, "time": 63, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11296614576" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/mrcieu/actions/runs/37186161210", "_status": "success", "_upstream": "https://github.com/ZhaotongL/GraphMRcML", "_commit": { "id": "a0942082654a1efe87fdc01a47cf4f1966ac0c45", "author": "Tom Palmer ", "committer": "Tom Palmer ", "message": "Document\n", "time": 1778180262 }, "_maintainer": { "name": "Zhaotong Lin", "email": "lin00374@umn.edu", "login": "zhaotongl", "description": "", "uuid": 45536679 }, "_distro": "resolute", "_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", "followers": 257 }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/GraphMRcML" }, "_devurl": "https://github.com/zhaotongl/graphmrcml", "_searchresults": 0, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/GraphMRcML.html", "extra/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": "2026-10-04T07:38:01.000Z", "distro": "resolute", "commit": "a0942082654a1efe87fdc01a47cf4f1966ac0c45", "fileid": "https://r2.ropensci.org/c1869be91923f845ebc2e805605c8ca47d6c468394ad8cf0d64eaaab0c83c562", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/37186161210" }, { "r": "4.6.1", "os": "linux", "version": "0.1.0", "date": "2026-10-04T07:38:52.000Z", "distro": "resolute", "commit": "a0942082654a1efe87fdc01a47cf4f1966ac0c45", "fileid": "https://r2.ropensci.org/5ac7dd0a13e5f788a8c50b59b5844d3afb1733257fe3de04c059849e1dd377c6", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/37186161210" }, { "r": "4.5.3", "os": "mac", "version": "0.1.0", "date": "2026-10-04T07:44:58.000Z", "commit": "a0942082654a1efe87fdc01a47cf4f1966ac0c45", "fileid": "https://r2.ropensci.org/b08a33492ab603e1fc2e212a14710fcb85b3bffb21e9d5046a56a779abdfe43c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/37186161210" }, { "r": "4.6.1", "os": "mac", "version": "0.1.0", "date": "2026-10-04T07:47:15.000Z", "commit": "a0942082654a1efe87fdc01a47cf4f1966ac0c45", "fileid": "https://r2.ropensci.org/c1c3533b19edb3c61733885cc3c4dedd1d80e9f5ed2367fd7eb00384095ddd1c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/37186161210" }, { "r": "4.6.0", "os": "wasm", "version": "0.1.0", "date": "2026-10-04T07:38:01.000Z", "commit": "a0942082654a1efe87fdc01a47cf4f1966ac0c45", "fileid": "https://r2.ropensci.org/91a4cb4bc5e891509586397f03d68fe11162bb09c9a24a9edce8d6823c4b25cc", "status": "success", "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/37186161210" }, { "r": "4.7.0", "os": "win", "version": "0.1.0", "date": "2026-10-04T07:37:37.000Z", "commit": "a0942082654a1efe87fdc01a47cf4f1966ac0c45", "fileid": "https://r2.ropensci.org/01b901e5368b8ad6e70ee6b33b3741c1e0e5abed9192c7ed36184bc6e34534d6", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/37186161210" }, { "r": "4.5.3", "os": "win", "version": "0.1.0", "date": "2026-10-04T07:37:16.000Z", "commit": "a0942082654a1efe87fdc01a47cf4f1966ac0c45", "fileid": "https://r2.ropensci.org/256c6c969919d82a84663396d53a989a1ec61a1f92ba757137a8b86ac3c0c676", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/37186161210" }, { "r": "4.6.1", "os": "win", "version": "0.1.0", "date": "2026-10-04T07:37:22.000Z", "commit": "a0942082654a1efe87fdc01a47cf4f1966ac0c45", "fileid": "https://r2.ropensci.org/343f29ac5486d17c0bcc97484ed55c356412046b2af46bbf9a8fd926b0f02539", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mrcieu/actions/runs/37186161210" } ] }